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Lohia S, Latosinska A, Zoidakis J, Makridakis M, Mischak H, Glorieux G, Vlahou A, Jankowski V. Glycosylation Analysis of Urinary Peptidome Highlights IGF2 Glycopeptides in Association with CKD. Int J Mol Sci 2023; 24:ijms24065402. [PMID: 36982475 PMCID: PMC10048973 DOI: 10.3390/ijms24065402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Chronic kidney disease (CKD) is prevalent in 10% of world’s adult population. The role of protein glycosylation in causal mechanisms of CKD progression is largely unknown. The aim of this study was to identify urinary O-linked glycopeptides in association to CKD for better characterization of CKD molecular manifestations. Urine samples from eight CKD and two healthy subjects were analyzed by CE-MS/MS and glycopeptides were identified by a specific software followed by manual inspection of the spectra. Distribution of the identified glycopeptides and their correlation with Age, eGFR and Albuminuria were evaluated in 3810 existing datasets. In total, 17 O-linked glycopeptides from 7 different proteins were identified, derived primarily from Insulin-like growth factor-II (IGF2). Glycosylation occurred at the surface exposed IGF2 Threonine 96 position. Three glycopeptides (DVStPPTVLPDNFPRYPVGKF, DVStPPTVLPDNFPRYPVG and DVStPPTVLPDNFPRYP) exhibited positive correlation with Age. The IGF2 glycopeptide (tPPTVLPDNFPRYP) showed a strong negative association with eGFR. These results suggest that with aging and deteriorating kidney function, alterations in IGF2 proteoforms take place, which may reflect changes in mature IGF2 protein. Further experiments corroborated this hypothesis as IGF2 increased plasma levels were observed in CKD patients. Protease predictions, considering also available transcriptomics data, suggest activation of cathepsin S with CKD, meriting further investigation.
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Affiliation(s)
- Sonnal Lohia
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | | | - Jerome Zoidakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Division, Ghent University Hospital, 9000 Gent, Belgium
| | - Antonia Vlahou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, 52074 Aachen, Germany
- Correspondence: ; Tel.: +49-(0241)-80-80580
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2
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Scurt FG, Bose K, Hammoud B, Brandt S, Bernhardt A, Gross C, Mertens PR, Chatzikyrkou C. Old known and possible new biomarkers of ANCA-associated vasculitis. J Autoimmun 2022; 133:102953. [PMID: 36410262 DOI: 10.1016/j.jaut.2022.102953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/06/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022]
Abstract
Antineutrophil cytoplasm antibody (ANCA)-associated vasculitis (AAV) comprises a group of multisystem disorders involving severe, systemic, small-vessel vasculitis with short- and long term serious and life-threating complications. Despite the simplification of treatment, fundamental aspects concerning assessment of its efficacy and its adaptation to encountered complications or to the relapsing/remitting/subclinical disease course remain still unknown. The pathogenesis of AAV is complex and unique, and despite the progress achieved in the last years, much has not to be learnt. Foremost, there is still no accurate marker enabling us to monitoring disease and guide therapy. Therefore, the disease management relays often on clinical judgment and follows a" trial and error approach". In the recent years, an increasing number of new molecules s have been explored and used for this purpose including genomics, B- and T-cell subpopulations, complement system factors, cytokines, metabolomics, biospectroscopy and components of our microbiome. The aim of this review is to discuss both the role of known historical and clinically established biomarkers of AAV, as well as to highlight potential new ones, which could be used for timely diagnosis and monitoring of this devastating disease, with the goal to improve the effectiveness and ameliorate the complications of its demanding therapy.
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Affiliation(s)
- Florian G Scurt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany.
| | - K Bose
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - Ben Hammoud
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - S Brandt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - A Bernhardt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - C Gross
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - Peter R Mertens
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
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3
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Forouzandeh A, Rutar A, Kalmady SV, Greiner R. Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets. PLoS One 2022; 17:e0252697. [PMID: 35901020 PMCID: PMC9333302 DOI: 10.1371/journal.pone.0252697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/29/2022] [Indexed: 11/19/2022] Open
Abstract
Many researchers try to understand a biological condition by identifying biomarkers. This is typically done using univariate hypothesis testing over a labeled dataset, declaring a feature to be a biomarker if there is a significant statistical difference between its values for the subjects with different outcomes. However, such sets of proposed biomarkers are often not reproducible – subsequent studies often fail to identify the same sets. Indeed, there is often only a very small overlap between the biomarkers proposed in pairs of related studies that explore the same phenotypes over the same distribution of subjects. This paper first defines the Reproducibility Score for a labeled dataset as a measure (taking values between 0 and 1) of the reproducibility of the results produced by a specified fixed biomarker discovery process for a given distribution of subjects. We then provide ways to reliably estimate this score by defining algorithms that produce an over-bound and an under-bound for this score for a given dataset and biomarker discovery process, for the case of univariate hypothesis testing on dichotomous groups. We confirm that these approximations are meaningful by providing empirical results on a large number of datasets and show that these predictions match known reproducibility results. To encourage others to apply this technique to analyze their biomarker sets, we have also created a publicly available website, https://biomarker.shinyapps.io/BiomarkerReprod/, that produces these Reproducibility Score approximations for any given dataset (with continuous or discrete features and binary class labels).
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Affiliation(s)
- Amir Forouzandeh
- Department of Computing Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Alex Rutar
- Department of Pure Math, University of Waterloo, Waterloo, ON, Canada
| | - Sunil V. Kalmady
- Department of Computing Science, University of Alberta, Edmonton, Canada
- Canadian VIGOUR Centre, University of Alberta, Edmonton, Canada
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, Canada
- Alberta Machine Intelligence Institute, Edmonton, Canada
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4
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Wei D, Melgarejo J, Vanassche T, Van Aelst L, Janssens S, Verhamme P, Zhang ZY. Urinary matrix Gla protein is associated with mortality risk in Flemish population: A prospective study. Front Cardiovasc Med 2022; 9:894447. [PMID: 35935627 PMCID: PMC9353515 DOI: 10.3389/fcvm.2022.894447] [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: 03/11/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background Vascular calcification is strongly related to the risk of mortality and cardiovascular (CV) diseases. In vascular calcification, matrix Gla protein (MGP), a small vitamin K-dependent protein, is an important mineralization inhibitor. Recent studies showed that circulating MGP is associated with mortality risk. However, the longitudinal association between urinary excretion of MGP and all-cause mortality was not established. Materials and methods Urinary MGP was measured in 776 randomly recruited Flemish population (mean age: 51.2 years; 50.9% women) at baseline (during 2005–2010) using capillary electrophoresis coupled with mass spectrometry. Plasma inactive MGP [desphospho-uncarboxylated MGP (dp-ucMGP)] levels were quantified in 646 individuals by ELISA kits. Mortality status was ascertained through the Belgian Population Registry until 2016. The longitudinal association with mortality was determined by the multivariate-adjusted Cox proportional hazards regression models. The multivariate linear regression models were used to identify determinants of urinary MGP level. Results Over the 9.2 years, 47 (6.06%) participants died, including 15 CV deaths. For a doubling of urinary MGP, the hazard ratios (HRs) were 1.31 (95% CI: 1.01–1.69, P = 0.040) for all-cause mortality and 2.05 (95% CI: 1.11–3.79, P = 0.023) for CV mortality with adjustment for covariates, including estimated glomerular filtration rate and urine microalbumin. The addition of urinary MGP to the basic models improved the reclassification as suggested by the increased net reclassification improvement [64.01% (95% CI: 32.64–98.63)] and integrated discrimination improvement [2.33% (95% CI: 0.24–4.71)]. Circulating inactive MGP, total cholesterol, urine microalbumin, and smoking were significantly associated with urinary MGP levels (P ≤ 0.041), independent of sex and age. Conclusion Elevated urinary MGP was associated with an increased risk of all-cause mortality and CV mortality and improved the risk reclassification for all-cause mortality. These findings suggested that urinary MGP might be useful in mortality risk assessment in the general population. However, these observations need to be replicated in larger studies with a longer follow-up time.
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Affiliation(s)
- Dongmei Wei
- Studies Coordinating Center, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Jesus Melgarejo
- Studies Coordinating Center, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Thomas Vanassche
- Division of Cardiology, University Hospitals Leuven, Leuven, Belgium
| | - Lucas Van Aelst
- Division of Cardiology, University Hospitals Leuven, Leuven, Belgium
| | - Stefan Janssens
- Division of Cardiology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Verhamme
- Division of Cardiology, University Hospitals Leuven, Leuven, Belgium
| | - Zhen-Yu Zhang
- Studies Coordinating Center, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
- *Correspondence: Zhen-Yu Zhang,
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5
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Sparding N, Genovese F, Rasmussen DGK, Karsdal MA, Neprasova M, Maixnerova D, Satrapova V, Frausova D, Hornum M, Bartonova L, Honsova E, Kollar M, Koprivova H, Hruskova Z, Tesar V. Endotrophin, a collagen type VI-derived matrikine, reflects the degree of renal fibrosis in patients with IgA nephropathy and in patients with ANCA-associated vasculitis. Nephrol Dial Transplant 2022; 37:1099-1108. [PMID: 33914059 PMCID: PMC9130028 DOI: 10.1093/ndt/gfab163] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Renal fibrosis is the hallmark of chronic kidney disease (CKD) and is characterized by an imbalanced extracellular matrix remodelling. Endotrophin (ETP) is a signalling molecule released from collagen type VI (COL VI). ETP can be measured by the PRO-C6 assay, which quantifies the levels of COL VI formation. ETP levels were previously associated with mortality and disease progression in patients with CKD. We hypothesized that serum and urinary ETP levels correlate with the degree of interstitial fibrosis in kidney biopsies from patients with immunoglobulin A nephropathy (IgAN) and patients with anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). METHODS We examined a cohort of 49 IgAN and 47 AAV patients. A validation cohort of 85 IgAN patients was included. ETP was measured in serum (S-ETP) and urine (U-ETP/Cr) samples, taken on the same day before renal biopsy was performed, using the enzyme-linked immunosorbent assay PRO-C6. The biopsies were evaluated for interstitial fibrosis and tubular atrophy according to the Banff and MEST-C scores. RESULTS S-ETP and U-ETP/Cr levels correlated with kidney function, increased CKD severity, correlated with the extent of interstitial fibrosis and gradually increased with increasing degree of interstitial fibrosis and tubular atrophy. ETP outperformed the known fibrosis biomarker Dickkopf-3 for discrimination of patients with high fibrotic burden. The association of S-ETP and U-ETP/Cr with the level of kidney fibrosis was confirmed in the validation cohort. CONCLUSIONS We demonstrated that high levels of circulating and excreted ETP are not only indicative of lower kidney function, but also reflect the burden of fibrosis in the kidneys.
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Affiliation(s)
- Nadja Sparding
- Nordic Bioscience, Herlev, Denmark
- Faculty of Health and Medical Science, Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Michaela Neprasova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Dita Maixnerova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Veronika Satrapova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Doubravka Frausova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Mads Hornum
- Department of Nephrology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lenka Bartonova
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Eva Honsova
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Marek Kollar
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Helena Koprivova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenka Hruskova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
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6
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Wei D, D Melgarejo J, Thijs L, Temmerman X, Vanassche T, Van Aelst L, Janssens S, Staessen JA, Verhamme P, Zhang ZY. Urinary Proteomic Profile of Arterial Stiffness Is Associated With Mortality and Cardiovascular Outcomes. J Am Heart Assoc 2022; 11:e024769. [PMID: 35411793 PMCID: PMC9238473 DOI: 10.1161/jaha.121.024769] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background The underlying mechanisms of arterial stiffness remain not fully understood. This study aimed to identify a urinary proteomic profile to illuminate its pathogenesis and to determine the prognostic value of the profile for adverse outcomes. Methods and Results We measured aortic stiffness using pulse wave velocity (PWV) and analyzed urinary proteome using capillary electrophoresis coupled with mass spectrometry in 669 randomly recruited Flemish patients (mean age, 50.2 years; 51.1% women). We developed a PWV‐derived urinary proteomic score (PWV‐UP) by modeling PWV with proteomics data at baseline through orthogonal projections to latent structures. PWV‐UP that consisted of 2336 peptides explained the 65% variance of PWV, higher than 36% explained by clinical risk factors. PWV‐UP was significantly associated with PWV (adjusted β=0.73 [95% CI, 0.67–0.79]; P<0.0001). Over 9.2 years (median), 36 participants died, and 75 experienced cardiovascular events. The adjusted hazard ratios (+1 SD) were 1.46 (95% CI, 1.08–1.97) for all‐cause mortality, 2.04 (95% CI, 1.07–3.87) for cardiovascular mortality, and 1.39 (95% CI, 1.11–1.74) for cardiovascular events (P≤0.031). For PWV, the corresponding estimates were 1.25 (95% CI, 0.97–1.60), 1.35 (95% CI, 0.85–2.15), and 1.22 (95% CI, 1.02–1.47), respectively (P≥0.033). Pathway analysis revealed that the peptides in PWV‐UP mostly involved multiple pathways, including collagen turnover, cell adhesion, inflammation, and lipid metabolism. Conclusions PWV‐UP was highly associated with PWV and could be used as a biomarker of arterial stiffness. PWV‐UP, but not PWV, was associated with all‐cause mortality and cardiovascular mortality, implying that PWV‐UP–associated peptides may be multifaceted and involved in diverse pathological processes beyond arterial stiffness.
