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Chen YC, Smith M, Ying YL, Makridakis M, Noonan J, Kanellakis P, Rai A, Salim A, Murphy A, Bobik A, Vlahou A, Greening DW, Peter K. Quantitative proteomic landscape of unstable atherosclerosis identifies molecular signatures and therapeutic targets for plaque stabilization. Commun Biol 2023; 6:265. [PMID: 36914713 PMCID: PMC10011552 DOI: 10.1038/s42003-023-04641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Atherosclerotic plaque rupture leading to myocardial infarction is a major global health burden. Applying the tandem stenosis (TS) mouse model, which distinctively exhibits the characteristics of human plaque instability/rupture, we use quantitative proteomics to understand and directly compare unstable and stable atherosclerosis. Our data highlight the disparate natures and define unique protein signatures of unstable and stable atherosclerosis. Key proteins and pathway networks are identified such as the innate immune system, and neutrophil degranulation. The latter includes calprotectin S100A8/A9, which we validate in mouse and human unstable plaques, and we demonstrate the plaque-stabilizing effects of its inhibition. Overall, we provide critical insights into the unique proteomic landscape of unstable atherosclerosis (as distinct from stable atherosclerosis and vascular tissue). We further establish the TS model as a reliable preclinical tool for the discovery and testing of plaque-stabilizing drugs. Finally, we provide a knowledge resource defining unstable atherosclerosis that will facilitate the identification and validation of long-sought-after therapeutic targets and drugs for plaque stabilization.
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Affiliation(s)
- Yung-Chih Chen
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Meaghan Smith
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ya-Lan Ying
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Manousos Makridakis
- Proteomics Research Unit, Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jonathan Noonan
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Kanellakis
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Alin Rai
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
| | - Agus Salim
- Department of Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Andrew Murphy
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
- Haematopoiseis and Leukocyte Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Alex Bobik
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Immunology, Monash University, Centre for Inflammatory Disease, School of Clinical Sciences, Monash Health, Melbourne, VIC, Australia
| | - Antonia Vlahou
- Proteomics Research Unit, Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - David W Greening
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
| | - Karlheinz Peter
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
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Yu A, Zhao J, Peng W, Yadav SPS, Molitoris BA, Wagner MC, Mechref Y. Proteomics profiling of kidney brush border membrane from rats using LC-MS/MS analysis. Proteomics Clin Appl 2023; 17:e2200063. [PMID: 36189891 DOI: 10.1002/prca.202200063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/12/1912] [Accepted: 09/30/2022] [Indexed: 03/15/2023]
Abstract
PURPOSE Chronic kidney disease (CKD) is defined by a reduced renal function, that is, glomerular filtration rate, and the extent of kidney damage is assessed by determining serum creatinine levels and proteins in urine, diagnosed as proteinuria/albuminuria. Albuminuria increases with age and can result from glomerular and/or proximal tubule (PT) alterations. Brush border membranes (BBMs) on PT cells are important in maintaining the stability of PT functions. EXPERIMENTAL DESIGN An LC-MS/MS bottom-up proteomics analysis of BBMs from four groups of rat models was applied to investigate protein abundance alterations associated with CKD progression. Moreover, systems biology analyses were used to identify key proteins that can provide insight into the different regulated molecular pathways and processes associated with CKD. RESULTS Our results indicated that 303 proteins showed significantly altered expressions from the severe CKD BBM group when compared to the control. Focusing on renal diseases, several proteins including Ctnnb1, Fah, and Icam1 were annotated to kidney damage and urination disorder. The up-regulation of Ctnnb1 (β-catenin) could contribute to CKD through the regulation of the WNT signaling pathway. CONCLUSION AND CLINICAL RELEVANCE Overall, the study of protein abundance changes in BBMs from rat models helps to reveal protein corrections with important pathways and regulator effects involved in CKD. Although this study is focused on rat models, the results provided more information for a deeper insight into possible CKD mechanisms in humans.
