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Dekker PM, Boeren S, Saccenti E, Hettinga KA. Network analysis of the proteome and peptidome sheds light on human milk as a biological system. Sci Rep 2024; 14:7569. [PMID: 38555284 PMCID: PMC10981717 DOI: 10.1038/s41598-024-58127-2] [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: 09/27/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
Proteins and peptides found in human milk have bioactive potential to benefit the newborn and support healthy development. Research has been carried out on the health benefits of proteins and peptides, but many questions still need to be answered about the nature of these components, how they are formed, and how they end up in the milk. This study explored and elucidated the complexity of the human milk proteome and peptidome. Proteins and peptides were analyzed with non-targeted nanoLC-Orbitrap-MS/MS in a selection of 297 milk samples from the CHILD Cohort Study. Protein and peptide abundances were determined, and a network was inferred using Gaussian graphical modeling (GGM), allowing an investigation of direct associations. This study showed that signatures of (1) specific mechanisms of transport of different groups of proteins, (2) proteolytic degradation by proteases and aminopeptidases, and (3) coagulation and complement activation are present in human milk. These results show the value of an integrated approach in evaluating large-scale omics data sets and provide valuable information for studies that aim to associate protein or peptide profiles from biofluids such as milk with specific physiological characteristics.
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Affiliation(s)
- Pieter M Dekker
- Food Quality and Design Group, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Kasper A Hettinga
- Food Quality and Design Group, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands.
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2
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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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Israr MZ, Bernieh D, Salzano A, Cassambai S, Yazaki Y, Suzuki T. Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications. Clin Chem Lab Med 2021; 58:883-896. [PMID: 32229653 DOI: 10.1515/cclm-2019-0868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/21/2020] [Indexed: 01/23/2023]
Abstract
Background Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics. Content This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories. Summary MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases. Outlook There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.
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Affiliation(s)
- Muhammad Zubair Israr
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dennis Bernieh
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Andrea Salzano
- IRCCS SDN, Diagnostic and Nuclear Research Institute, Naples, Italy
| | - Shabana Cassambai
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Yoshiyuki Yazaki
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Toru Suzuki
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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Pathophysiological Implications of Urinary Peptides in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13153786. [PMID: 34359689 PMCID: PMC8345155 DOI: 10.3390/cancers13153786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary In this study, the application of capillary electrophoresis mass spectrometry enabled identification of 31 urinary peptides significantly associated with hepatocellular carcinoma diagnosis and prognosis. Further assessment of these peptides lead to prediction of cellular proteases involved in their development namely Meprin A subunit α and Kallikrein-6. Subsequent identification of the proteases was verified by immunohistochemistry in normal liver, cirrhosis and hepatocellular carcinoma. Histopathological assessment of the proteases revealed numerical gradient staining signifying their involvement in liver fibrosis and hepatocellular carcinoma formation. The discovered urinary peptides offered a potential noninvasive tool for diagnosis and prognosis of hepatocellular carcinoma. Abstract Hepatocellular carcinoma (HCC) is known to be associated with protein alterations and extracellular fibrous deposition. We investigated the urinary proteomic profiles of HCC patients in this prospective cross sectional multicentre study. 195 patients were recruited from the UK (Coventry) and Germany (Hannover) between 1 January 2013 and 30 June 2019. Out of these, 57 were HCC patients with a background of liver cirrhosis (LC) and 138 were non-HCC controls; 72 patients with LC, 57 with non-cirrhotic liver disease and 9 with normal liver function. Analysis of the urine samples was performed by capillary electrophoresis (CE) coupled to mass spectrometry (MS). Peptide sequences were obtained and 31 specific peptide markers for HCC were identified and further integrated into a multivariate classification model. The peptide model demonstrated 79.5% sensitivity and 85.1% specificity (95% CI: 0.81–0.93, p < 0.0001) for HCC and 4.1-fold increased risk of death (95% CI: 1.7–9.8, p = 0.0005). Proteases potentially involved in HCC progression were mapped to the N- and C-terminal sequence motifs of the CE-MS peptide markers. In silico protease prediction revealed that kallikrein-6 (KLK6) elicits increased activity, whilst Meprin A subunit α (MEP1A) has reduced activity in HCC compared to the controls. Tissue expression of KLK6 and MEP1A was subsequently verified by immunohistochemistry.