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Affiliation(s)
- Dongmei Wei
- Studies Coordinating Centre Research Unit Hypertension and Cardiovascular Epidemiology KU Leuven Department of Cardiovascular Sciences University of Leuven Belgium
| | - Jesus D Melgarejo
- Studies Coordinating Centre Research Unit Hypertension and Cardiovascular Epidemiology KU Leuven Department of Cardiovascular Sciences University of Leuven Belgium
| | - Lutgarde Thijs
- Studies Coordinating Centre Research Unit Hypertension and Cardiovascular Epidemiology KU Leuven Department of Cardiovascular Sciences University of Leuven Belgium
| | - Xander Temmerman
- Biomedical Sciences Group Faculty of Medicine University of Leuven Belgium
| | - Thomas Vanassche
- Division of Cardiology University Hospitals Leuven Leuven Belgium
| | - Lucas Van Aelst
- Division of Cardiology University Hospitals Leuven Leuven Belgium
| | - Stefan Janssens
- Division of Cardiology University Hospitals Leuven Leuven Belgium
| | - Jan A Staessen
- Biomedical Sciences Group Faculty of Medicine University of Leuven Belgium.,Non-Profit Research Institute Alliance for the Promotion of Preventive Medicine Mechelen Belgium
| | - Peter Verhamme
- Division of Cardiology University Hospitals Leuven Leuven Belgium
| | - Zhen-Yu Zhang
- Studies Coordinating Centre Research Unit Hypertension and Cardiovascular Epidemiology KU Leuven Department of Cardiovascular Sciences University of Leuven Belgium
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7
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Rudnicki M, Siwy J, Wendt R, Lipphardt M, Koziolek MJ, Maixnerova D, Peters B, Kerschbaum J, Leierer J, Neprasova M, Banasik M, Sanz AB, Perez-Gomez MV, Ortiz A, Stegmayr B, Tesar V, Mischak H, Beige J, Reich HN. Urine proteomics for prediction of disease progression in patients with IgA nephropathy. Nephrol Dial Transplant 2021; 37:42-52. [PMID: 33313853 PMCID: PMC8719618 DOI: 10.1093/ndt/gfaa307] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Risk of kidney function decline in immunoglobulin A (IgA) nephropathy (IgAN) is significant and may not be predicted by available clinical and histological tools. To serve this unmet need, we aimed at developing a urinary biomarker-based algorithm that predicts rapid disease progression in IgAN, thus enabling a personalized risk stratification. METHODS In this multicentre study, urine samples were collected in 209 patients with biopsy-proven IgAN. Progression was defined by tertiles of the annual change of estimated glomerular filtration rate (eGFR) during follow-up. Urine samples were analysed using capillary electrophoresis coupled mass spectrometry. The area under the receiver operating characteristic curve (AUC) was used to evaluate the risk prediction models. RESULTS Of the 209 patients, 64% were male. Mean age was 42 years, mean eGFR was 63 mL/min/1.73 m2 and median proteinuria was 1.2 g/day. We identified 237 urine peptides showing significant difference in abundance according to the tertile of eGFR change. These included fragments of apolipoprotein C-III, alpha-1 antitrypsin, different collagens, fibrinogen alpha and beta, titin, haemoglobin subunits, sodium/potassium-transporting ATPase subunit gamma, uromodulin, mucin-2, fractalkine, polymeric Ig receptor and insulin. An algorithm based on these protein fragments (IgAN237) showed a significant added value for the prediction of IgAN progression [AUC 0.89; 95% confidence interval (CI) 0.83-0.95], as compared with the clinical parameters (age, gender, proteinuria, eGFR and mean arterial pressure) alone (0.72; 95% CI 0.64-0.81). CONCLUSIONS A urinary peptide classifier predicts progressive loss of kidney function in patients with IgAN significantly better than clinical parameters alone.
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Affiliation(s)
- Michael Rudnicki
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | - Ralph Wendt
- Division of Nephrology and KfH Renal Unit, Hospital St Georg, Leipzig, Germany
| | - Mark Lipphardt
- Department of Nephrology and Rheumatology, University Medical Centre Göttingen, Göttingen, Germany
| | - Michael J Koziolek
- Department of Nephrology and Rheumatology, University Medical Centre Göttingen, Göttingen, Germany
| | - Dita Maixnerova
- Department of Nephrology, 1st School of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Björn Peters
- Department of Nephrology, Skaraborg Hospital, Skövde, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Julia Kerschbaum
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Johannes Leierer
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Michaela Neprasova
- Department of Nephrology, 1st School of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Miroslaw Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Ana Belen Sanz
- Research Health Institute, Fundación Jiménez Díaz University, Madrid, Spain
| | | | - Alberto Ortiz
- Research Health Institute, Fundación Jiménez Díaz University, Madrid, Spain
| | - Bernd Stegmayr
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Vladimir Tesar
- Department of Nephrology, 1st School of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | | | - Joachim Beige
- Division of Nephrology and KfH Renal Unit, Hospital St Georg, Leipzig, Germany
- Martin-Luther-University Halle/Wittenberg, Halle/Saale, Germany
| | - Heather N Reich
- Department of Medicine, Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
- Nephrology Research, University of Toronto, Toronto, Ontario, Canada
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8
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Govender MA, Brandenburg JT, Fabian J, Ramsay M. The Use of 'Omics for Diagnosing and Predicting Progression of Chronic Kidney Disease: A Scoping Review. Front Genet 2021; 12:682929. [PMID: 34819944 PMCID: PMC8606569 DOI: 10.3389/fgene.2021.682929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022] Open
Abstract
Globally, chronic kidney disease (CKD) contributes substantial morbidity and mortality. Recently, various 'omics platforms have provided insight into the molecular basis of kidney dysfunction. This scoping review is a synthesis of the current literature on the use of different 'omics platforms to identify biomarkers that could be used to detect early-stage CKD, predict disease progression, and identify pathways leading to CKD. This review includes 123 articles published from January 2007 to May 2021, following a structured selection process. The most common type of 'omic platform was proteomics, appearing in 55 of the studies and two of these included a metabolomics component. Most studies (n = 91) reported on CKD associated with diabetes mellitus. Thirteen studies that provided information on the biomarkers associated with CKD and explored potential pathways involved in CKD are discussed. The biomarkers that are associated with risk or early detection of CKD are SNPs in the MYH9/APOL1 and UMOD genes, the proteomic CKD273 biomarker panel and metabolite pantothenic acid. Pantothenic acid and the CKD273 biomarker panel were also involved in predicting CKD progression. Retinoic acid pathway genes, UMOD, and pantothenic acid provided insight into potential pathways leading to CKD. The biomarkers were mainly used to detect CKD and predict progression in high-income, European ancestry populations, highlighting the need for representative 'omics research in other populations with disparate socio-economic strata, including Africans, since disease etiologies may differ across ethnic groups. To assess the transferability of findings, it is essential to do research in diverse populations.
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Affiliation(s)
- Melanie A. Govender
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - June Fabian
- Wits Donald Gordon Medical Centre, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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9
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Mavrogeorgis E, Mischak H, Beige J, Latosinska A, Siwy J. Understanding glomerular diseases through proteomics. Expert Rev Proteomics 2021; 18:137-157. [PMID: 33779448 DOI: 10.1080/14789450.2021.1908893] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Chronic kidney disease is avery common and complex chronic disease. Uncovering the pathological patterns of CKD on the molecular level of bio-fluids and tissue appears to be both vital and promising for a more favorable outcome. We reviewed recently discovered proteomics biomarkers for CKD to provide new insight into disease pathology. AREAS COVERED We review the application of proteome analysis in the context of CKD with various etiologies within the last 5 years. Proteins and peptides associated with CKD as derived from multiple sources (urine, blood and tissue) are reported along with their various biological pathways. EXPERT OPINION A systematic and theoretical comprehension of the CKD pathology is essential for its successful management. The underlying complexity of the disease further requires specific conditions for reliable and interpretable results. In this context, clinical proteomics has resulted in first encouraging findings in CKD. A more complete understanding of the biological pathways related to the disease, based on the scope of a holistic proteomic approach, could improve substantially the management of CKD, especially when in conjunction with the current trend of personalized medicine.
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Affiliation(s)
| | - H Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J Beige
- Division of Nephrology and KfH Renal Unit, Hospital St. Georg, Leipzig, Germany.,Department of Internal Medicine 2 (Nephrology, Rheumatology, Endocrinology), Martin-Luther-University Halle, Wittenberg, Germany
| | | | - J Siwy
- Mosaiques Diagnostics GmbH, Hannover, Germany
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10
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Prikryl P, Satrapova V, Frydlova J, Hruskova Z, Zima T, Tesar V, Vokurka M. Mass spectrometry-based proteomic exploration of the small urinary extracellular vesicles in ANCA-associated vasculitis in comparison with total urine. J Proteomics 2020; 233:104067. [PMID: 33307252 DOI: 10.1016/j.jprot.2020.104067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 11/29/2020] [Indexed: 01/07/2023]
Abstract
ANCA-associated vasculitis (AAV) is a rare, but potentially severe autoimmune disease, even nowadays displaying increased mortality and morbidity. Finding early biomarkers of activity and prognosis is thus very important. Small extracellular vesicles (EVs) isolated from urine can be considered as a non-invasive source of biomarkers. We evaluated several protocols for urinary EV isolation. To eliminate contaminating non-vesicular proteins due to AAV associated proteinuria we used proteinase K treatment. We investigated the differences in proteomes of small EVs of patients with AAV compared to healthy controls by label-free LC-MS/MS. In parallel, we performed an analogous proteomic analysis of urine samples from identical patients. The study results showed significant differences and similarities in both EV and urine proteome, the latter one being highly affected by proteinuria. Using bioinformatics tools we explored differentially changed proteins and their related pathways with a focus on the pathophysiology of AAV. Our findings indicate significant regulation of Golgi enzymes, such as MAN1A1, which can be involved in T cell activation by N-glycans glycosylation and may thus play a key role in pathogenesis and diagnosis of AAV. SIGNIFICANCE: The present study explores for the first time the changes in proteomes of small extracellular vesicles and urine of patients with renal ANCA-associated vasculitis compared to healthy controls by label-free LC-MS/MS. Isolation of vesicles from proteinuric urine samples has been modified to minimize contamination by plasma proteins and to reduce co-isolation of extraluminal proteins. Differentially changed proteins and their related pathways with a role in the pathophysiology of AAV were described and discussed. The results could be helpful for the research of potential biomarkers in renal vasculitis associated with ANCA.
