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Liang K, Li Q, Song Z, Zhao K, Su R, Huang S, Guo X, Li Y. Endogenous Plasma Peptides Modulated by Protease in a Time-Dependent Manner as Effective Biomarkers for Preanalytical Quality Control. J Proteome Res 2023; 22:3029-3039. [PMID: 37530177 DOI: 10.1021/acs.jproteome.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Non-cryopreservation temperature exposure (NCE) is a vital preanalytical factor for assessing plasma quality. NCE can introduce undesirable errors in clinical diagnosis or when developing biomarkers of diseases. Biomarkers that can effectively indicate the changes in sample quality caused by long-term NCE (0-several days) are limited. Low-molecular-weight (LMW) peptides in the plasma are modulated by endogenous proteases. These protease activities are significantly correlated with NCE temperatures and duration, indicating a potential link of these protease reactions with the preanalytical quality of plasma samples. In this study, two groups of plasma samples were aged at room temperature (RT, 57 samples) and 4 °C (69 samples) for different durations (0, 1, 2, 5, and 10 days), and LMW peptidomics were analyzed through nanopore-assisted matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The analysis revealed 10 peptides that consistently exhibited time-dependent changes, which were used to develop multiple-variable models for predicting the changes in sample quality resulting from extended NCE. These biomarker models exhibited outstanding performance in distinguishing poor-quality samples aged at both RT and 4 °C. To validate the findings, tests on samples from validation sets were conducted by analysts who were blinded to the detailed conditions, which revealed a high specificity (94.3-96.9%) and sensitivity (90.5-99.3%). These results indicate the potential of these peptides as novel biomarkers of quality control.
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Affiliation(s)
- Kai Liang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Western Institute of Health Data Science, Chongqin 400050, China
| | - Qianqian Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijing Song
- Western Institute of Health Data Science, Chongqin 400050, China
| | - Keli Zhao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Su
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Shengchun Huang
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Xueyan Guo
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Western Institute of Health Data Science, Chongqin 400050, China
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2
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Gummadi S, Kang T, Fonseka P, Chitti SV, Ang CS, Mathivanan S. Pep2Graph: A standalone tool to analyse proteolytic cleavages by proteases from gel-based mass spectrometry data. Proteomics 2022; 22:e2200147. [PMID: 35924633 DOI: 10.1002/pmic.202200147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 12/29/2022]
Abstract
Proteases are enzymes that regulate substrates via proteolytic activation and coordinate essential cellular functions including DNA replication, DNA transcription, cell proliferation, differentiation, migration and apoptosis. However, techniques to identify proteolytic events in a high-throughput manner is limited. PROtein TOpography and Migration Analysis Platform (PROTOMAP) is a technique that relies on mass spectrometry-based proteomics to globally identify the shifts in the in-gel migration of proteins and their corresponding fragments that are obtained by proteolysis. However, user-friendly software tool to analyse the proteomic data to identify proteolytic events is needed. Here, we report Pep2Graph, a user-friendly standalone tool that integrates peptide sequence information from in-gel proteomics and presents the data as two-dimensional peptographs with in-gel migration, sequence coverage and MS/MS spectra counts. Pep2Graph (http://www.mathivananlab.org/Pep2Graph) allows users to utilize in-gel proteomics data to study proteolytic events that may play a significant role in normal physiology and pathology.
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Affiliation(s)
- Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
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3
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Chen C, Wen M, Jin Y. 1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC-MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins. J Proteome Res 2022; 21:2311-2330. [PMID: 36018058 DOI: 10.1021/acs.jproteome.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (Mws) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury1 was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent Mws and calculated Mws. Only 56% of the proteins showed narrow distributions and matched Mws, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.