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Ciociola T, Zanello PP, D’Adda T, Galati S, Conti S, Magliani W, Giovati L. A Peptide Found in Human Serum, Derived from the C-Terminus of Albumin, Shows Antifungal Activity In Vitro and In Vivo. Microorganisms 2020; 8:E1627. [PMID: 33096923 PMCID: PMC7588913 DOI: 10.3390/microorganisms8101627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 01/19/2023] Open
Abstract
The growing problem of antimicrobial resistance highlights the need for alternative strategies to combat infections. From this perspective, there is a considerable interest in natural molecules obtained from different sources, which are shown to be active against microorganisms, either alone or in association with conventional drugs. In this paper, peptides with the same sequence of fragments, found in human serum, derived from physiological proteins, were evaluated for their antifungal activity. A 13-residue peptide, representing the 597-609 fragment within the albumin C-terminus, was proved to exert a fungicidal activity in vitro against pathogenic yeasts and a therapeutic effect in vivo in the experimental model of candidal infection in Galleria mellonella. Studies by confocal microscopy and transmission and scanning electron microscopy demonstrated that the peptide penetrates and accumulates in Candida albicans cells, causing gross morphological alterations in cellular structure. These findings add albumin to the group of proteins, which already includes hemoglobin and antibodies, that could give rise to cryptic antimicrobial fragments, and could suggest their role in anti-infective homeostasis. The study of bioactive fragments from serum proteins could open interesting perspectives for the development of new antimicrobial molecules derived by natural sources.
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Affiliation(s)
- Tecla Ciociola
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
| | - Pier Paolo Zanello
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
| | - Tiziana D’Adda
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
| | - Serena Galati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
| | - Stefania Conti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
| | - Walter Magliani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
| | - Laura Giovati
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (P.P.Z.); (T.D.); (W.M.); (L.G.)
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Sharma MK, Dhakne P, Nn S, Reddy PA, Sengupta P. Paradigm Shift in the Arena of Sample Preparation and Bioanalytical Approaches Involving Liquid Chromatography Mass Spectroscopic Technique. ANAL SCI 2019; 35:1069-1082. [PMID: 31105088 DOI: 10.2116/analsci.19r003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sample preparation is a highly important and integral part of bioanalysis for cleaning up the complex biological matrices and thereby minimizing matrix effect. Matrix effect can jeopardize the precise quantification and adversely affect the reliability of liquid chromatography-mass spectrometry-based analytical results by alteration of analyte ionization. Matrix components result in suppression or enhancement of the intensity of analyte response. In spite of the high specificity and selectivity of tandem mass spectrometry, a relatively higher concentration of coeluted matrix elements present in biofluids may alter the efficiency of quantification of a bioanalytical method. Numerous literature reports different types of sample preparation techniques employed in bioanalysis. In this review, the strategies for selection of the appropriate sample clean-up technique in bioanalysis are discussed extensively. A paradigm shift in the arena of sample preparation and bioanalytical approaches involving the liquid chromatography-mass spectroscopic technique has been scrutinized. Current trends and possible future advancements in the field of biological sample extraction methods, including instrumental techniques are analyzed in detail.
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Affiliation(s)
- Manish Kumar Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad
| | - Pooja Dhakne
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad
| | - Sidhartha Nn
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad
| | - P Ajitha Reddy
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad
| | - Pinaki Sengupta
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad
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7
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Cao Z, Kamlage B, Wagner-Golbs A, Maisha M, Sun J, Schnackenberg LK, Pence L, Schmitt TC, Daniels JR, Rogstad S, Beger RD, Yu LR. An Integrated Analysis of Metabolites, Peptides, and Inflammation Biomarkers for Assessment of Preanalytical Variability of Human Plasma. J Proteome Res 2019; 18:2411-2421. [PMID: 31074987 DOI: 10.1021/acs.jproteome.8b00903] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Discrepancies in blood sample collection and processing could have a significant impact on levels of metabolites, peptides, and protein biomarkers of inflammation in the blood; thus, sample quality control is critical for successful biomarker identification and validation. In this study, we analyzed the effects of several preanalytical processing conditions, including different storage times and temperatures for blood or plasma samples and different centrifugation forces on the levels of metabolites, peptides, and inflammation biomarkers in human plasma samples using ethylenediaminetetraacetic acid (EDTA) as an anticoagulant. Temperature was found to be the major factor for metabolite variation, and both time and temperature were identified as major factors for peptide variation. For inflammation biomarkers, temperature played different roles depending on the sample type (blood or plasma). Low temperature affected inflammation biomarkers in blood, while room temperature impacted inflammation biomarkers in plasma.