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Affiliation(s)
- Petr Prikryl
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Satrapova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jana Frydlova
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zdenka Hruskova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Zima
- Institute of Clinical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Martin Vokurka
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
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11
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Siwy J, Mischak H, Zürbig P. Proteomics and personalized medicine: a focus on kidney disease. Expert Rev Proteomics 2019; 16:773-782. [DOI: 10.1080/14789450.2019.1659138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Justyna Siwy
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Harald Mischak
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Petra Zürbig
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
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12
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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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13
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Ricci P, Magalhães P, Krochmal M, Pejchinovski M, Daina E, Caruso MR, Goea L, Belczacka I, Remuzzi G, Umbhauer M, Drube J, Pape L, Mischak H, Decramer S, Schaefer F, Schanstra JP, Cereghini S, Zürbig P. Urinary proteome signature of Renal Cysts and Diabetes syndrome in children. Sci Rep 2019; 9:2225. [PMID: 30778115 PMCID: PMC6379363 DOI: 10.1038/s41598-019-38713-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Renal Cysts and Diabetes Syndrome (RCAD) is an autosomal dominant disorder caused by mutations in the HNF1B gene encoding for the transcriptional factor hepatocyte nuclear factor-1B. RCAD is characterized as a multi-organ disease, with a broad spectrum of symptoms including kidney abnormalities (renal cysts, renal hypodysplasia, single kidney, horseshoe kidneys, hydronephrosis), early-onset diabetes mellitus, abnormal liver function, pancreatic hypoplasia and genital tract malformations. In the present study, using capillary electrophoresis coupled to mass spectrometry (CE-MS), we investigated the urinary proteome of a pediatric cohort of RCAD patients and different controls to identify peptide biomarkers and obtain further insights into the pathophysiology of this disorder. As a result, 146 peptides were found to be associated with RCAD in 22 pediatric patients when compared to 22 healthy age-matched controls. A classifier based on these peptides was generated and further tested on an independent cohort, clearly discriminating RCAD patients from different groups of controls. This study demonstrates that the urinary proteome of pediatric RCAD patients differs from autosomal dominant polycystic kidney disease (PKD1, PKD2), congenital nephrotic syndrome (NPHS1, NPHS2, NPHS4, NPHS9) as well as from chronic kidney disease conditions, suggesting differences between the pathophysiology behind these disorders.
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Affiliation(s)
- Pierbruno Ricci
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Pedro Magalhães
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | | | - Erica Daina
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri - Clinical Research Center for Rare Diseases Aldo e Cele Daccò, Ranica Bergamo, Italy
| | | | - Laura Goea
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Iwona Belczacka
- Mosaiques Diagnostics GmbH, Hannover, Germany
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | - Giuseppe Remuzzi
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri - Clinical Research Center for Rare Diseases Aldo e Cele Daccò, Ranica Bergamo, Italy
| | - Muriel Umbhauer
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Jens Drube
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | - Lars Pape
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Stéphane Decramer
- Service de Néphrologie Pédiatrique, Hôpital des Enfants, CHU Toulouse, Toulouse, France
- Centre De Référence des Maladies Rénales Rares du Sud Ouest (SORARE), Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Franz Schaefer
- University Children Hospital, Pediatric Nephrology, Heidelberg, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Silvia Cereghini
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
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14
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Siwy J, Klein T, Rosler M, von Eynatten M. Urinary Proteomics as a Tool to Identify Kidney Responders to Dipeptidyl Peptidase-4 Inhibition: A Hypothesis-Generating Analysis from the MARLINA-T2D Trial. Proteomics Clin Appl 2019; 13:e1800144. [PMID: 30632692 DOI: 10.1002/prca.201800144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/27/2018] [Indexed: 01/13/2023]
Abstract
PURPOSE Chronic kidney disease (CKD) is a serious complication of hyperglycemia and treatment options to slow its progression are scarce. Dipeptidyl peptidase-4 (DPP-4) inhibitors are common glucose-lowering drugs in type 2 diabetes (T2D). Among these, linagliptin has been suggested to exert kidney protective effects. It is investigated whether an effect of linagliptin on kidney function could be unmasked by characterizing the urinary proteome profile (UPP) in albuminuric T2D individuals. EXPERIMENTAL DESIGN Participants of the MARLINA-T2D trial (NCT01792518) are randomized 1:1 to receive either linagliptin 5 mg or placebo for 24 weeks. A previously developed proteome-based classifier, CKD273, is assessed. RESULTS Results confirm a significant correlation between CKD273 and clinical kidney parameters as well as with eGFR decline. Patient stratification using CKD273 at baseline, show a trend toward attenuation of renal function loss in high CKD-risk patients treated with linagliptin. Moreover, characterized are linagliptin affected peptides of which the majority contained a DPP-4 target sequence. CONCLUSIONS AND CLINICAL RELEVANCE CKD273 is a promising tool for identifying patients at high risk for CKD progression and may unmask a potential of linagliptin to slow progressive kidney function loss in high CKD-risk patients. UPP characterization reveals a significant impact of linagliptin on urinary peptides.
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Affiliation(s)
- Justyna Siwy
- mosaiques-diagnostics GmbH, Rotenburger Str. 20, 30659, Hannover, Germany
| | - Thomas Klein
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riß, Germany
| | - Marcel Rosler
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riß, Germany
| | - Maximilian von Eynatten
- Boehringer Ingelheim International GmbH. KG, Binger Str. 173, 55216, Ingelheim am Rhein, Germany
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15
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Wallbach M, Zürbig P, Dihazi H, Müller GA, Wachter R, Beige J, Koziolek MJ, Mischak H. Kidney protective effects of baroreflex activation therapy in patients with resistant hypertension. J Clin Hypertens (Greenwich) 2018; 20:1519-1526. [PMID: 30203514 DOI: 10.1111/jch.13365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/27/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
Baroreflex activation therapy (BAT) is approved for the treatment of resistant hypertension. In addition to blood pressure (BP) reduction, pilot studies suggested several organoprotective effects of BAT. Thirty-two patients with resistant hypertension were prospectively treated with BAT. Besides office BP and 24-hour ambulatory BP (ABP) measurements, detection of a urinary proteome-based classifier (CKD273), which has been shown to predict chronic kidney disease (CKD) progression, was carried out at baseline and after 6 months of BAT. Office BP significantly decreased from 170 ± 25/90 ± 18 to 149 ± 29/82 ± 18 mm Hg. Analysis of CKD273 score and eGFR with CKD-EPI equation at baseline revealed strong correlation (r = 0.568, P < 0.001). After 6 months of BAT, there was no significant change in CKD273 score (-0.061 [95% CI: -0.262 to 0.140], P = 0.601). However, by stratification of the data regarding ABP response, there was a statistically significant (P = 0.0113) reduction in the CKD273 score from a mean of 0.161 [95% CI: -0.093 to 0.414] to -0.346 [95% CI: -0.632 to -0.060] after BAT in patients with systolic ABP decrease of ≥5 mm Hg. These data emphasized potential nephroprotective effects of BAT in patients with sufficient BP response.
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Affiliation(s)
- Manuel Wallbach
- Department of Nephrology & Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Hassan Dihazi
- Department of Nephrology & Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Gerhard A Müller
- Department of Nephrology & Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Rolf Wachter
- Department of Cardiology & Pneumology, University Medical Center Göttingen, Göttingen, Germany.,Clinic and Policlinic for Cardiology, University Hospital Leipzig, Leipzig, Germany
| | - Joachim Beige
- Department of Nephrology/KfH Renal Unit, Hospital Sankt Georg, Leipzig, Germany.,Martin-Luther-University Halle/Wittenberg, Halle, Germany
| | - Michael J Koziolek
- Department of Nephrology & Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
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16
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Ozen S, Batu ED. Vasculitis Pathogenesis: Can We Talk About Precision Medicine? Front Immunol 2018; 9:1892. [PMID: 30154798 PMCID: PMC6102378 DOI: 10.3389/fimmu.2018.01892] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/31/2018] [Indexed: 12/27/2022] Open
Abstract
Precision medicine is designing the medical care by taking into account the individual variability for each person. We have tried to address whether the existing data may guide precision medicine in primary systemic vasculitides (PSV). We have reviewed genome-wide association studies (GWAS) data, lessons from monogenic mimics of these diseases, and biomarker studies in immunoglobulin A vasculitis/Henoch–Schönlein purpura, Kawasaki disease, anti-neutrophil cytoplasmic antibody-associated vasculitis, polyarteritis nodosa (PAN), Takayasu arteritis, and Behçet’s disease (BD). GWAS provide insights about the pathogenesis of PSV while whole exome sequencing studies lead to discovery of monogenic vasculitides, phenotype of which could mimic other types of vasculitis such as PAN and BD. Monogenic vasculitides form a subgroup of vasculitis which are caused by single gene alterations and discovery of these diseases has enabled more specific therapies in these patients. With increasing number of studies on biomarkers, new targets for treatment appear and better and structured follow-up of PSV patients will become possible. Proteomics and metabolomics studies are required to better categorize our patients with PSV so that we can manage them appropriately and offer more targeted therapy.
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Affiliation(s)
- Seza Ozen
- Division of Rheumatology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ezgi Deniz Batu
- Division of Rheumatology, Department of Pediatrics, University of Health Sciences, Ankara Training and Research Hospital, Ankara, Turkey
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17
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Siwy J, Zürbig P, Argiles A, Beige J, Haubitz M, Jankowski J, Julian BA, Linde PG, Marx D, Mischak H, Mullen W, Novak J, Ortiz A, Persson F, Pontillo C, Rossing P, Rupprecht H, Schanstra JP, Vlahou A, Vanholder R. Noninvasive diagnosis of chronic kidney diseases using urinary proteome analysis. Nephrol Dial Transplant 2018; 32:2079-2089. [PMID: 27984204 DOI: 10.1093/ndt/gfw337] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
Background In spite of its invasive nature and risks, kidney biopsy is currently required for precise diagnosis of many chronic kidney diseases (CKDs). Here, we explored the hypothesis that analysis of the urinary proteome can discriminate different types of CKD irrespective of the underlying mechanism of disease. Methods We used data from the proteome analyses of 1180 urine samples from patients with different types of CKD, generated by capillary electrophoresis coupled to mass spectrometry. A set of 706 samples served as the discovery cohort, and 474 samples were used for independent validation. For each CKD type, peptide biomarkers were defined using statistical analysis adjusted for multiple testing. Potential biomarkers of statistical significance were combined in support vector machine (SVM)-based classifiers. Results For seven different types of CKD, several potential urinary biomarker peptides (ranging from 116 to 619 peptides) were defined and combined into SVM-based classifiers specific for each CKD. These classifiers were validated in an independent cohort and showed good to excellent accuracy for discrimination of one CKD type from the others (area under the receiver operating characteristic curve ranged from 0.77 to 0.95). Sequence analysis of the biomarkers provided further information that may clarify the underlying pathophysiology. Conclusions Our data indicate that urinary proteome analysis has the potential to identify various types of CKD defined by pathological assessment of renal biopsies and current clinical practice in general. Moreover, these approaches may provide information to model molecular changes per CKD.