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Affiliation(s)
- Changming Chen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Meiling Wen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
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4
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Vaughan RH, Kresse J, Farmer LK, Thézénas ML, Kessler BM, Lindeman JHN, Sharples EJ, Welsh GI, Nørregaard R, Ploeg RJ, Kaisar M. Cytoskeletal protein degradation in brain death donor kidneys associates with adverse posttransplant outcomes. Am J Transplant 2022; 22:1073-1087. [PMID: 34878723 PMCID: PMC9305475 DOI: 10.1111/ajt.16912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/25/2023]
Abstract
In brain death, cerebral injury contributes to systemic biological dysregulation, causing significant cellular stress in donor kidneys adversely impacting the quality of grafts. Here, we hypothesized that donation after brain death (DBD) kidneys undergo proteolytic processes that may deem grafts susceptible to posttransplant dysfunction. Using mass spectrometry and immunoblotting, we mapped degradation profiles of cytoskeletal proteins in deceased and living donor kidney biopsies. We found that key cytoskeletal proteins in DBD kidneys were proteolytically cleaved, generating peptide fragments, predominantly in grafts with suboptimal posttransplant function. Interestingly, α-actinin-4 and talin-1 proteolytic fragments were detected in brain death but not in circulatory death or living donor kidneys with similar donor characteristics. As talin-1 is a specific proteolytic target of calpain-1, we investigated a potential trigger of calpain activation and talin-1 degradation using human ex vivo precision-cut kidney slices and in vitro podocytes. Notably, we showed that activation of calpain-1 by transforming growth factor-β generated proteolytic fragments of talin-1 that matched the degradation fragments detected in DBD preimplantation kidneys, also causing dysregulation of the actin cytoskeleton in human podocytes; events that were reversed by calpain-1 inhibition. Our data provide initial evidence that brain death donor kidneys are more susceptible to cytoskeletal protein degradation. Correlation to posttransplant outcomes may be established by future studies.
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Affiliation(s)
- Rebecca H. Vaughan
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK
| | | | - Louise K. Farmer
- Bristol RenalBristol Medical SchoolUniversity of BristolBristolUK
| | - Marie L. Thézénas
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Jan H. N. Lindeman
- Department of SurgeryLeiden University Medical CentreLeidenThe Netherlands
| | | | - Gavin I. Welsh
- Bristol RenalBristol Medical SchoolUniversity of BristolBristolUK
| | | | - Rutger J. Ploeg
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK,Department of SurgeryLeiden University Medical CentreLeidenThe Netherlands
| | - Maria Kaisar
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK
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5
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Rolland DC, Lim MS, Elenitoba-Johnson KS. Mass spectrometry and proteomics in hematology. Semin Hematol 2019; 56:52-57. [DOI: 10.1053/j.seminhematol.2018.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 01/02/2023]
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6
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Padoan A. The Impact of Pre-Analytical Conditions on Human Serum Peptidome Profiling. Proteomics Clin Appl 2018; 12:e1700183. [PMID: 29476601 DOI: 10.1002/prca.201700183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 12/20/2022]
Abstract
The successful use of proteomic technology for the discovery of clinically relevant, new candidate biomarkers, especially in the low molecular weight range (peptidome), calls for a careful consideration of standardized operating procedures (SOP) for pre-analytical variables, including samples handling and storage. The current lack of standardization, widely considered a relevant source of random and systematic errors, underlies the uncertainty of analytical results and poor comparability, especially in multi-centric or inter-laboratory studies. In their recent study, Tsuchida et al. used the MALDI-TOF/MS technique to investigate the effect of long-term storage at -20 °C, -80 °C, and in liquid nitrogen on serum samples obtained for peptidomic analyses. The authors have also evaluated the effects of different sample thawing modalities. By including results from the same series as that reported on in a previous publication, they have effectively defined some important requirements for the peptidomic analysis of serum samples (e.g., maximum time intervals between venepuncture and serum separation [1 h], minimum temperature for long-term sera storage temperature [-80 °C], ideal conditions for sample thawing).
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Affiliation(s)
- Andrea Padoan
- Department of Medicine (DIMED), University of Padova, Padova, Italy
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7
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Fuhrman-Luck RA, Silva LM, Hastie ML, Gorman JJ, Clements JA. Determining Protease Substrates Within a Complex Protein Background Using the PROtein TOpography and Migration Analysis Platform (PROTOMAP). Methods Mol Biol 2017; 1574:145-170. [PMID: 28315249 DOI: 10.1007/978-1-4939-6850-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The PROtein TOpography and Migration Analysis Platform (PROTOMAP) approach is a degradomics technique used to determine protease substrates within complex protein backgrounds. The method involves protein separation according to protein relative mobility, using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Gel lanes are then sliced into horizontal sections, and in-gel trypsin digestion performed for each gel slice. Extracted peptides and corresponding proteins are identified using liquid chromatography-tandem mass spectrometry and bioinformatics. Results are compiled in silico to generate a peptograph for every identified protein, being a pictorial representation of sodium dodecyl sulfate polyacrylamide gel electrophoresis. Proteins shown by their peptograph to have migrated further through the gel (i.e., to a lower gel slice) in the lane containing the active protease(s) of interest, as compared to the control, are deemed putative protease substrates. PROTOMAP has broad applicability to a range of experimental conditions and protein pools. Coupling this with its simple and robust methodology, the PROTOMAP approach has emerged as a valuable tool with which to determine protease substrates in complex systems.