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Affiliation(s)
- Zhijun Cao
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | | | | | - Mackean Maisha
- Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Jinchun Sun
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Laura K Schnackenberg
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Lisa Pence
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Thomas C Schmitt
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Jaclyn R Daniels
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Sarah Rogstad
- Center for Drug Evaluation and Research , FDA , Silver Spring , Maryland 20993 , United States
| | - Richard D Beger
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
| | - Li-Rong Yu
- Division of Systems Biology , National Center for Toxicological Research, FDA , Jefferson , Arkansas 72079 , United States
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8
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Semis M, Gugiu GB, Bernstein EA, Bernstein KE, Kalkum M. The Plethora of Angiotensin-Converting Enzyme-Processed Peptides in Mouse Plasma. Anal Chem 2019; 91:6440-6453. [PMID: 31021607 DOI: 10.1021/acs.analchem.8b03828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Angiotensin-converting enzyme (ACE) converts angiotensin I into the potent vasoconstrictor angiotensin II, which regulates blood pressure. However, ACE activity is also essential for other physiological functions, presumably through processing of peptides unrelated to angiotensin. The goal of this study was to identify novel natural substrates and products of ACE through a series of mass-spectrometric experiments. This included comparing the ACE-treated and untreated plasma peptidomes of ACE-knockout (KO) mice, validation with select synthetic peptides, and a quantitative in vivo study of ACE substrates in mice with distinct genetic ACE backgrounds. In total, 244 natural peptides were identified ex vivo as possible substrates or products of ACE, demonstrating high promiscuity of the enzyme. ACE prefers to cleave substrates with Phe or Leu at the C-terminal P2' position and Gly in the P6 position. Pro in P1' and Iso in P1 are typical residues in peptides that ACE does not cleave. Several of the novel ACE substrates are known to have biological activities, including a fragment of complement C3, the spasmogenic C3f, which was processed by ACE ex vivo and in vitro. Analyses with N-domain-inactive (NKO) ACE allowed clarification of domain selectivity toward substrates. The in vivo ACE-substrate concentrations in WT, transgenic ACE-KO, NKO, and CKO mice correspond well with the in vitro observations in that higher levels of the ACE substrates were observed when the processing domain was knocked out. This study highlights the vast extent of ACE promiscuity and provides a valuable platform for further investigations of ACE functionality.
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Affiliation(s)
- Margarita Semis
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Gabriel B Gugiu
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States.,Mass Spectrometry & Proteomics Core Facility , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Ellen A Bernstein
- Departments of Biomedical Sciences, Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Kenneth E Bernstein
- Departments of Biomedical Sciences, Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States.,Mass Spectrometry & Proteomics Core Facility , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
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9
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Zaki A, Ramadan RA, Moez P, Ghareeb H, Elkarmouty A. Plasma Peptidome Pattern of Breast Cancer Using Magnetic Beads-Based Plasma Fractionation and MALDI-TOF MS: A Case Control Study in Egypt. Asian Pac J Cancer Prev 2019; 20:175-184. [PMID: 30678429 PMCID: PMC6485569 DOI: 10.31557/apjcp.2019.20.1.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Objective: The present study aimed to determine peptidome patterns in breast cancer (BC). Methods: We analyzed
the plasma proteomic profiling of 80 BC patients and 50 healthy controls, using hydrophobic interaction chromatography
magnetic beads (MB-HIC8) separation followed by Matrix assisted laser desorption ionization/ time of flight mass
spectrometry (MALDI-TOF MS). Results: ClinProTools software identified 92 peaks that differed among the analyzed
groups, 33 peaks were significantly different (P < 0.05). Of those, 22 peaks were up-regulated while 11 peaks were
down-regulated in BC patients compared with the healthy controls. Three peptide ion signatures (m/z 1,570.31, 1,897.4
and 2,568.17) were provided by the Quick Classifier model to discriminate BC patients from healthy control subjects
with 96.4% accuracy. External validation was performed by an independent group and this achieved a sensitivity of
100% and a specificity of 76.9%. Conclusion: MALDI-TOF MS has good analytical performance in distinguishing
BC patients from healthy controls.