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Shiv Pratap S Yadav
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Bruce A Molitoris
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Mark C Wagner
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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Sanni A, Goli M, Zhao J, Wang J, Barsa C, El Hayek S, Talih F, Lanuzza B, Kobeissy F, Plazzi G, Moresco M, Mondello S, Ferri R, Mechref Y. LC-MS/MS-Based Proteomics Approach for the Identification of Candidate Serum Biomarkers in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:420. [PMID: 36979356 PMCID: PMC10046664 DOI: 10.3390/biom13030420] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Narcolepsy type 1 (NT1) is the most common type of narcolepsy known to be caused by the loss of specific neurons responsible for producing peptide neurotransmitters (orexins/hypocretins), resulting in a sleep-wake cycle disorder. It is characterized by its association with cataplexy and abnormalities in rapid eye movement. To date, no cure has been established for this life-threatening condition. Misdiagnosis of NT1 is also quite common, although it is not exceedingly rare. Therefore, successfully identifying candidate serum biomarkers for NT1 would be a head start for accurate diagnosis and development of therapeutics for this disorder. This study aims to identify such potential serum biomarkers. A depletion protocol was employed for 27 human serum samples (16 NT1 and 11 healthy controls), followed by applying LC-MS/MS bottom-up proteomics analysis, then LC-PRM-MS for validation. The comparison of the proteome profiles of the low-abundant proteins in the samples was then investigated based on age, sex, sample groups, and the presence of the Human Leukocyte Antigen (HLA) DQB1*0602 allele. The results were tracked to gene expression studies as well as system biology to identify key proteins and understand their relationship in the pathogenesis of NT1. Our results revealed 36 proteins significantly and differentially expressed. Among the impaired pathways and bioprocesses, the complement activation pathway is impaired by six of the differentially expressed proteins (DEPs). They are coded by the genes C2, CFB, C5, C1R, C1S, and MASP1, while 11 DEPs are involved in Acute Phase Response Signaling (APRS), which are coded by the genes FN1, AMBP, APOH, CFB, CP, ITIH2, C5, C2, F2, C1, and ITIH4. The combined AUCs of the downregulated and upregulated DEPs are 0.95 and 0.76, respectively. Overall, this study reveals potential serum-protein biomarkers of NT1 and explains the possible correlation between the biomarkers and pathophysiological effects, as well as important biochemical pathways involved in NT1.
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Affiliation(s)
- Akeem Sanni
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Mona Goli
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Jingfu Zhao
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Junyao Wang
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Chloe Barsa
- Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Samer El Hayek
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33124, USA
| | - Farid Talih
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Bartolo Lanuzza
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Firas Kobeissy
- Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
- Multiomics & Biomarkers, Department of Neurobiology, Center for Neurotrauma, Morehouse School of Medicine (MSM), Atlanta, GA 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98122 Messina, Italy
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Yehia Mechref
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
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de Beer D, Mels CMC, Schutte AE, Delles C, Mary S, Mullen W, Mischak H, Kruger R. A urinary peptidomics approach for early stages of cardiovascular disease risk: The African-PREDICT study. Hypertens Res 2023; 46:485-494. [PMID: 36396816 DOI: 10.1038/s41440-022-01097-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022]
Abstract
Cardiovascular disease (CVD) affects individuals across the lifespan, with multiple cardiovascular (CV) risk factors increasingly present in young populations. The underlying mechanisms in early cardiovascular disease development are complex and still poorly understood. We therefore employed urinary proteomics as a novel approach to gain better insight into early CVD-related molecular pathways based on a CVD risk stratification approach. This study included 964 apparently healthy (no self-reported chronic illnesses, free from clinical symptoms of CVD) black and white men and women (aged 20-30 years old) from the African Prospective study on the Early Detection and Identification of Cardiovascular disease and Hypertension (African-PREDICT) study. Cardiovascular risk factors used for stratification included obesity, physical inactivity, tobacco use, high alcohol intake, hyperglycemia, dyslipidemia and hypertension. Participants were divided into low (0 risk factors), medium (1-2 risk factors) and high (≥3 risk factors) CV risk groups. We analyzed urinary peptidomics by capillary electrophoresis time-of-flight mass spectrometry. After adjusting for ethnicity, sex and age, 65 sequenced urinary peptides were differentially expressed between the CV risk groups (all q-values ≤ 0.01). These peptides included a lower abundance of collagen type I- and III-derived peptides in the high compared to the low CV risk group. With regard to noncollagen peptides, we found a lower abundance of alpha-1-antitrypsin fragments in the high compared to the low CV risk group (all q-values ≤ 0.01). Our findings indicate lower abundances of collagen types I and III in the high compared to the low CV risk group, suggesting potential early alterations in the CV extracellular matrix.