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Affiliation(s)
- R A Fuhrman-Luck
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - L M Silva
- Translational Research Institute, Brisbane, Queensland, Australia
- Cancer Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - M L Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - J J Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - J A Clements
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Translational Research Institute, Brisbane, Queensland, Australia.
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8
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Bingeman TS, Perlman DH, Storey DG, Lewis IA. Digestomics: an emerging strategy for comprehensive analysis of protein catabolism. Curr Opin Biotechnol 2016; 43:134-140. [PMID: 28025112 DOI: 10.1016/j.copbio.2016.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/01/2016] [Accepted: 11/04/2016] [Indexed: 11/29/2022]
Abstract
When cells mobilize nutrients from protein, they generate a fingerprint of peptide fragments that reflects the net action of proteases and the identities of the affected proteins. Analyzing these mixtures falls into a grey area between proteomics and metabolomics that is poorly served by existing technology. Herein, we describe an emerging digestomics strategy that bridges this gap and allows mixtures of proteolytic fragments to be quantitatively mapped with an amino acid level of resolution. We describe recent successes using this technique, including a case where digestomics provided the link between hemoglobin digestion by the malaria parasite and the world-wide distribution of chloroquine resistance. We highlight other areas of microbiology and cancer research that are well-suited to this emerging technology.
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Affiliation(s)
- Travis S Bingeman
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - David H Perlman
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - Douglas G Storey
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4.
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9
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Kaisar M, van Dullemen LFA, Thézénas ML, Zeeshan Akhtar M, Huang H, Rendel S, Charles PD, Fischer R, Ploeg RJ, Kessler BM. Plasma degradome affected by variable storage of human blood. Clin Proteomics 2016; 13:26. [PMID: 27708557 PMCID: PMC5037888 DOI: 10.1186/s12014-016-9126-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/16/2016] [Indexed: 01/01/2023] Open
Abstract
Background The successful application of—omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding of disease mechanisms and may represent a source of biomarkers. However, a major confounding factor for defining disease-specific proteomic signatures in plasma is the variation in handling and processing of clinical samples leading to protein degradation. To address this, we defined a plasma proteolytic signature (degradome) reflecting pre-analytical variability in blood samples that remained at ambient temperature for different time periods after collection and prior to processing. Methods We obtained EDTA blood samples from five healthy volunteers (n = 5), and blood tubes remained at ambient temperature for 30 min, 8, 24 and 48 h prior to centrifugation and isolation of plasma. Naturally occurred peptides derived from plasma samples were compared by label-free quantitative LC–MS/MS. To profile protein degradation, we analysed pooled plasma samples at T = 30 min and 48 h using PROTOMAP analysis. The proteolytic pattern of selected protein candidates was further validated by immunoblotting. Results A total of 820 plasma proteins were surveyed by PROTOMAP, and for 4 % of these, marked degradation was observed. We show distinct proteolysis patterns for talin-1, coagulation factor XI, complement protein C1r, C3, C4 and thrombospondin, and several proteins including S100A8, A9, annexin A1, profiling-1 and platelet glycoprotein V are enriched after 48 h blood storage at ambient temperature. In particular, thrombospondin protein levels increased after 8 h and proteolytic fragments appeared after 24 h storage time. Conclusions The overall impact of blood storage at ambient temperature for variable times on the plasma proteome and degradome is relatively minor, but in some cases can cause a potential bias in identifying and assigning relevant proteomic markers. The observed effects on the plasma proteome and degradome are predominantly triggered by limited leucocyte and platelet cell activation due to blood handling and storage. The baseline plasma degradome signature presented here can help filtering candidate protein markers relevant for clinical biomarker studies. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9126-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Kaisar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,NHS Blood and Transplant, Watford, WD24 4QN UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Leon F A van Dullemen