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Affiliation(s)
- Ahmad Zaki
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
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10
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Perera NCN, Godahewa GI, Jung S, Kim MJ, Nam BH, Lee J. Identification and characterization of a carboxypeptidase N1 from red lip mullet (Liza haematocheila); revealing its immune relevance. FISH & SHELLFISH IMMUNOLOGY 2019; 84:223-232. [PMID: 30300741 DOI: 10.1016/j.fsi.2018.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
Complement system orchestrates the innate and adaptive immunity via the activation, recruitment, and regulation of immune molecules to destroy pathogens. However, regulation of the complement is essential to avoid injuries to the autologous tissues. The present study unveils the characteristic features of an important complement component, anaphylatoxin inactivator from red lip mullet at its molecular and functional level. Mullet carboxypeptidase N1 (MuCPN1) cDNA sequence possessed an open reading frame of 1347 bp, which encoded a protein of 449 amino acids with a predicted molecular weight of 51 kDa. In silico analysis discovered two domains of PM14-Zn carboxypeptidase and a C-terminal domain of M14 N/E carboxypeptidase, two zinc-binding signature motifs, and an N-glycosylation site in the MuCPN1 sequence. Homology analysis revealed that most of the residues in the sequence are conserved among the other selected homologs. Phylogeny analysis showed that MuCPN1 closely cladded with the Maylandia zebra CPN1 and clustered together with the teleostean counterparts. A challenge experiment showed modulated expression of MuCPN1 upon polyinosinic:polycytidylic acid and Lactococcus garviae in head kidney, spleen, gill, and liver tissues. The highest upregulation of MuCPN1 was observed 24 h post infection against poly I:C in each tissue. Moreover, the highest relative expressions upon L. garviae challenge were observed at 24 h post infection in head kidney tissue and 48 h post infection in spleen, gill, and liver tissues. MuCPN1 transfected cells triggered a 2.2-fold increase of nitric oxide (NO) production upon LPS stimulation compared to the un-transfected controls suggesting that MuCPN1 is an active protease which releases arginine from complement C3a, C4a, and C5a. These results have driven certain way towards enhancing the understanding of immune role of MuCPN1 in the complement defense mechanism of red lip mullet.
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Affiliation(s)
- N C N Perera
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - G I Godahewa
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Sumi Jung
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Myoung-Jin Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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11
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Wu Y, Han M, Wang Y, Gao Y, Cui X, Xu P, Ji C, Zhong T, You L, Zeng Y. A Comparative Peptidomic Characterization of Cultured Skeletal Muscle Tissues Derived From db/db Mice. Front Endocrinol (Lausanne) 2019; 10:741. [PMID: 31736878 PMCID: PMC6828820 DOI: 10.3389/fendo.2019.00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
As an important secretory organ, skeletal muscle has drawn attention as a potential target tissue for type 2 diabetic mellitus (T2DM). Recent peptidomics approaches have been applied to identify secreted peptides with potential bioactive. However, comprehensive analysis of the secreted peptides from skeletal muscle tissues of db/db mice and elucidation of their possible roles in insulin resistance remains poorly characterized. Here, we adopted a label-free discovery using liquid chromatography tandem mass spectrometry (LC-MS/MS) technology and identified 63 peptides (42 up-regulated peptides and 21 down-regulated peptides) differentially secreted from cultured skeletal muscle tissues of db/db mice. Analysis of relative molecular mass (Mr), isoelectric point (pI) and distribution of Mr vs pI of differentially secreted peptides presented the general feature. Furthermore, Gene ontology (GO) and pathway analyses for the parent proteins made a comprehensive functional assessment of these differential peptides, indicating the enrichment in glycolysis/gluconeogenesis and striated muscle contraction processes. Intercellular location analysis pointed out most precursor proteins of peptides were cytoplasmic or cytoskeletal. Additionally, cleavage site analysis revealed that Lysine (N-terminal)-Alanine (C-terminal) and Lysine (N-terminal)-Leucine (C-terminal) represents the preferred cleavage sites for identified peptides and proceeding peptides respectively. Mapped to the precursors' sequences, most identified peptides were observed cleaved from creatine kinase m-type (KCRM) and fructose-bisphosphate aldolase A (Aldo A). Based on UniProt and Pfam database for specific domain structure or motif, 44 peptides out of total were positioned in the functional motif or domain from their parent proteins. Using C2C12 myotubes as cell model in vitro, we found several candidate peptides displayed promotive or inhibitory effects on insulin and mitochondrial-related pathways by an autocrine manner. Taken together, this study will encourage us to investigate the biologic functions and the potential regulatory mechanism of these secreted peptides from skeletal muscle tissues, thus representing a promising strategy to treat insulin resistance as well as the associated metabolic disorders.