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Affiliation(s)
| | | | | | - Joachim Beige
- KfH Renal Unit, Department Nephrology, Leipzig and Martin Luther University, Halle/Wittenberg, Germany
| | - Marion Haubitz
- Department of Nephrology, Klinikum Fulda gAG, Fulda, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany.,School for Cardiovascular Diseases (CARIM), University of Maastricht, Maastricht, The Netherlands
| | - Bruce A Julian
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - David Marx
- Department of Nephrology and Kidney Transplantation, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hanover, Germany.,BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alberto Ortiz
- School of Medicine, Jimenez Diaz Foundation Institute for Health Research, Autonomous University of Madrid, Madrid, Spain
| | | | - Claudia Pontillo
- Mosaiques Diagnostics GmbH, Hanover, Germany.,Charite-Universitätsmedizin, Berlin, Germany
| | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark.,Faculty of Health, University of Aarhus, Aarhus, Denmark.,Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, French Institute of Health and Medical Research U1048, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Antonia Vlahou
- Division of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Raymond Vanholder
- Nephrology Section, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
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18
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Pontillo C, Jacobs L, Staessen JA, Schanstra JP, Rossing P, Heerspink HJL, Siwy J, Mullen W, Vlahou A, Mischak H, Vanholder R, Zürbig P, Jankowski J. A urinary proteome-based classifier for the early detection of decline in glomerular filtration. Nephrol Dial Transplant 2018; 32:1510-1516. [PMID: 27387473 DOI: 10.1093/ndt/gfw239] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/02/2016] [Indexed: 12/13/2022] Open
Abstract
Background Chronic kidney disease (CKD) progression is currently assessed by a decline in estimated glomerular filtration rate (eGFR) and/or an increase in urinary albumin excretion (UAE). However, these markers are considered either to be late-stage markers or to have low sensitivity or specificity. In this study, we investigated the performance of the urinary proteome-based classifier CKD273, compared with UAE, in a number of different narrow ranges of CKD severity, with each range separated by an eGFR of 10 mL/min/1.73 m 2 . Methods A total of 2672 patients with different CKD stages were included in the study. Of these, 394 individuals displayed a decline in eGFR of >5 mL/min/1.73 m 2 /year (progressors) and the remaining individuals were considered non-progressors. For all samples, UAE values and CKD273 classification scores were obtained. To assess UAE values and CKD273 scores at different disease stages, the cohort was divided according to baseline eGFRs of ≥80, 70-79, 60-69, 50-59, 40-49, 30-39 and <29 mL/min/1.73 m 2 . In addition, areas under the curve for CKD273 and UAE were calculated. Results In early stage CKD, the urinary proteome-based classifier performed significantly better than UAE in detecting progressors. In contrast, UAE performed better in patients with late-stage CKD. No significant difference in performance was found between CKD273 and UAE in patients with moderately reduced renal function. Conclusions These results suggest that urinary peptides, as combined in the CKD273 classifier, allow the detection of progressive CKD at early stages, a point where therapeutic intervention is more likely to be effective. However, late-stage disease, where irreversible damage of the kidney is already present, is better detected by UAE.
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Affiliation(s)
- Claudia Pontillo
- Mosaiques Diagnostics, Hanover, Germany.,Charité-Universitatsmedizin, Berlin, Germany
| | - Lotte Jacobs
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Jan A Staessen
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium.,R&D VitaK Group, Maastricht University, Maastricht, The Netherlands
| | - Joost P Schanstra
- Institute of Metabolic and Cardiovascular Diseases, Inserm U1048, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark.,University of Aarhus, Aarhus, Denmark.,Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Harald Mischak
- Mosaiques Diagnostics, Hanover, Germany.,University of Glasgow, Glasgow, UK
| | - Ray Vanholder
- Nephrology Section, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Joachim Jankowski
- Charité-Universitatsmedizin, Berlin, Germany.,Institute for Molecular Cardiovascular Research, University Hospital RWTH, Aachen, Germany.,Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), University of Maastricht, Maastricht, The Netherlands
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19
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Lindhardt M, Persson F, Zürbig P, Stalmach A, Mischak H, de Zeeuw D, Lambers Heerspink H, Klein R, Orchard T, Porta M, Fuller J, Bilous R, Chaturvedi N, Parving HH, Rossing P. Urinary proteomics predict onset of microalbuminuria in normoalbuminuric type 2 diabetic patients, a sub-study of the DIRECT-Protect 2 study. Nephrol Dial Transplant 2018; 32:1866-1873. [PMID: 27507891 DOI: 10.1093/ndt/gfw292] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/13/2016] [Indexed: 11/12/2022] Open
Abstract
Background Early prevention of diabetic nephropathy is not successful as early interventions have shown conflicting results, partly because of a lack of early and precise indicators of disease development. Urinary proteomics has shown promise in this regard and could identify those at high risk who might benefit from treatment. In this study we investigate its utility in a large type 2 diabetic cohort with normoalbuminuria. Methods We performed a post hoc analysis in the Diabetic Retinopathy Candesartan Trials (DIRECT-Protect 2 study), a multi centric randomized clinical controlled trial. Patients were allocated to candesartan or placebo, with the aim of slowing the progression of retinopathy. The secondary endpoint was development of persistent microalbuminuria (three of four samples). We used a previously defined chronic kidney disease risk score based on proteomic measurement of 273 urinary peptides (CKD273-classifier). A Cox regression model for the progression of albuminuria was developed and evaluated with integrated discrimination improvement (IDI), continuous net reclassification index (cNRI) and receiver operating characteristic curve statistics. Results Seven hundred and thirty-seven patients were analysed and 89 developed persistent microalbuminuria (12%) with a mean follow-up of 4.1 years. At baseline the CKD273-classifier predicted development of microalbuminuria during follow-up, independent of treatment (candesartan/placebo), age, gender, systolic blood pressure, urine albumin excretion rate, estimated glomerular filtration rate, HbA1c and diabetes duration, with hazard ratio 2.5 [95% confidence interval (CI) 1.4-4.3; P = 0.002] and area under the curve 0.79 (95% CI 0.75-0.84; P < 0.0001). The CKD273-classifier improved the risk prediction (relative IDI 14%, P = 0.002; cNRI 0.10, P = 0.043). Conclusions In this cohort of patients with type 2 diabetes and normoalbuminuria from a large intervention study, the CKD273-classifier was an independent predictor of microalbuminuria. This may help identify high-risk normoalbuminuric patients for preventive strategies for diabetic nephropathy.
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Affiliation(s)
| | | | | | | | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,University of Glasgow, Glasgow, UK
| | - Dick de Zeeuw
- Department of Clinical Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hiddo Lambers Heerspink
- Department of Clinical Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Trevor Orchard
- Department of Epidemiology, Medicine & Pediatrics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Massimo Porta
- Department of Medical Sciences, University of Turin, Torino, Italy
| | - John Fuller
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Rudolf Bilous
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.,South Tees NHS Trust, Middlesbrough, UK
| | - Nish Chaturvedi
- Institute of Cardiovascular Sciences, University College London, London, UK
| | - Hans-Henrik Parving
- Department of Medical Endocrinology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark.,Faculty of Health Science, University of Aarhus, Aarhus, Denmark.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
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20
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Monocyte Chemoattractant Protein-1 in Antineutrophil Cytoplasmic Autoantibody-Associated Vasculitis: Biomarker Potential and Association with Polymorphisms in the MCP-1 and the CC Chemokine Receptor-2 Gene. Mediators Inflamm 2018; 2018:6861257. [PMID: 29720895 PMCID: PMC5867591 DOI: 10.1155/2018/6861257] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 11/23/2022] Open
Abstract
Antineutrophil cytoplasmic autoantibody- (ANCA-) associated vasculitis (AAV) are relapsing-remitting disorders with unpredictable prognosis. There is a need of biomarkers for distinguishing which patients will have a more severe outcome and also for predicting relapses in disease activity. This study confirms the previous results of urinary MCP-1 (uMCP-1) as a prognostic marker and explores its potential as a marker of disease activity. Method. 114 patients with AAV were followed regularly between 2002 and 2011 at Skåne University Hospital. Urine samples, blood samples, and clinical status were registered. The urine samples were analyzed in an in-house-developed ELISA. PCR-RLFP was used to analyze the MCP-1 and CCR2 genes. Results. Patients with severe prognosis had significantly higher levels of uMCP-1 compared to patients with nonsevere prognosis and healthy controls. Patients with renal damage had higher levels compared to patients who did not have renal damage. There was also a tendency of higher uMCP-1 levels in active disease as compared to remission. AA in the -2518 position in the MCP-1 gene was associated with a more severe outcome compared to the A/G or the G/G genotype. The A/A genotype were also associated with higher levels of uMCP-1. No significant associations were seen for the CCR2-V64I. Conclusion. This study confirmed the connection between high uMCP-1 levels and poor prognosis and also disease activity. It also suggests an association of the A/A genotype at position -2518 in the MCP-1 gene and poor prognosis in AAV. uMCP-1 is clearly a candidate biomarker of potential clinical value. The A/A genotype association needs further evaluation.
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21
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Krochmal M, Schanstra JP, Mischak H. Urinary peptidomics in kidney disease and drug research. Expert Opin Drug Discov 2017; 13:259-268. [DOI: 10.1080/17460441.2018.1418320] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Magdalena Krochmal
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, Greece
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Joost P Schanstra
- Institut of Cardiovascular and Metabolic Disease, Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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22
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Cherney D, Perkins BA, Lytvyn Y, Heerspink H, Rodríguez-Ortiz ME, Mischak H. The effect of sodium/glucose cotransporter 2 (SGLT2) inhibition on the urinary proteome. PLoS One 2017; 12:e0186910. [PMID: 29084249 PMCID: PMC5662219 DOI: 10.1371/journal.pone.0186910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/14/2017] [Indexed: 12/02/2022] Open
Abstract
Treatment with empagliflozin, an inhibitor of the sodium/glucose cotransporter 2 (SGLT2), is associated with slower progression of diabetic kidney disease. In this analysis, we explored the hypothesis that empagliflozin may have an impact on urinary peptides associated with chronic kidney disease (CKD). In this post-hoc, exploratory analysis, we investigated urine samples obtained from 40 patients with uncomplicated type 1 diabetes (T1D) before and after treatment with empagliflozin for 8 weeks to for significant post-therapy changes in urinary peptides. We further assessed the association of these changes with CKD in an independent cohort, and with a previously established urinary proteomic panel, termed CKD273. 107 individual peptides significantly changed after treatment. The majority of the empagliflozin-induced changes were in the direction of “CKD absent” when compare to patients with CKD and controls. A classifier consisting of these 107 peptides scored significantly different in controls, in comparison to CKD patients. However, empagliflozin did not impact the CKD273 classifier. Our data indicate that empagliflozin induces multiple significant changes in the urinary proteomic markers such as mucin and clusterin. The relationship between empagliflozin-induced proteomic changes and clinical outcomes merits further investigation.
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Affiliation(s)
- David Cherney
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - Bruce A. Perkins
- Division of Endocrinology, University Health Network, University of Toronto, Toronto, Canada
| | - Yuliya Lytvyn
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - Hiddo Heerspink
- Department of Clinical Pharmacology University Medical Center Groningen, Groningen, the Netherlands
| | - María E. Rodríguez-Ortiz
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz. Fundación Renal Iñigo Álvarez de Toledo. Universidad Autónoma de Madrid. REDinREN, Madrid, Spain
| | - Harald Mischak
- Mosaiques diagnostics GmbH, Hanover, Germany
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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23
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Markoska K, Pejchinovski M, Pontillo C, Zürbig P, Jacobs L, Smith A, Masin-Spasovska J, Stojceva-Taneva O, Polenakovic M, Magni F, Mischak H, Spasovski G. Urinary peptide biomarker panel associated with an improvement in estimated glomerular filtration rate in chronic kidney disease patients. Nephrol Dial Transplant 2017; 33:751-759. [DOI: 10.1093/ndt/gfx263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/09/2017] [Indexed: 01/21/2023] Open
Affiliation(s)
| | | | - Claudia Pontillo
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Petra Zürbig
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Lotte Jacobs
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Andrew Smith
- Unit of Proteomics, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | | | | | - Fulvio Magni
- Unit of Proteomics, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Harald Mischak
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Goce Spasovski
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
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24
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Zhang ZY, Ravassa S, Nkuipou-Kenfack E, Yang WY, Kerr SM, Koeck T, Campbell A, Kuznetsova T, Mischak H, Padmanabhan S, Dominiczak AF, Delles C, Staessen JA. Novel Urinary Peptidomic Classifier Predicts Incident Heart Failure. J Am Heart Assoc 2017; 6:e005432. [PMID: 28784649 PMCID: PMC5586413 DOI: 10.1161/jaha.116.005432] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/05/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Detection of preclinical cardiac dysfunction and prognosis of left ventricular heart failure (HF) would allow targeted intervention, and appears to be the most promising approach in its management. Novel biomarker panels may support this approach and provide new insights into the pathophysiology. METHODS AND RESULTS A retrospective comparison of urinary proteomic profiles generated by mass spectrometric analysis from 49 HF patients, 36 patients who progressed to HF within 2.6±1.6 years, and 192 sex- and age-matched controls who did not progress to HF enabled identification of 96 potentially HF-specific peptide biomarkers. Based on these 96 peptides, the classifier called Heart Failure Predictor (HFP) was established by support vector machine modeling. The incremental prognostic value of HFP was subsequently evaluated in urine samples from 175 individuals with asymptomatic diastolic dysfunction from an independent population cohort. Within 4.8 years, 17 of these individuals progressed to overt HF. The area under receiver-operating characteristic curve was 0.70 (95% CI, 0.56-0.82); P=0.0047 for HFP and 0.57 (0.42-0.72; P=0.62) for N-terminal pro b-type natriuretic peptide. Hazard ratios were 1.63 (CI, 1.04-2.55; P=0.032) per 1-SD increment in HFP and 0.70 (CI, 0.35-1.41; P=0.32) for a doubling of the logarithmically transformed N-terminal pro b-type natriuretic peptide. CONCLUSIONS HFP is a novel biomarker derived from the urinary proteome and might serve as a sensitive tool to improve risk stratification, patient management, and understanding of the pathophysiology of HF.