- Surgical Research Laboratory, University Medical Center, University of Groningen, Groningen, 9713 GZ The Netherlands
| | - Marie-Laëtitia Thézénas
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - M Zeeshan Akhtar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK
| | - Honglei Huang
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Sandrine Rendel
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Rutger J Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,NHS Blood and Transplant, Watford, WD24 4QN UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
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10
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Kaisar M, van Dullemen LFA, Thézénas ML, Charles PD, Ploeg RJ, Kessler BM. Plasma Biomarker Profile Alterations during Variable Blood Storage. Clin Chem 2016; 62:1272-4. [PMID: 27440514 DOI: 10.1373/clinchem.2016.257246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Maria Kaisar
- Nuffield Department of Surgical Sciences University of Oxford, Oxford, UK NHS Blood and Transplant Hertfordshire, UK Target Discovery Institute Nuffield Department of Medicine University of Oxford, Oxford, UK
| | - Leon F A van Dullemen
- Nuffield Department of Surgical Sciences University of Oxford, Oxford, UK Surgical Research Laboratory University of Groningen Groningen, The Netherlands
| | | | - Philip D Charles
- Target Discovery Institute Nuffield Department of Medicine University of Oxford, Oxford, UK
| | - Rutger J Ploeg
- Nuffield Department of Surgical Sciences University of Oxford, Oxford, UK NHS Blood and Transplant Hertfordshire, UK Oxford Biomedical Research Centre Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute Nuffield Department of Medicine University of Oxford, Oxford, UK
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11
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Yu Y, Prassas I, Diamandis EP. Putative kallikrein substrates and their (patho)biological functions. Biol Chem 2015; 395:931-43. [PMID: 24854536 DOI: 10.1515/hsz-2014-0129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/08/2014] [Indexed: 12/31/2022]
Abstract
Human tissue kallikreins (KLKs) represent the largest contiguous group of protease genes within our genome. All 15 KLK genes co-localize within approximately 260 kb in human chromosome 19q13.3-13.4 (14 640 kb→274 990 kb). They are widely expressed in several tissues and mediate a wide range of critical physiological and pathological processes. Despite the recent developments in KLK research, elucidation of their physiological substrate repertoires remains a largely unfulfilled goal. Phage display, positional scanning and combinatorial peptide library screens have provided some valuable insights into the preferred specificities of these powerful enzymes. More recently, advances in proteomic technologies have enabled more systemic approaches towards identification of KLK substrates in a physiological setting. The advent of degradomic technologies has brought to light several putative physiological substrates and has allowed a deeper appreciation of the in vivo functional roles of KLKs. The aim of this review is to provide an overview of the different techniques that have been utilized towards the elucidation of the substrate specificities of these enzymes and elaborate on their emerging in vivo substrates.
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12
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Ferraz Franco C, Santos R, Varela Coelho A. Proteolytic events are relevant cellular responses during nervous system regeneration of the starfish Marthasterias glacialis. J Proteomics 2014; 99:1-25. [DOI: 10.1016/j.jprot.2013.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 01/12/2023]
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13
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Shahinian H, Tholen S, Schilling O. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications. Expert Rev Proteomics 2014; 10:421-33. [DOI: 10.1586/14789450.2013.841547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Theopold U, Krautz R, Dushay MS. The Drosophila clotting system and its messages for mammals. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 42:42-46. [PMID: 23545286 DOI: 10.1016/j.dci.2013.03.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/07/2013] [Accepted: 03/24/2013] [Indexed: 06/02/2023]
Abstract
Drosophila has been increasingly used as a model to study hemolymph clotting. Proteomics and bioinformatics identified candidate clotting-factors, several of which were tested using genetics. Mutants and lines with reduced expression of clotting-factors show subtle effects after wounding, indicating that sealing wounds may rely on redundant mechanisms. More striking effects are observed after infection, in particular when a natural infection model involving entomopathogenic nematodes is used. When translated into mammalian models these results reveal that mammalian blood clots serve a similar immune function, thus providing a new example of the usefulness of studying invertebrate models.