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Affiliation(s)
- Dalene de Beer
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Catharina M C Mels
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Aletta E Schutte
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
- School of Population Health, University of New South Wales; The George Institute for Global Health, Sydney, NSW, Australia
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sheon Mary
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | | | - Ruan Kruger
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa.
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa.
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Advances in capillary electrophoresis for the life sciences. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1118-1119:116-136. [PMID: 31035134 DOI: 10.1016/j.jchromb.2019.04.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/15/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022]
Abstract
Capillary electrophoresis (CE) played an important role in developments in the life sciences. The technique is nowadays used for the analysis of both large and small molecules in applications where it performs better than or is complementary to liquid chromatographic techniques. In this review, principles of different electromigration techniques, especially capillary isoelectric focusing (CIEF), capillary gel (CGE) and capillary zone electrophoresis (CZE), are described and recent developments in instrumentation, with an emphasis on mass spectrometry (MS) coupling and microchip CE, are discussed. The role of CE in the life sciences is shown with applications in which it had a high impact over the past few decades. In this context, current practice for the characterization of biopharmaceuticals (therapeutic proteins) is shown with CIEF, CGE and CZE using different detection techniques, including MS. Subsequently, the application of CGE and CZE, in combination with laser induced fluorescence detection and CZE-MS are demonstrated for the analysis of protein-released glycans in the characterization of biopharmaceuticals and glycan biomarker discovery in biological samples. Special attention is paid to developments in capillary coatings and derivatization strategies for glycans. Finally, routine CE analysis in clinical chemistry and latest developments in metabolomics approaches for the profiling of small molecules in biological samples are discussed. The large number of CE applications published for these topics in recent years clearly demonstrates the established role of CE in life sciences.
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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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Ramautar R. Sheathless Capillary Electrophoresis-Mass Spectrometry for the Profiling of Charged Metabolites in Biological Samples. Methods Mol Biol 2019; 1738:183-192. [PMID: 29654590 DOI: 10.1007/978-1-4939-7643-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Capillary electrophoresis (CE) is well suited for the profiling of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. The protocol presented here is based on using a recently developed sheathless interfacing design, i.e., a porous tip interface, for coupling CE to electrospray ionization mass spectrometry (MS). It is demonstrated that sheathless CE-MS employing a bare fused-silica capillary at low-pH separation conditions can be used for the profiling of both cationic and anionic metabolites by only switching the MS detection and electrophoretic separation voltage polarity. The proposed sheathless CE-MS protocol allows efficient and sensitive profiles to be obtained for a broad array of charged metabolites, including amino acids, organic acids, nucleotides, and sugar phosphates, in various biological samples, such as urine and extracts of the glioblastoma cell line.
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Affiliation(s)
- Rawi Ramautar
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018). J Sep Sci 2018; 42:398-414. [DOI: 10.1002/jssc.201801090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
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Frantzi M, Latosinska A, Belczacka I, Mischak H. Urinary proteomic biomarkers in oncology: ready for implementation? Expert Rev Proteomics 2018; 16:49-63. [PMID: 30412678 DOI: 10.1080/14789450.2018.1547193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Biomarkers are expected to improve the management of cancer patients by enabling early detection and prediction of therapeutic response. Proteins reflect a molecular phenotype, have high potential as biomarkers, and also are key targets for intervention. Given the ease of collection and proximity to certain tumors, the urinary proteome is a rich source of biomarkers and several proteins have been already implemented. Areas covered: We examined the literature on urine proteins and proteome analysis in oncology from reports published during the last 5 years to generate an overview on the status of urine protein and peptide biomarkers, with emphasis on their actual clinical value. Expert commentary: A few studies report on biomarkers that are ready to be implemented in patient management, among others in bladder cancer and cholangiocarcinoma. These reports are based on multi-marker approaches. A high number of biomarkers, though, has been described in studies with low statistical power. In fact, several of them have been consistently reported across different studies. The latter should be the focus of attention and be tested in properly designed confirmatory and ultimately, prospective investigations. It is expected that multi-marker classifiers for a specific context-of-use, will be the preferred path toward clinical implementation.