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Affiliation(s)
- Zhen-Yu Zhang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Susana Ravassa
- Program of Cardiovascular Diseases, Centre for Applied Medical Research, Navarra Institute for Health Research, University of Navarra, Pamplona, Spain
- CIBERCV Carlos III Institute of Health, Madrid, Spain
| | | | - Wen-Yi Yang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Shona M Kerr
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom
| | - Thomas Koeck
- Mosaiques Diagnostics and Therapeutics AG, Hanover, Germany
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom
| | - Tatiana Kuznetsova
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Harald Mischak
- Mosaiques Diagnostics and Therapeutics AG, Hanover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, United Kingdom
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, United Kingdom
| | - Anna F Dominiczak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, United Kingdom
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, United Kingdom
| | - Jan A Staessen
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
- R & D Group VitaK, Maastricht University, Maastricht, The Netherlands
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25
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Pontillo C, Mischak H. Urinary peptide-based classifier CKD273: towards clinical application in chronic kidney disease. Clin Kidney J 2017; 10:192-201. [PMID: 28694965 PMCID: PMC5499684 DOI: 10.1093/ckj/sfx002] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Capillary electrophoresis coupled with mass spectrometry (CE-MS) has been used as a platform for discovery and validation of urinary peptides associated with chronic kidney disease (CKD). CKD affects ∼ 10% of the population, with high associated costs for treatments. A urinary proteome-based classifier (CKD273) has been discovered and validated in cross-sectional and longitudinal studies to assess and predict the progression of CKD. It has been implemented in studies employing cohorts of > 1000 patients. CKD273 is commercially available as an in vitro diagnostic test for early detection of CKD and is currently being used for patient stratification in a multicentre randomized clinical trial (PRIORITY). The validity of the CKD273 classifier has recently been evaluated applying the Oxford Evidence-Based Medicine and Southampton Oxford Retrieval Team guidelines and a letter of support for CKD273 was issued by the US Food and Drug Administration. In this article we review the current evidence published on CKD273 and the challenges associated with implementation. Definition of a possible surrogate early endpoint combined with CKD273 as a biomarker for patient stratification currently appears as the most promising strategy to enable the development of effective drugs to be used at an early time point when intervention can still be effective.
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Affiliation(s)
| | - Harald Mischak
- Mosaiques Diagnostics, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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26
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Htun NM, Magliano DJ, Zhang ZY, Lyons J, Petit T, Nkuipou-Kenfack E, Ramirez-Torres A, von zur Muhlen C, Maahs D, Schanstra JP, Pontillo C, Pejchinovski M, Snell-Bergeon JK, Delles C, Mischak H, Staessen JA, Shaw JE, Koeck T, Peter K. Prediction of acute coronary syndromes by urinary proteome analysis. PLoS One 2017; 12:e0172036. [PMID: 28273075 PMCID: PMC5342174 DOI: 10.1371/journal.pone.0172036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/30/2017] [Indexed: 01/20/2023] Open
Abstract
Identification of individuals who are at risk of suffering from acute coronary syndromes (ACS) may allow to introduce preventative measures. We aimed to identify ACS-related urinary peptides, that combined as a pattern can be used as prognostic biomarker. Proteomic data of 252 individuals enrolled in four prospective studies from Australia, Europe and North America were analyzed. 126 of these had suffered from ACS within a period of up to 5 years post urine sampling (cases). Proteomic analysis of 84 cases and 84 matched controls resulted in the discovery of 75 ACS-related urinary peptides. Combining these to a peptide pattern, we established a prognostic biomarker named Acute Coronary Syndrome Predictor 75 (ACSP75). ACSP75 demonstrated reasonable prognostic discrimination (c-statistic = 0.664), which was similar to Framingham risk scoring (c-statistics = 0.644) in a validation cohort of 42 cases and 42 controls. However, generating by a composite algorithm named Acute Coronary Syndrome Composite Predictor (ACSCP), combining the biomarker pattern ACSP75 with the previously established urinary proteomic biomarker CAD238 characterizing coronary artery disease as the underlying aetiology, and age as a risk factor, further improved discrimination (c-statistic = 0.751) resulting in an added prognostic value over Framingham risk scoring expressed by an integrated discrimination improvement of 0.273 ± 0.048 (P < 0.0001) and net reclassification improvement of 0.405 ± 0.113 (P = 0.0007). In conclusion, we demonstrate that urinary peptide biomarkers have the potential to predict future ACS events in asymptomatic patients. Further large scale studies are warranted to determine the role of urinary biomarkers in clinical practice.
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Affiliation(s)
- Nay M. Htun
- Atherothrombosis and Vascular Biology, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
- Department of Medicine, Monash University, Melbourne, Australia
| | - Dianna J. Magliano
- Clinical Diabetes and Epidemiology, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Zhen-Yu Zhang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Jasmine Lyons
- Clinical Diabetes and Epidemiology, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Thibault Petit
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | | | - Adela Ramirez-Torres
- Mosaiques Diagnostics GmbH, Hanover, Germany
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | | | - David Maahs
- Department of Paediatrics, Stanford School of Medicine, Stanford, California, United States of America
- Barbara Davis Centre for Diabetes, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Joost P. Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | | | - Janet K. Snell-Bergeon
- Barbara Davis Centre for Diabetes, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hanover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jan A. Staessen
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
- R&D VitaK Group, Maastricht University, Maastricht, Netherlands
| | - Jonathan E. Shaw
- Clinical Diabetes and Epidemiology, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | | | - Karlheinz Peter
- Atherothrombosis and Vascular Biology, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
- Department of Medicine, Monash University, Melbourne, Australia
- * E-mail:
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27
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Nkuipou-Kenfack E, Zürbig P, Mischak H. The long path towards implementation of clinical proteomics: Exemplified based on CKD273. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/28/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Harald Mischak
- Mosaiques Diagnostics GmbH; Hannover Germany
- BHF Glasgow Cardiovascular Research Centre; University of Glasgow; Glasgow United Kingdom
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28
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Siebert S, Porter D, Paterson C, Hampson R, Gaya D, Latosinska A, Mischak H, Schanstra J, Mullen W, McInnes I. Urinary proteomics can define distinct diagnostic inflammatory arthritis subgroups. Sci Rep 2017; 7:40473. [PMID: 28091549 PMCID: PMC5320079 DOI: 10.1038/srep40473] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/06/2016] [Indexed: 01/17/2023] Open
Abstract
Current diagnostic tests applied to inflammatory arthritis lack the necessary specificity to appropriately categorise patients. There is a need for novel approaches to classify patients with these conditions. Herein we explored whether urinary proteomic biomarkers specific for different forms of arthritis (rheumatoid arthritis (RA), psoriatic arthritis (PsA), osteoarthritis (OA)) or chronic inflammatory conditions (inflammatory bowel disease (IBD)) can be identified. Fifty subjects per group with RA, PsA, OA or IBD and 50 healthy controls were included in the study. Two-thirds of these populations were randomly selected to serve as a training set, while the remaining one-third was reserved for validation. Sequential comparison of one group to the other four enabled identification of multiple urinary peptides significantly associated with discrete pathological conditions. Classifiers for the five groups were developed and subsequently tested blind in the validation test set. Upon unblinding, the classifiers demonstrated excellent performance, with an area under the curve between 0.90 and 0.97 per group. Identification of the peptide markers pointed to dysregulation of collagen synthesis and inflammation, but also novel inflammatory markers. We conclude that urinary peptide signatures can reliably differentiate between chronic arthropathies and inflammatory conditions with discrete pathogenesis.
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Affiliation(s)
- Stefan Siebert
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Duncan Porter
- Rheumatology Department, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Caron Paterson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rosie Hampson
- Rheumatology Department, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Daniel Gaya
- Gastroenterology Department, NHS Greater Glasgow and Clyde, Glasgow, UK
| | | | - Harald Mischak
- Mosaiques Diagnostics, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Joost Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, 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
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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29
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Stanley E, Delatola EI, Nkuipou-Kenfack E, Spooner W, Kolch W, Schanstra JP, Mischak H, Koeck T. Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease. BMC Bioinformatics 2016; 17:496. [PMID: 27923348 PMCID: PMC5139137 DOI: 10.1186/s12859-016-1390-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 11/26/2022] Open
Abstract
Background When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomarkers. The purpose of this study was thus to evaluate the effectiveness of different statistical methods applied for urinary proteomic biomarker discovery and different methods of classifier modelling in respect of the diagnosis of coronary artery disease in 197 study subjects and the prognostication of acute coronary syndromes in 368 study subjects. Results Computing the discovery sub-cohorts comprising \documentclass[12pt]{minimal}
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\begin{document}$$ {\scriptscriptstyle \raisebox{1ex}{$2$}\!\left/ \!\raisebox{-1ex}{$3$}\right.} $$\end{document}23 of the study subjects based on the Wilcoxon rank sum test, t-score, cat-score, binary discriminant analysis and random forests provided largely different numbers (ranging from 2 to 398) of potential peptide biomarkers. Moreover, these biomarker patterns showed very little overlap limited to fragments of type I and III collagens as the common denominator. However, these differences in biomarker patterns did mostly not translate into significant differently performing diagnostic or prognostic classifiers modelled by support vector machine, diagonal discriminant analysis, linear discriminant analysis, binary discriminant analysis and random forest. This was even true when different biomarker patterns were combined into master-patterns. Conclusion In conclusion, our study revealed a very considerable dependence of peptide biomarker discovery on statistical computing of urinary peptide profiles while the observed diagnostic and/or prognostic reliability of classifiers was widely independent of the modelling approach. This may however be due to the limited statistical power in classifier testing. Nonetheless, our study showed that urinary proteome analysis has the potential to provide valuable biomarkers for coronary artery disease mirroring especially alterations in the extracellular matrix. It further showed that for a comprehensive discovery of biomarkers and thus of pathological information, the results of different statistical methods may best be combined into a master pattern that then can be used for classifier modelling. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1390-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eleanor Stanley
- Eagle Genomics Ltd, The Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK
| | | | | | - William Spooner
- Eagle Genomics Ltd, The Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hanover, Germany. .,Institute of Cardiovascular and Medical Sciences, University of Glasgow, G12 8TA, Glasgow, UK.
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30
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Rossing K, Bosselmann HS, Gustafsson F, Zhang ZY, Gu YM, Kuznetsova T, Nkuipou-Kenfack E, Mischak H, Staessen JA, Koeck T, Schou M. Urinary Proteomics Pilot Study for Biomarker Discovery and Diagnosis in Heart Failure with Reduced Ejection Fraction. PLoS One 2016; 11:e0157167. [PMID: 27308822 PMCID: PMC4911082 DOI: 10.1371/journal.pone.0157167] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/25/2016] [Indexed: 01/06/2023] Open
Abstract
Background Biomarker discovery and new insights into the pathophysiology of heart failure with reduced ejection fraction (HFrEF) may emerge from recent advances in high-throughput urinary proteomics. This could lead to improved diagnosis, risk stratification and management of HFrEF. Methods and Results Urine samples were analyzed by on-line capillary electrophoresis coupled to electrospray ionization micro time-of-flight mass spectrometry (CE-MS) to generate individual urinary proteome profiles. In an initial biomarker discovery cohort, analysis of urinary proteome profiles from 33 HFrEF patients and 29 age- and sex-matched individuals without HFrEF resulted in identification of 103 peptides that were significantly differentially excreted in HFrEF. These 103 peptides were used to establish the support vector machine-based HFrEF classifier HFrEF103. In a subsequent validation cohort, HFrEF103 very accurately (area under the curve, AUC = 0.972) discriminated between HFrEF patients (N = 94, sensitivity = 93.6%) and control individuals with and without impaired renal function and hypertension (N = 552, specificity = 92.9%). Interestingly, HFrEF103 showed low sensitivity (12.6%) in individuals with diastolic left ventricular dysfunction (N = 176). The HFrEF-related peptide biomarkers mainly included fragments of fibrillar type I and III collagen but also, e.g., of fibrinogen beta and alpha-1-antitrypsin. Conclusion CE-MS based urine proteome analysis served as a sensitive tool to determine a vast array of HFrEF-related urinary peptide biomarkers which might help improving our understanding and diagnosis of heart failure.