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Affiliation(s)
- Ulrich Theopold
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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15
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Findeisen P, Thumfart JO, Costina V, Hofheinz R, Neumaier M. MS-based monitoring of proteolytic decay of synthetic reporter peptides for quality control of plasma and serum specimens. Am J Clin Pathol 2013; 140:314-23. [PMID: 23955449 DOI: 10.1309/ajcpos9z5kvzsfsc] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES To determine the preanalytical quality of serum and plasma by monitoring the time-dependent ex vivo decay of a synthetic reporter peptide (RP) with liquid chromatography/mass spectrometry (LC/MS). METHODS Serum and plasma specimens were spiked with the RP and proteolytic fragments were monitored with LC/MS at different preanalytical time points ranging from 2 to 24 hours after blood withdrawal. RESULTS The concentration of fragments changed in a time-dependent manner, and respective peptide profiles were used to classify specimens according to their preanalytical time span. Classification accuracy was high, with values always above 0.89 for areas under receiver operating characteristic curves. CONCLUSIONS This "proteomics degradation clock" can be used to estimate the preanalytical quality of serum and plasma and might have impact on quality control procedures of biobanking repositories.
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Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Jörg Oliver Thumfart
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Victor Costina
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Ralf Hofheinz
- Third Medical Clinic, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
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16
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Admission Rapid Thrombelastography Can Replace Conventional Coagulation Tests in the Emergency Department. Ann Surg 2012; 256:476-86. [DOI: 10.1097/sla.0b013e3182658180] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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17
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Shen C, Yu Y, Li H, Yan G, Liu M, Shen H, Yang P. Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network. Proteomics 2012; 12:1917-27. [DOI: 10.1002/pmic.201200027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chengpin Shen
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Yanyan Yu
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Hong Li
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Mingqi Liu
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Huali Shen
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
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Findeisen P, Costina V, Yepes D, Hofheinz R, Neumaier M. Functional protease profiling with reporter peptides in serum specimens of colorectal cancer patients: demonstration of its routine diagnostic applicability. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2012; 31:56. [PMID: 22682081 PMCID: PMC3780806 DOI: 10.1186/1756-9966-31-56] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/04/2012] [Indexed: 01/18/2023]
Abstract
Background The progression of many solid tumors is characterized by the release of tumor-associated proteases and the detection of tumor specific proteolytic activity in serum specimens is a promising diagnostic tool in oncology. Here we describe a mass spectrometry-based functional proteomic profiling approach that tracks the ex-vivo degradation of a synthetic endoprotease substrate in serum specimens of colorectal tumor patients. Methods A reporter peptide (RP) with the amino acid sequence WKPYDAAD was synthesized that has a known cleavage site for the cysteine-endopeptidase cancer procoagulant (EC 3.4.22.26). The RP was added to serum specimens from colorectal cancer patients (n = 30), inflammatory controls (n = 30) and healthy controls (n = 30) and incubated under strictly standardized conditions. The proteolytic fragment of the RP was quantified with liquid chromatography / mass spectrometry (LC/MS). Results RP-spiking showed good intra- and inter-day reproducibility with coefficients of variation (CVs) that did not exceed a value of 10%. The calibration curve for the anchor peptide was linear in the concentration range of 0.4 – 50 μmol/L. The median concentration of the RP-fragment in serum specimens from tumor patients (TU: 17.6 μmol/L, SD 9.0) was significantly higher when compared to non-malignant inflammatory controls (IC: 11.1 μmol/L, SD 6.1) and healthy controls (HC: 10.3 μmol/L, SD 3.1). Highest area under receiver operating characteristic (AUROC) values were seen for discrimination of TU versus HC (0.89) followed by TU versus IC (0.77). IC and HC could barely be separated indicated by an AUROC value of 0.57. The proteolytic activity towards the RP was conserved in serum specimens that were kept at room temperature for up to 24 hours prior to the analysis. Conclusion The proteolytic cleavage of reporter peptides is a surrogate marker for tumor associated proteolytic activity in serum specimens of cancer patients. A simple, robust and highly reproducible LC/MS method has been developed that allows the quantification of proteolytic fragments in serum specimens. The preanalytical impact of sample handling is minimal as the tumor-associated proteolytic activity towards the reporter peptide is stable for at least up to 24 h. Taken together, the functional protease profiling shows characteristics that are in line with routinely performed diagnostic assays. Further work will focus on the identification of additional reporter peptides for the construction of a multiplex assay to increase diagnostic accuracy of the functional protease profiling.
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Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Theodor-Kutzer-Ufer 1-3, Mannheim, Germany.
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Findeisen P, Neumaier M. Functional protease profiling for diagnosis of malignant disease. Proteomics Clin Appl 2011; 6:60-78. [PMID: 22213637 DOI: 10.1002/prca.201100058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/27/2011] [Accepted: 10/19/2011] [Indexed: 12/24/2022]
Abstract
Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches.
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Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany.
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