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Affiliation(s)
- Maria Frantzi
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
| | | | - Iwona Belczacka
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
| | - Harald Mischak
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
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Belczacka I, Pejchinovski M, Krochmal M, Magalhães P, Frantzi M, Mullen W, Vlahou A, Mischak H, Jankowski V. Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers. Proteomics Clin Appl 2018; 13:e1800111. [PMID: 30334612 DOI: 10.1002/prca.201800111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Indexed: 12/20/2022]
Abstract
PURPOSE Urine is a rich source of potential biomarkers, including glycoproteins. Glycoproteomic analysis remains difficult due to the high heterogeneity of glycans. Nevertheless, recent advances in glycoproteomics software solutions facilitate glycopeptide identification and characterization. The aim is to investigate intact glycopeptides in the urinary peptide profiles of normal subjects using a novel PTM-centric software-Byonic. EXPERIMENTAL DESIGN The urinary peptide profiles of 238 normal subjects, previously analyzed using CE-MS and CE-MS/MS and/or LC-MS/MS, are subjected to glycopeptide analysis. Additionally, glycopeptide distribution is assessed in a set of 969 patients with five different cancer types: bladder, prostate and pancreatic cancer, cholangiocarcinoma, and renal cell carcinoma. RESULTS A total of 37 intact O-glycopeptides and 23 intact N-glycopeptides are identified in the urinary profiles of 238 normal subjects. Among the most commonly identified O-glycoproteins are Apolipoprotein C-III and insulin-like growth factor II, while titin among the N-glycoproteins. Further statistical analysis reveals that three O-glycopeptides and five N-glycopeptides differed significantly in their abundance among the different cancer types, comparing to normal subjects. CONCLUSIONS AND CLINICAL RELEVANCE Through the established glycoproteomics workflow, intact O- and N-glycopeptides in human urine are identified and characterized, providing novel insights for further exploration of the glycoproteome with respect to specific diseases.
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Affiliation(s)
- Iwona Belczacka
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.,University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
| | | | | | | | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, G128QQ Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens (BRFAA), 11527 Athens, Greece
| | | | - Vera Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
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Frantzi M, Latosinska A, Kontostathi G, Mischak H. Clinical Proteomics: Closing the Gap from Discovery to Implementation. Proteomics 2018; 18:e1700463. [PMID: 29785737 DOI: 10.1002/pmic.201700463] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/10/2018] [Indexed: 12/15/2022]
Abstract
Clinical proteomics, the application of proteome analysis to serve a clinical purpose, represents a major field in the area of proteome research. Over 1000 manuscripts on this topic are published each year, with numbers continuously increasing. However, the anticipated outcome, the transformation of the reported findings into improvements in patient management, is not immediately evident. In this article, the value and validity of selected clinical proteomics findings are investigated, and it is assessed how far implementation has progressed. A main conclusion from this assessment is that to achieve implementation, well-powered clinical studies are required in the appropriate population, addressing a specific clinical need and with a clear context-of-use. Efforts toward implementation, to be feasible, must be supported by the key players in science: publishers and funders. The authors propose a change on objectives, from additional discovery studies toward studies aiming at validation of the plethora of potential biomarkers that have been described, to demonstrate practical value of clinical proteomics. All elements required, potential biomarkers, technologies, and bio-banked samples are available (based on today's literature), hence a change in focus from discovery toward validation and application is not only urgently necessary, but also possible based on resources available today.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Hannover, 30659, Germany
| | | | - Georgia Kontostathi
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, 11527, Greece
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12
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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Urinary proteomics using capillary electrophoresis coupled to mass spectrometry for diagnosis and prognosis in kidney diseases. Curr Opin Nephrol Hypertens 2018; 25:494-501. [PMID: 27584928 DOI: 10.1097/mnh.0000000000000278] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PURPOSE OF REVIEW Urine is the most useful of body fluids for biomarker research. Therefore, we have focused on urinary proteomics, using capillary electrophoresis coupled to mass spectrometry, to investigate kidney diseases in recent years. RECENT FINDINGS Several urinary proteomics studies for the detection of various kidney diseases have indicated the potential of this approach aimed at diagnostic and prognostic assessment. Urinary protein biomarkers such as collagen fragments, serum albumin, α-1-antitrypsin, and uromodulin can help to explain the processes involved during disease progression. SUMMARY Urinary proteomics has been used in several studies in order to identify and validate biomarkers associated with different kidney diseases. These biomarkers, with improved sensitivity and specificity when compared with the current gold standards, provide a significant alternative for diagnosis and prognosis, as well as improving clinical decision-making.