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Affiliation(s)
- Kasper Rossing
- Department of Cardiology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Helle Skovmand Bosselmann
- Department of Cardio-, Nephro-, and Endocrinology, North Zealand Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Finn Gustafsson
- Department of Cardiology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Zhen-Yu Zhang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Yu-Mei Gu
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Tatiana Kuznetsova
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | | | - Harald Mischak
- Mosaiques Diagnostics and Therapeutics AG, Hanover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jan A. Staessen
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Thomas Koeck
- Mosaiques Diagnostics and Therapeutics AG, Hanover, Germany
| | - Morten Schou
- Institute for Clinical Medicine, Herlev Hospital, Herlev, Denmark
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31
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Mischak H. Pro: urine proteomics as a liquid kidney biopsy: no more kidney punctures! Nephrol Dial Transplant 2016; 30:532-7. [PMID: 25801638 DOI: 10.1093/ndt/gfv046] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this article, the benefits of urinary proteomics in comparison with kidney biopsy are discussed. The majority of urinary proteins are generated by the kidney, hence the urinary proteome holds substantial information on the kidney, and assessment of the urinary proteome could be considered a 'liquid biopsy'. The main question is how well the information contained in the urinary proteome can be assessed today, if it is ready to be routinely used, and what are the advantages and possible disadvantages in comparison with current standards. Since chronic kidney disease (CKD) is by far the largest area in nephrology based on the number of patients affected, the focus of this article is on CKD. Substantial progress was made in the last decade in urinary proteomics, and today we have comparable urinary proteome datasets of tens of thousands of subjects available. Clinical proteomics studies in CKD including close to, or even exceeding, 1000 subjects have recently been published, demonstrating a benefit over the current state-of-the-art in diagnosis and especially prognosis. The first large multicentric randomized controlled intervention trial aiming at preventing CKD by employing urinary proteomics-guided intervention has been initiated recently. These data provide ample evidence for the utility and value of urinary proteomics in nephrology. A further consideration is that the purpose of the biopsy, be it 'liquid' or 'solid', is to guide intervention. However, essentially all drug targets are proteins, not microscopic structures. Therefore, obtaining information on the proteome to guide intervention appears to be the most appropriate approach. Presenting more detailed evidence, I argue that urinary proteome analysis can, in most cases, be employed to guide therapeutic intervention, can be repeated multiple times as it is without any direct risk or discomfort and can be considered as a liquid biopsy.
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Affiliation(s)
- Harald Mischak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK Mosaiques Diagnostics GmbH, Hannover D-30625, Germany
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Farmakis D, Koeck T, Mullen W, Parissis J, Gogas BD, Nikolaou M, Lekakis J, Mischak H, Filippatos G. Urine proteome analysis in heart failure with reduced ejection fraction complicated by chronic kidney disease: feasibility, and clinical and pathogenetic correlates. Eur J Heart Fail 2016; 18:822-9. [DOI: 10.1002/ejhf.544] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/12/2016] [Accepted: 03/12/2016] [Indexed: 12/27/2022] Open
Affiliation(s)
- Dimitrios Farmakis
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
| | - Thomas Koeck
- Mosaiques Diagnostics and Therapeutics AG; Hanover Germany
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre; University of Glasgow; Glasgow UK
| | - John Parissis
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
| | - Bill D. Gogas
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
| | - Maria Nikolaou
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
| | - John Lekakis
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
| | - Harald Mischak
- Mosaiques Diagnostics and Therapeutics AG; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Gerasimos Filippatos
- Heart Failure Unit, Department of Cardiology; Athens University Hospital Attikon; Athens Greece
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von Zur Mühlen C, Koeck T, Schiffer E, Sackmann C, Zürbig P, Hilgendorf I, Reinöhl J, Rivera J, Zirlik A, Hehrlein C, Mischak H, Bode C, Peter K. Urine proteome analysis as a discovery tool in patients with deep vein thrombosis and pulmonary embolism. Proteomics Clin Appl 2016; 10:574-84. [PMID: 26898369 DOI: 10.1002/prca.201500105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/15/2015] [Accepted: 02/08/2016] [Indexed: 02/03/2023]
Abstract
PURPOSE Early and accurate detection of deep vein thrombosis (DVT) is an important clinical need. Based on the hypothesis that urinary peptides may hold information on DVT in conjunction with pulmonary embolism (PE), the study was aimed at identifying such peptide biomarkers using capillary electrophoresis coupled mass spectrometry. EXPERIMENTAL DESIGN Patients with symptoms of unprovoked/idiopathic DVT and/or PE were examined by doppler-sonography or angio-computed tomography. Urinary proteome analysis allowed for identification of respective peptide biomarkers. To confirm their biological relevance, we induced PE in mice and assessed human ex vivo thrombi. RESULTS We identified 62 urinary peptides as DVT-specific biomarkers, i.e. fragments of collagen type I and a fragment of fibrinogen β-chain. The presence of fibrinogen α/β in the acute thrombus, and collagen type I and osteopontin in the older, organized thrombus was demonstrated. The classifier DVT62 established through support vector machine (SVM) modeling based on the 62 identified peptides was validated in an independent cohort of 47 subjects (six cases and 41 controls) with a sensitivity of 100% and specificity of 83%. CONCLUSIONS AND CLINICAL RELEVANCE Urine proteome analysis enabled the detection of DVT-specific peptides, which were validated in human and mouse tissue. Furthermore, it allowed for the establishment of an urinary-proteome based classifier that is relatively specific for DVT. The data provide the basis for assessment of these biomarkers in a prospective clinical study.
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Affiliation(s)
| | | | | | - Christine Sackmann
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | | | - Ingo Hilgendorf
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Jochen Reinöhl
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Jennifer Rivera
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Andreas Zirlik
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Christoph Hehrlein
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,BHF Glasgow Cardiovascular Research, University of Glasgow, UK
| | - Christoph Bode
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Karlheinz Peter
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
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Jankowski J, Schanstra JP, Mischak H. Body fluid peptide and protein signatures in diabetic kidney diseases. Nephrol Dial Transplant 2016. [PMID: 26209737 DOI: 10.1093/ndt/gfv091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Body fluid protein-based biomarkers carry the hope of improving patient management in diabetes by enabling more accurate and earlier detection of diabetic kidney disease (DKD), but also of defining the most suitable therapeutic targets. We present the data on some of the best studied individual protein markers in body fluids and conclude that their potential in clinical application for assessing DKD is moderate. Proteome-based approaches aiming at the identification of panels of body fluid biomarkers might be a valid alternative. We discuss the past (first) clinical proteomics studies in DKD, stressing their drawbacks but also the lessons that could be learned from them, as well as the more recent studies that have a potential for actual clinical implementation. We also highlight relevant issues and current problems associated with clinical proteomics from discovery towards application, and give suggestions for solutions that may help guiding proteomic studies, thereby removing some of the current hurdles for implementation of potentially beneficial results.
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Affiliation(s)
- Joachim Jankowski
- Universitätsklinikum RWTH Aachen, Institute of Molecular Cardiovascular Research, Aachen, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, Faculty of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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35
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Implementation of CE-MS-identified proteome-based biomarker panels in drug development and patient management. Bioanalysis 2016; 8:439-55. [DOI: 10.4155/bio.16.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The recent advancements in clinical proteomics enabled identification of biomarker panels for a large range of diseases. A number of CE-MS-identified biomarker panels were verified and implemented in clinical studies. Despite multiple challenges, accumulating evidence supports the value and the need for proteome-based biomarker panels. In this perspective, we provide an overview of clinical studies indicating the added value of CE-MS biomarker panels over traditional diagnostics and monitoring methods. We outline apparent advantages of applying novel proteomic biomarker panels for disease diagnosis, prognosis, staging, drug development and patient management. Facing the plethora of benefits associated with the use of CE-MS biomarker panels, we envision their implementation into the medical practice in the near future.
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Lalmahomed ZS, Bröker MEE, van Huizen NA, van den Braak RRJC, Dekker LJM, Rizopoulos D, Verhoef C, Steyerberg EW, Luider TM, IJzermans JNM. Hydroxylated collagen peptide in urine as biomarker for detecting colorectal liver metastases. Am J Cancer Res 2016; 6:321-330. [PMID: 27186406 PMCID: PMC4859663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023] Open
Abstract
The clinical efficacy of carcinoembryonic antigen (CEA) as a marker of colorectal liver metastasis is limited, motivating a search for new biomarkers. Recently, urine proteomic analysis revealed AGPP(-OH)GEAGKP(-OH)GEQGVP(-OH)GDLGAP(-OH)GP (AGP), a promising peptide for this application. This study aimed to determine whether combining urine AGP testing with serum CEA analyses improves the sensitivity of detecting colorectal liver metastases. Urine samples from 100 patients with CRLM were collected prospectively and compared to three control groups: healthy kidney donors, patients who were relapse-free for 24 months after curative CRLM surgery, and primary colorectal cancer patients. A stable isotope labeled peptide standard was used to quantify the abundance of AGP in urine samples by selective reaction monitoring. Combined testing of urine AGP levels and serum CEA levels revealed a significantly increased sensitivity compared to CEA alone (85% vs. 68%, P<0.001; specificity 84% and 91%, respectively). No correlation was found between CEA and AGP-positive test results within individual patients (r(2) = 0.08). Urine AGP testing was negative in the three control groups. These results indicate that collagen-derived urine AGP peptide with a specific hydroxylation pattern combined with serum CEA levels may significantly improve the detection of colorectal liver metastases in patients at risk.
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Affiliation(s)
- Zarina S Lalmahomed
- Division of Transplantation and Hepatobiliary Surgery, Department of Surgery, Erasmus MCRotterdam, The Netherlands
| | - Mirelle EE Bröker
- Division of Transplantation and Hepatobiliary Surgery, Department of Surgery, Erasmus MCRotterdam, The Netherlands
| | - Nick A van Huizen
- Division of Transplantation and Hepatobiliary Surgery, Department of Surgery, Erasmus MCRotterdam, The Netherlands
- Department of Neurology, Erasmus MCRotterdam, The Netherlands
| | | | | | | | - Cornelis Verhoef
- Division of Surgical Oncology, Department of Surgery, Erasmus MCRotterdam, The Netherlands
| | | | - Theo M Luider
- Department of Neurology, Erasmus MCRotterdam, The Netherlands
| | - Jan NM IJzermans
- Division of Transplantation and Hepatobiliary Surgery, Department of Surgery, Erasmus MCRotterdam, The Netherlands
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He X, Yin W, Ding Y, Cui SJ, Luan J, Zhao P, Yue X, Yu C, Laing X, Zhao Y. Higher Serum Angiotensinogen Is an Indicator of IgA Vasculitis with Nephritis Revealed by Comparative Proteomes Analysis. PLoS One 2015; 10:e0130536. [PMID: 26098644 PMCID: PMC4476708 DOI: 10.1371/journal.pone.0130536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/21/2015] [Indexed: 11/28/2022] Open
Abstract
IgA vasculitis (IgAV), previously named as Henoch–Schönlein purpura, is the most common systematic vasculitis with unknown etiology. Lack of appropriate study system and/or animal model limits the understanding of its molecular pathogenesis and hinders the identification of targets for rational therapy, especially for its long-term complication, IgAV nephritis (IgAVN). In this study, we applied comparative analysis of serum proteomes to obtain an insight about disease pathogenesis. This study has utilized high sensitivity nanoscale ultra performance liquid chromatography-mass spectrometry (nanoLC-MS/MS) to investigate the alterations in serum proteomic profiles in patients with IgAV (n=6), IgAVN (n=6) and healthy subjects (n=7). The differentially expressed proteins were subjected to functional pathway analysis by PANTHER and DAVID software. We identified 107 differentially expressed proteins among three different groups, and functional analysis suggested that, in addition to earlier reported pathways, such as acute phase response, immune response, complement and blood coagulation pathways, hemostasis and Wnt signaling pathway were probably involved in pathogenesis of IgAV. A few differentially abundant proteins identified, such as C4a, serum amyloid A, angiotensinogen, and kininogen 1, were further validated by ELISA. More importantly, we found that angiotensinogen concentration is correlated with IgAVN and could be used as a potential marker for the progression of IgAV. This is the first report of analyzing the proteomic alterations in IgAV patients and the differentially proteins identified in this study may enhance understanding of the pathology of IgAV and a few of them may be used to monitor disease progression.