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González-Ruiz V, Codesido S, Rudaz S, Schappler J. Evolution in the design of a low sheath-flow interface for CE-MS and application to biological samples. Electrophoresis 2017; 39:853-861. [DOI: 10.1002/elps.201700328] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
| | | | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
| | - Julie Schappler
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
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15
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017). Electrophoresis 2017; 39:209-234. [PMID: 28836681 DOI: 10.1002/elps.201700295] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/17/2022]
Abstract
The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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16
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Phillips TM. Recent advances in CE and microchip-CE in clinical applications: 2014 to mid-2017. Electrophoresis 2017; 39:126-135. [PMID: 28853177 DOI: 10.1002/elps.201700283] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/11/2022]
Abstract
CE and microchip CE (ME) are powerful tools for the analysis of a number of different analytes and have been applied to a variety of clinical fields and human samples. This review will present an overview of the most recent applications of these techniques to different areas of clinical medicine during the period of 2014 to mid-2017. CE and ME have been applied to clinical chemistry, drug detection and monitoring, hematology, infectious diseases, oncology, endocrinology, neonatology, nephrology, and genetic screening. Samples examined range from serum, plasma, and urine to lest utilized materials such as tears, cerebral spinal fluid, sweat, saliva, condensed breath, single cells, and biopsy tissue. Examples of clinical applications will be given along with the various detection systems employed.
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Affiliation(s)
- Terry M Phillips
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
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17
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Jiang Y, He MY, Zhang WJ, Luo P, Guo D, Fang X, Xu W. Recent advances of capillary electrophoresis-mass spectrometry instrumentation and methodology. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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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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19
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Next-generation capillary electrophoresis–mass spectrometry approaches in metabolomics. Curr Opin Biotechnol 2017; 43:1-7. [DOI: 10.1016/j.copbio.2016.07.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/28/2016] [Accepted: 07/04/2016] [Indexed: 12/14/2022]
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20
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Rodrigues KT, Cieslarová Z, Tavares MFM, Simionato AVC. Strategies Involving Mass Spectrometry Combined with Capillary Electrophoresis in Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:99-141. [DOI: 10.1007/978-3-319-47656-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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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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22
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Gamat SN, Fotouhi L, Talebpour Z. The application of electrochemical detection in capillary electrophoresis. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-016-1023-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Magalhães P, Schanstra JP, Carrick E, Mischak H, Zürbig P. Urinary biomarkers for renal tract malformations. Expert Rev Proteomics 2016; 13:1121-1129. [PMID: 27791437 DOI: 10.1080/14789450.2016.1254555] [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: 10/20/2022]
Abstract
INTRODUCTION Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications. Areas covered: In this review, we summarized relevant studies identified in "Pubmed" using the keywords "urinary biomarkers" and "proteomics" and "renal tract malformations" or "hydronephrosis" or "ureteropelvic junction obstruction" or "posterior urethral valves" or "vesicoureteral reflux". These publications represent studies on potential protein-based biomarkers, either individually or combined in panels, of RTMs in human and animal models. Expert commentary: Successful use in the clinic of these protein-based biomarkers will need to involve larger scale studies to reach sufficient power. Improved performance will potentially come from combining immunoassay- and MS-based markers.
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Affiliation(s)
- Pedro Magalhães
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,b Department of Pediatric Nephrology, Hannover Medical School , Hannover , Germany
| | - Joost P Schanstra
- c Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease , Toulouse , France.,d Université Toulouse III Paul-Sabatier , Toulouse , France
| | - Emma Carrick
- e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Harald Mischak
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Petra Zürbig
- a Mosaiques Diagnostics GmbH , Hannover , Germany
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24
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Ramautar R, Somsen GW, de Jong GJ. CE-MS for metabolomics: Developments and applications in the period 2014-2016. Electrophoresis 2016; 38:190-202. [PMID: 27718257 PMCID: PMC5248609 DOI: 10.1002/elps.201600370] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 12/11/2022]
Abstract
CE–MS can be considered a useful analytical technique for the global profiling of (highly) polar and charged metabolites in various samples. Over the past few years, significant advancements have been made in CE–MS approaches for metabolomics studies. In this paper, which is a follow‐up of a previous review paper covering the years 2012–2014 (Electrophoresis 2015, 36, 212–224), recent CE–MS strategies developed for metabolomics covering the literature from July 2014 to June 2016 are outlined. Attention will be paid to new CE–MS approaches for the profiling of anionic metabolites and the potential of SPE coupled to CE–MS is also demonstrated. Representative examples illustrate the applicability of CE–MS in the fields of biomedical, clinical, microbial, plant, and food metabolomics. A complete overview of recent CE–MS‐based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings, and MS detection mode. Finally, general conclusions and perspectives are given.
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Affiliation(s)
- Rawi Ramautar
- Division of Analytical Biosciences, LACDR, Leiden University, Leiden, The Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerhardus J de Jong
- Biomolecular Analysis, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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25
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Týčová A, Ledvina V, Klepárník K. Recent advances in CE-MS coupling: Instrumentation, methodology, and applications. Electrophoresis 2016; 38:115-134. [DOI: 10.1002/elps.201600366] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Týčová
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
| | - Vojtěch Ledvina
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
| | - Karel Klepárník
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
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26
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Nkuipou-Kenfack E, Bhat A, Klein J, Jankowski V, Mullen W, Vlahou A, Dakna M, Koeck T, Schanstra JP, Zürbig P, Rudolph KL, Schumacher B, Pich A, Mischak H. Identification of ageing-associated naturally occurring peptides in human urine. Oncotarget 2016; 6:34106-17. [PMID: 26431327 PMCID: PMC4741439 DOI: 10.18632/oncotarget.5896] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 01/25/2023] Open
Abstract
To assess normal and pathological peptidomic changes that may lead to an improved understanding of molecular mechanisms underlying ageing, urinarypeptidomes of 1227 healthy and 10333 diseased individuals between 20 and 86 years of age were investigated. The diseases thereby comprised diabetes mellitus, renal and cardiovascular diseases. Using age as a continuous variable, 116 peptides were identified that significantly (p < 0.05; |ρ|≥0.2) correlated with age in the healthy cohort. The same approach was applied to the diseased cohort. Upon comparison of the peptide patterns of the two cohorts 112 common age-correlated peptides were identified. These 112 peptides predominantly originated from collagen, uromodulin and fibrinogen. While most fibrillar and basement membrane collagen fragments showed a decreased age-related excretion, uromodulin, beta-2-microglobulin and fibrinogen fragments showed an increase. Peptide-based in silico protease analysis was performed and 32 proteases, including matrix metalloproteinases and cathepsins, were predicted to be involved in ageing. Identified peptides, predicted proteases and patient information were combined in a systems biology pathway analysis to identify molecular pathways associated with normal and/or pathological ageing. While perturbations in collagen homeostasis, trafficking of toll-like receptors and endosomal pathways were commonly identified, degradation of insulin-like growth factor-binding proteins was uniquely identified in pathological ageing.