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Affiliation(s)
- Xuelian He
- Clinical research center, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
- * E-mail: (XH); (XL); (YZ)
| | - Wei Yin
- Department of Rheumatology, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Yan Ding
- Department of Rheumatology, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Shu-jian Cui
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiangwei Luan
- Department of Nephrology, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Peiwei Zhao
- Clinical research center, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Xin Yue
- Clinical research center, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Chunhua Yu
- Clinical research center, Wuhan Children’s Hospital, No. 100 Hongkong Rd,Wuhan, China
| | - Xiaohui Laing
- School of Public Health, Wuhan University, Wuhan, China
- * E-mail: (XH); (XL); (YZ)
| | - YuLan Zhao
- Institute of Advanced Interdisciplinary Research, East China Normal University, Shanghai, China
- * E-mail: (XH); (XL); (YZ)
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Pejchinovski M, Klein J, Ramírez-Torres A, Bitsika V, Mermelekas G, Vlahou A, Mullen W, Mischak H, Jankowski V. Comparison of higher energy collisional dissociation and collision-induced dissociation MS/MS sequencing methods for identification of naturally occurring peptides in human urine. Proteomics Clin Appl 2015; 9:531-42. [DOI: 10.1002/prca.201400163] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/27/2015] [Accepted: 03/23/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Martin Pejchinovski
- Charite-Universitätsmedizin Berlin; Berlin Germany
- Mosaiques Diagnostics GmbH; Hanover Germany
| | | | | | - Vasiliki Bitsika
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - George Mermelekas
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Vera Jankowski
- Universitätsklinikum RWTH Aachen; Institute of Molecular Cardiovascular Research; Aachen Germany
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39
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Pejchinovski M, Hrnjez D, Ramirez-Torres A, Bitsika V, Mermelekas G, Vlahou A, Zürbig P, Mischak H, Metzger J, Koeck T. Capillary zone electrophoresis on-line coupled to mass spectrometry: A perspective application for clinical proteomics. Proteomics Clin Appl 2015; 9:453-68. [DOI: 10.1002/prca.201400113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | - Vasiliki Bitsika
- Biotechnology Division; Biomedical Research Foundation, Academy of Athens; Athens Greece
| | - George Mermelekas
- Biotechnology Division; Biomedical Research Foundation, Academy of Athens; Athens Greece
| | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation, Academy of Athens; Athens Greece
- School of Biomedical and Healthcare Sciences; Plymouth University, Plymouth; UK
| | | | - Harald Mischak
- Mosaiques Diagnostics GmbH; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; UK
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Floege J. Moderator's view: Will 'modern' urine proteomics replace 'old-fashioned' renal biopsy? Nephrol Dial Transplant 2015; 30:538-40. [DOI: 10.1093/ndt/gfv040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Lee MY, Huang CH, Kuo CJ, Lin CLS, Lai WT, Chiou SH. Clinical proteomics identifies urinary CD14 as a potential biomarker for diagnosis of stable coronary artery disease. PLoS One 2015; 10:e0117169. [PMID: 25668619 PMCID: PMC4323104 DOI: 10.1371/journal.pone.0117169] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/19/2014] [Indexed: 01/08/2023] Open
Abstract
Inflammation plays a key role in coronary artery disease (CAD) and other manifestations of atherosclerosis. Recently, urinary proteins were found to be useful markers for reflecting inflammation status of different organs. To identify potential biomarker for diagnosis of CAD, we performed one-dimensional SDS-gel electrophoresis followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Among the proteins differentially expressed in urine samples, monocyte antigen CD14 was found to be consistently expressed in higher amounts in the CAD patients as compared to normal controls. Using enzyme-linked immunosorbent assays to analyze the concentrations of CD14 in urine and serum, we confirmed that urinary CD14 levels were significantly higher in patients (n = 73) with multi-vessel and single vessel CAD than in normal control (n = 35) (P < 0.001). Logistic regression analysis further showed that urinary CD14 concentration level is associated with severity or number of diseased vessels and SYNTAX score after adjustment for potential confounders. Concomitantly, the proportion of CD14+ monocytes was significantly increased in CAD patients (59.7 ± 3.6%) as compared with healthy controls (14.9 ± 2.1%) (P < 0.001), implicating that a high level of urinary CD14 may be potentially involved in mechanism(s) leading to CAD pathogenesis. By performing shotgun proteomics, we further revealed that CD14-associated inflammatory response networks may play an essential role in CAD. In conclusion, the current study has demonstrated that release of CD14 in urine coupled with more CD14+ monocytes in CAD patients is significantly correlated with severity of CAD, pointing to the potential application of urinary CD14 as a novel noninvasive biomarker for large-scale diagnostic screening of susceptible CAD patients.
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Affiliation(s)
- Min-Yi Lee
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Cardiology, Department of Internal Medicine, Kaohsiung Municipal Ming-Sheng Hospital, Kaohsiung, Taiwan
| | - Chun-Hao Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chao-Jen Kuo
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Quantitative Proteomics Center, Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Lung Steve Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wen-Ter Lai
- Division of Cardiology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- * E-mail: (WTL); (SHC)
| | - Shyh-Horng Chiou
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Quantitative Proteomics Center, Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail: (WTL); (SHC)
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Abstract
Proteomic biomarkers offer the hope of improving the management of patients with kidney diseases by enabling more accurate and earlier detection of renal pathology than is possible with currently available biomarkers, serum creatinine and urinary albumin. In addition, proteomic biomarkers could also be useful to define the most suitable therapeutic targets in a given patient or disease setting. This Review describes the current status of proteomic and protein biomarkers in the context of kidney diseases. The valuable lessons learned from early clinical studies of potential proteomic biomarkers in kidney disease are presented to give context to the newly identified biomarkers, which have potential for actual clinical implementation. This article also includes an overview of protein-based biomarker candidates that are undergoing development for use in nephrology, focusing on those with the greatest potential for clinical implementation. Relevant issues and problems associated with the discovery, validation and clinical application of proteomic biomarkers are discussed, along with suggestions for solutions that might help to guide the design of future proteomic studies. These improvements might remove some of the current obstacles to the utilization of proteomic biomarkers, with potentially beneficial results.
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Schanstra JP, Zürbig P, Alkhalaf A, Argiles A, Bakker SJL, Beige J, Bilo HJG, Chatzikyrkou C, Dakna M, Dawson J, Delles C, Haller H, Haubitz M, Husi H, Jankowski J, Jerums G, Kleefstra N, Kuznetsova T, Maahs DM, Menne J, Mullen W, Ortiz A, Persson F, Rossing P, Ruggenenti P, Rychlik I, Serra AL, Siwy J, Snell-Bergeon J, Spasovski G, Staessen JA, Vlahou A, Mischak H, Vanholder R. Diagnosis and Prediction of CKD Progression by Assessment of Urinary Peptides. J Am Soc Nephrol 2015; 26:1999-2010. [PMID: 25589610 DOI: 10.1681/asn.2014050423] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/30/2014] [Indexed: 01/13/2023] Open
Abstract
Progressive CKD is generally detected at a late stage by a sustained decline in eGFR and/or the presence of significant albuminuria. With the aim of early and improved risk stratification of patients with CKD, we studied urinary peptides in a large cross-sectional multicenter cohort of 1990 individuals, including 522 with follow-up data, using proteome analysis. We validated that a previously established multipeptide urinary biomarker classifier performed significantly better in detecting and predicting progression of CKD than the current clinical standard, urinary albumin. The classifier was also more sensitive for identifying patients with rapidly progressing CKD. Compared with the combination of baseline eGFR and albuminuria (area under the curve [AUC]=0.758), the addition of the multipeptide biomarker classifier significantly improved CKD risk prediction (AUC=0.831) as assessed by the net reclassification index (0.303±-0.065; P<0.001) and integrated discrimination improvement (0.058±0.014; P<0.001). Correlation of individual urinary peptides with CKD stage and progression showed that the peptides that associated with CKD, irrespective of CKD stage or CKD progression, were either fragments of the major circulating proteins, suggesting failure of the glomerular filtration barrier sieving properties, or different collagen fragments, suggesting accumulation of intrarenal extracellular matrix. Furthermore, protein fragments associated with progression of CKD originated mostly from proteins related to inflammation and tissue repair. Results of this study suggest that urinary proteome analysis might significantly improve the current state of the art of CKD detection and outcome prediction and that identification of the urinary peptides allows insight into various ongoing pathophysiologic processes in CKD.
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Affiliation(s)
- Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, French Institute of Health and Medical Research U1048, Toulouse, France; Paul Sabatier University (Toulouse III), Toulouse, France
| | | | - Alaa Alkhalaf
- University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | | | - Stephan J L Bakker
- University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Joachim Beige
- KfH Renal Unit, Department Nephrology, Leipzig and Martin-Luther-University, Halle/Wittenberg, Germany
| | - Henk J G Bilo
- University Medical Center Groningen and University of Groningen, Groningen, The Netherlands; Diabetes Centre, Isala Clinics, Zwolle, The Netherlands
| | - Christos Chatzikyrkou
- Department of Nephrology and Hypertension, University Hospital of Magdeburg, Magdeburg, Germany
| | | | - Jesse Dawson
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christian Delles
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hermann Haller
- Department of Nephrology and Hypertension, Medical School of Hanover, Hanover, Germany
| | - Marion Haubitz
- Department of Nephrology, Klinikum Fulda gAG, Fulda, Germany
| | - Holger Husi
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany; Department of Internal Medicine IV, Charity Medical University of Berlin, Berlin, Germany
| | - George Jerums
- Austin Health, University of Melbourne, Heidelberg, Australia
| | - Nanne Kleefstra
- University Medical Center Groningen and University of Groningen, Groningen, The Netherlands; Diabetes Centre, Isala Clinics, Zwolle, The Netherlands
| | - Tatiana Kuznetsova
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium; Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David M Maahs
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Jan Menne
- Department of Nephrology and Hypertension, Medical School of Hanover, Hanover, Germany
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alberto Ortiz
- School of Medicine, Jimenez Diaz Foundation Institute for Health Research, Autonomous University of Madrid, Madrid, Spain
| | | | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark; Faculty of Health, University of Aarhus, Aarhus, Denmark; Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Ivan Rychlik
- Second Department of Internal Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andreas L Serra
- Division of Nephrology, University Hospital, and Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Switzerland
| | - Justyna Siwy
- mosaiques diagnostics GmbH, Hanover, Germany; Department of Internal Medicine IV, Charity Medical University of Berlin, Berlin, Germany
| | - Janet Snell-Bergeon
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Goce Spasovski
- University Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
| | - Jan A Staessen
- Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Antonia Vlahou
- Division of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece; School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom; and
| | - Harald Mischak
- Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Raymond Vanholder
- Nephrology Section, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
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Abstract
PURPOSE OF REVIEW Better biomarkers are needed for guiding management of patients with vasculitis. Large cohorts and technological advances had led to an increase in preclinical studies of potential biomarkers. RECENT FINDINGS The most interesting markers described recently include a gene expression signature in CD8+ T cells that predicts tendency to relapse or remain relapse-free in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis, and a pair of urinary proteins that are elevated in Kawasaki disease but not other febrile illnesses. Both of these studies used 'omics' technologies to generate and then test hypotheses. More conventional hypothesis-based studies have indicated that the following circulating proteins have potential to improve upon clinically available tests: pentraxin-3 in giant cell arteritis and Takayasu's arteritis; von Willebrand factor antigen in childhood central nervous system vasculitis; eotaxin-3 and other markers related to eosinophils or Th2 immune responses in eosinophilic granulomatosis with polyangiitis (Churg-Strauss syndrome); and matrix metalloproteinase-3, tissue inhibitor of metalloproteinase-1, and CXCL13 in ANCA-associated vasculitis. SUMMARY New markers testable in blood and urine have the potential to assist with diagnosis, staging, assessment of current disease activity, and prognosis. However, the standards for clinical usefulness, in particular, the demonstration of either very high sensitivity or very high specificity have yet to be met for clinically relevant outcomes.