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Affiliation(s)
- Esther Nkuipou-Kenfack
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Hannover Medical School, Core Facility Proteomics, Hannover, Germany
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Charité-Universitätsmedizin Berlin, Med. Klinik IV, Berlin, Germany
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Vera Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece.,School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom
| | | | | | - Joost P Schanstra
- Université Toulouse III Paul-Sabatier, Toulouse, France.,University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | | | - Karl L Rudolph
- Leibniz Institute of Age Research, Fritz Lipmann Institute, Jena, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
| | - Andreas Pich
- Hannover Medical School, Core Facility Proteomics, Hannover, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
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27
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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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28
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Metzger J, Mullen W, Husi H, Stalmach A, Herget-Rosenthal S, Groesdonk HV, Mischak H, Klingele M. Acute kidney injury prediction in cardiac surgery patients by a urinary peptide pattern: a case-control validation study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2016; 20:157. [PMID: 27230659 PMCID: PMC4882859 DOI: 10.1186/s13054-016-1344-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/12/2016] [Indexed: 12/14/2022]
Abstract
Background Acute kidney injury (AKI) is a prominent problem in hospitalized patients and associated with increased morbidity and mortality. Clinical medicine is currently hampered by the lack of accurate and early biomarkers for diagnosis of AKI and the evaluation of the severity of the disease. In 2010, we established a multivariate peptide marker pattern consisting of 20 naturally occurring urinary peptides to screen patients for early signs of renal failure. The current study now aims to evaluate if, in a different study population and potentially various AKI causes, AKI can be detected early and accurately by proteome analysis. Methods Urine samples from 60 patients who developed AKI after cardiac surgery were analyzed by capillary electrophoresis-mass spectrometry (CE-MS). The obtained peptide profiles were screened by the AKI peptide marker panel for early signs of AKI. Accuracy of the proteomic model in this patient collective was compared to that based on urinary neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1) ELISA levels. Sixty patients who did not develop AKI served as negative controls. Results From the 120 patients, 110 were successfully analyzed by CE-MS (59 with AKI, 51 controls). Application of the AKI panel demonstrated an AUC in receiver operating characteristics (ROC) analysis of 0.81 (95 % confidence interval: 0.72–0.88). Compared to the proteomic model, ROC analysis revealed poorer classification accuracy of NGAL and KIM-1 with the respective AUC values being outside the statistical significant range (0.63 for NGAL and 0.57 for KIM-1). Conclusions This study gives further proof for the general applicability of our proteomic multimarker model for early and accurate prediction of AKI irrespective of its underlying disease cause. Electronic supplementary material The online version of this article (doi:10.1186/s13054-016-1344-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | | | | | - Heiner V Groesdonk
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Saarland University Medical Centre, Homburg-Saar, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | - Matthias Klingele
- Department of Internal Medicine, Nephrology and Hypertension, Saarland University Medical Centre, Homburg-Saar, Germany.,Department of Internal Medicine, Hochtaunus-Kliniken, Usingen, Germany
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29
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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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30
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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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Thomas S, Hao L, Ricke WA, Li L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin Appl 2016; 10:358-70. [PMID: 26703953 DOI: 10.1002/prca.201500102] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/05/2015] [Accepted: 12/21/2015] [Indexed: 01/03/2023]
Abstract
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
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Affiliation(s)
- Samuel Thomas
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - William A Ricke
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Urology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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Abstract
In clinical metabolomics, capillary electrophoresis-mass spectrometry (CE-MS) has become a very useful technique for the analysis of highly polar and charged metabolites in complex biologic samples. A comprehensive overview of recent developments in CE-MS for metabolic profiling studies is presented. This review covers theory, CE separation modes, capillary coatings, and practical aspects of CE-MS coupling. Attention is also given to sample pretreatment and data analysis strategies used for metabolomics. The applicability of CE-MS for clinical metabolomics is illustrated using samples ranging from plasma and urine to cells and tissues. CE-MS application to large-scale and quantitative clinical metabolomics is addressed. Conclusions and perspectives on this unique analytic strategy are presented.
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Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomic and peptidomic analyses. J Sep Sci 2015; 39:198-211. [DOI: 10.1002/jssc.201500973] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague Czech Republic
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