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Zhang Z, Staessen JA, Thijs L, Gu Y, Liu Y, Jacobs L, Koeck T, Zürbig P, Mischak H, Kuznetsova T. Left ventricular diastolic function in relation to the urinary proteome: a proof-of-concept study in a general population. Int J Cardiol 2014; 176:158-65. [PMID: 25065337 PMCID: PMC4155932 DOI: 10.1016/j.ijcard.2014.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/06/2014] [Accepted: 07/05/2014] [Indexed: 01/09/2023]
Abstract
Background In previous studies, we identified two urinary proteomic classifiers, termed HF1 and HF2, which discriminated subclinical diastolic left ventricular (LV) dysfunction from normal. HF1 and HF2 combine information from 85 and 671 urinary peptides, mainly up- or down-regulated collagen fragments. We sought to validate these classifiers in a population study. Methods In 745 people randomly recruited from a Flemish population (49.8 years; 51.3% women), we measured early and late diastolic peak velocities of mitral inflow (E and A) and mitral annular velocities (e' and a') by conventional and tissue Doppler echocardiography, and the urinary proteome by capillary electrophoresis coupled with mass spectrometry. Results In the analyses adjusted for sex, age, body mass index, blood pressure, heart rate, LV mass index and intake of medications, we expressed effect sizes per 1-SD increment in the classifiers. HF1 was associated with 0.204 cm/s lower e' peak velocity (95% confidence interval, 0.057–0.351; p = 0.007) and 0.145 higher E/e' ratio (0.023–0.268; p = 0.020), while HF2 was associated with a 0.174 higher E/e' ratio (0.046–0.302; p = 0.008). According to published definitions, 67 (9.0%) participants had impaired LV relaxation and 96 (12.9%) had elevated LV filling pressure. The odds of impaired relaxation associated with HF1 was 1.38 (1.01–1.88; p = 0.043) and that of increased LV filling pressure associated with HF2 was 1.38 (1.00–1.90; p = 0.052). Conclusions In a general population, the urinary proteome correlated with diastolic LV dysfunction, proving its utility for early diagnosis of this condition. Aim: to validate urinary proteomic markers for LV dysfunction in a population. Result: LV diastolic dysfunction was associated with the urinary proteome. Perspective: Screening for subclinical LV dysfunction becomes possible.
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Affiliation(s)
- Zhenyu Zhang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | - Jan A Staessen
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium; Department of Epidemiology, Maastricht University, Maastricht, Netherlands.
| | - Lutgarde Thijs
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | - Yumei Gu
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | - Yanping Liu
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | - Lotte Jacobs
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | - Thomas Koeck
- Mosaiques Diagnostic and Therapeutics AG, Hannover, Germany
| | - Petra Zürbig
- Mosaiques Diagnostic and Therapeutics AG, Hannover, Germany
| | - Harald Mischak
- Mosaiques Diagnostic and Therapeutics AG, Hannover, Germany; BHF Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom
| | - Tatiana Kuznetsova
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
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Filip S, Pontillo C, Peter Schanstra J, Vlahou A, Mischak H, Klein J. Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases. Expert Rev Proteomics 2014; 11:535-48. [DOI: 10.1586/14789450.2014.926224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Smith CR, Batruch I, Bauça JM, Kosanam H, Ridley J, Bernardini MQ, Leung F, Diamandis EP, Kulasingam V. Deciphering the peptidome of urine from ovarian cancer patients and healthy controls. Clin Proteomics 2014; 11:23. [PMID: 24982608 PMCID: PMC4065538 DOI: 10.1186/1559-0275-11-23] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Background Ovarian cancer (OvCa) is the most lethal gynecological malignancy. The emergence of high-throughput technologies, such as mass spectrometry, has allowed for a paradigm shift in the way we search for novel biomarkers. Urine-based peptidomic profiling is a novel approach that may result in the discovery of noninvasive biomarkers for diagnosing patients with OvCa. In this study, the peptidome of urine from 6 ovarian cancer patients and 6 healthy controls was deciphered. Results Urine samples underwent ultrafiltration and the filtrate was subjected to solid phase extraction, followed by fractionation using strong cation exchange chromatography. These fractions were analyzed using an Orbitrap mass spectrometer. Over 4600 unique endogenous urine peptides arising from 713 proteins were catalogued, representing the largest urine peptidome reported to date. Each specimen was processed in triplicate and reproducibility at the protein (69-76%) and peptide (58-63%) levels were noted. More importantly, over 3100 unique peptides were detected solely in OvCa specimens. One such promising biomarker was leucine-rich alpha-2-glycoprotein (LRG1), where multiple peptides were found in all urines from OvCa patients, but only one peptide was found in one healthy control urine sample. Conclusions Mining the urine peptidome may yield highly promising novel OvCa biomarkers.
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Affiliation(s)
- Christopher R Smith
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ihor Batruch
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Josep Miquel Bauça
- Servei d'Anàlisis Clíniques, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Hari Kosanam
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julia Ridley
- Department of Psychosocial Oncology and Palliative Care, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada ; Division of Palliative Care, Department of Community and Palliative Medicine, University of Toronto, Toronto, ON, Canada
| | - Marcus Q Bernardini
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Felix Leung
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Eleftherios P Diamandis
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Vathany Kulasingam
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
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Nkuipou-Kenfack E, Duranton F, Gayrard N, Argilés À, Lundin U, Weinberger KM, Dakna M, Delles C, Mullen W, Husi H, Klein J, Koeck T, Zürbig P, Mischak H. Assessment of metabolomic and proteomic biomarkers in detection and prognosis of progression of renal function in chronic kidney disease. PLoS One 2014; 9:e96955. [PMID: 24817014 PMCID: PMC4016198 DOI: 10.1371/journal.pone.0096955] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Chronic kidney disease (CKD) is part of a number of systemic and renal diseases and may reach epidemic proportions over the next decade. Efforts have been made to improve diagnosis and management of CKD. We hypothesised that combining metabolomic and proteomic approaches could generate a more systemic and complete view of the disease mechanisms. To test this approach, we examined samples from a cohort of 49 patients representing different stages of CKD. Urine samples were analysed for proteomic changes using capillary electrophoresis-mass spectrometry and urine and plasma samples for metabolomic changes using different mass spectrometry-based techniques. The training set included 20 CKD patients selected according to their estimated glomerular filtration rate (eGFR) at mild (59.9±16.5 mL/min/1.73 m2; n = 10) or advanced (8.9±4.5 mL/min/1.73 m2; n = 10) CKD and the remaining 29 patients left for the test set. We identified a panel of 76 statistically significant metabolites and peptides that correlated with CKD in the training set. We combined these biomarkers in different classifiers and then performed correlation analyses with eGFR at baseline and follow-up after 2.8±0.8 years in the test set. A solely plasma metabolite biomarker-based classifier significantly correlated with the loss of kidney function in the test set at baseline and follow-up (ρ = -0.8031; p<0.0001 and ρ = -0.6009; p = 0.0019, respectively). Similarly, a urinary metabolite biomarker-based classifier did reveal significant association to kidney function (ρ = -0.6557; p = 0.0001 and ρ = -0.6574; p = 0.0005). A classifier utilising 46 identified urinary peptide biomarkers performed statistically equivalent to the urinary and plasma metabolite classifier (ρ = -0.7752; p<0.0001 and ρ = -0.8400; p<0.0001). The combination of both urinary proteomic and urinary and plasma metabolic biomarkers did not improve the correlation with eGFR. In conclusion, we found excellent association of plasma and urinary metabolites and urinary peptides with kidney function, and disease progression, but no added value in combining the different biomarkers data.
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Affiliation(s)
- Esther Nkuipou-Kenfack
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Toxicology, Hannover Medical School, Hannover, Germany
| | | | | | - Àngel Argilés
- RD Néphrologie, Montpellier, France
- Néphrologie Dialyse St Guilhem, Séte, France
- Service de Néphrologie, Dialyse Péritonéale et Transplantation, Montpellier, France
| | | | - Klaus M. Weinberger
- Biocrates life sciences AG, Innsbruck, Austria
- sAnalytiCo Ltd, Belfast, United Kingdom
- Department of Biomedical Informatics and Mechatronics, Private University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | | | - Christian Delles
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Holger Husi
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Julie Klein
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | | | | | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Rodríguez-Suárez E, Siwy J, Zürbig P, Mischak H. Urine as a source for clinical proteome analysis: From discovery to clinical application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:884-98. [DOI: 10.1016/j.bbapap.2013.06.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/10/2013] [Accepted: 06/20/2013] [Indexed: 01/03/2023]
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Boenisch M, Hurst R, Huber S, Koehn J, Krapfenbauer K. Improved prognostic diagnosis of systemic lupus erythematosus in an early stage of disease by a combination of different predictive biomarkers identified by proteome analysis. EPMA J 2014; 5:5. [PMID: 24650571 PMCID: PMC3998108 DOI: 10.1186/1878-5085-5-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/27/2014] [Indexed: 11/15/2022]
Abstract
Background Since the original characterizations of the pathological features defining glomerulonephritis in systemic lupus erythematosus (SLE) were reported, numerous studies have linked the development of pathology to the abnormal expression of protein in urine. The determination of proteinuria is important and necessary; however, this alone is not predictive enough to confirm a suspected diagnosis, especially in an early state of disease when symptoms are not yet observed. Furthermore, several studies have already highlighted the pitfalls of proteinuria both as a clinical prognostic marker and as a factor predicting the progressive loss of renal function. Therefore, the identification of more accurate and predictive biomarkers is urgently needed. To address this, comparative urinary and kidney profiling was performed in the MRL-lpr/lpr mouse as a model of lupus tubulointerstitial nephritis and lupus glomerulonephritis corresponding to SLE in humans. Results Tamm-Horsfall glycoprotein (THG; uromodulin) and beta2-microglubulin (β2M) were identified as immune process-related molecules in the urine and kidney of the MRL-lpr/lpr mouse model. Furthermore, we show that the combinatory expression profile of THG and β2M as biomarkers, normalized by the proteinuria level, is more predictive than proteinuria determination alone. Data were confirmed by comparative urinary profiling of SLE in mice by Western blot and quantitative polymerase chain reaction (qPCR) analysis. Conclusion Based on our results, we are able to diagnose SLE in the MRL-lpr/lpr mouse in a very early state of disease, when the proteinuria level alone is not able to confirm a suspected diagnosis. The pre-validation of our urinary biomarkers is associated with clinical outcomes of glomerulonephritis in humans and merits additional investigation. Further conformations of our predictive biomarkers in the urine of SLE patients in the course of a clinical study are still ongoing.
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Affiliation(s)
- Maximilian Boenisch
- University of Vienna, Universitätszentrum II, Althanstrasse 14, Vienna 1090, Austria
| | | | - Susanna Huber
- Medical University of Vienna, Waehringer Guertel 18-20, Vienna 1090, Austria
| | - Jadranka Koehn
- Medical University of Vienna, Waehringer Guertel 18-20, Vienna 1090, Austria
| | - Kurt Krapfenbauer
- Medical University of Vienna, Waehringer Guertel 18-20, Vienna 1090, Austria
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