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Affiliation(s)
- Yanting Wu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Affiliated Maternity and Child Health Care Hospital of Nantong University, NanTong, China
| | - Mei Han
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yan Wang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yao Gao
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Chenbo Ji
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tianying Zhong
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lianghui You
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- *Correspondence: Lianghui You
| | - Yu Zeng
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Yu Zeng
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12
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Dufresne J, Florentinus-Mefailoski A, Ajambo J, Ferwa A, Bowden P, Marshall J. Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:41. [PMID: 29234243 PMCID: PMC5721679 DOI: 10.1186/s12014-017-9176-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/26/2017] [Indexed: 12/12/2022] Open
Abstract
Background Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at – 80 °C prior to experiments. Plasma test samples from the – 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Methods Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) and correlated with X!TANDEM. Results Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than “no enzyme” correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours–days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. Conclusion The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides. Electronic supplementary material The online version of this article (10.1186/s12014-017-9176-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | | | - Juliet Ajambo
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Ammara Ferwa
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Peter Bowden
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - John Marshall
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada.,Integrated BioBank of Luxembourg, 6 r. Nicolas-Ernest Barblé, Dudelange, 1210 Luxembourg
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13
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The proteins cleaved by endogenous tryptic proteases in normal EDTA plasma by C18 collection of peptides for liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:39. [PMID: 29213220 PMCID: PMC5712186 DOI: 10.1186/s12014-017-9174-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/21/2017] [Indexed: 02/08/2023] Open
Abstract
The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed. A total of 583,927 precursor ions and MS/MS spectra were correlated to 94,669 best fit peptides that reduced to 22,287 correlations to the best accession within a gene symbol and to 7174 correlations to at least 510 gene symbols with ≥ 5 independent MS/MS correlations (peptide counts) that showed FDR q-values ranging from E−9 (i.e. FDR = 0.000000001) to E−227. A set of 528 gene symbols identified by X!TANDEM and SEQUEST including C4B showed ≥ fivefold variation between ice cold versus room temperature incubation. STRING analysis of the protein gene symbols observed from endogenous peptides in normal plasma revealed an extensive protein-interaction network of cellular factors associated with cell signalling and regulation, the formation of membrane bound organelles, cellular exosomes and exocytosis network proteins. Taken together the results indicated that a pool of cellular proteins, or protein complexes, in plasma are apparently not stable and degrade soon after incubation at room temperature.
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14
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Dufresne J, Hoang T, Ajambo J, Florentinus-Mefailoski A, Bowden P, Marshall J. Freeze-dried plasma proteins are stable at room temperature for at least 1 year. Clin Proteomics 2017; 14:35. [PMID: 29093647 PMCID: PMC5659006 DOI: 10.1186/s12014-017-9170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022] Open
Abstract
Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at -80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at -20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h. Random and independent sampling by liquid chromatography and tandem mass spectrometry (LC-ESI-MS/MS), as correlated by the MASCOT, OMSSA, X!TANDEM and SEQUEST algorithms, showed that tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature. Random sampling by LC-ESI-MS/MS showed that peptides from C4B were undetectable on ice, but peptides were cleaved from the mature C4B protein including NGFKSHALQLNNR within as little as 1 h at room temperature. The frequency and intensity of precursors within ± 3 m/z of the C4B peptide NGFKSHALQLNNR was confirmed by automated targeted analysis where the precursors from MS/MS spectra that correlated to the target sequence were analyzed in SQL/R. The C4B preproprotein was processed at the N terminus to release the mature chain that was cleaved on the carboxyl side of the isoprene C2 domain within a polar C terminal sequence of the mature C4B protein, to reveal the thioester reaction site, consistent with LC-ESI-MS/MS and Western blot. Random sampling showed that proteolytic peptides from complement component C4B were rarely observed with long term storage at - 80 °C in a freezer or in liquid nitrogen (LN2), freeze drying with storage at - 20 °C (FD-20 °C) or freeze drying and storage at room temperature (FDRT). Plasma samples maintained at room temperature (RT) showed at least 10-fold to 100-fold greater frequency of peptide correlation to C4B and measured peptide intensity compared to samples on ice for up to 72 h or stored at - 80 °C, LN2, FDRT or FD-20 °C for up to a year.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Trung Hoang
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Juliet Ajambo
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | | | - Peter Bowden
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - John Marshall
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada.,Integrated BioBank of Luxembourg, 6 r. Nicolas-Ernest Barblé, 1210 Luxembourg, Luxembourg
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15
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Greening DW, Kapp EA, Simpson RJ. The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. Enzymes 2017; 42:27-64. [PMID: 29054270 DOI: 10.1016/bs.enz.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.
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Affiliation(s)
- David W Greening
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
| | - Eugene A Kapp
- Systems Biology & Personalised Medicine Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Florey Institute of Neuroscience, Parkville, Victoria, Australia; University of Melbourne, Parkville, Victoria, Australia
| | - Richard J Simpson
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
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16
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Hamamura K, Yanagida M, Ishikawa H, Banzai M, Yoshitake H, Nonaka D, Tanaka K, Sakuraba M, Miyakuni Y, Takamori K, Nojima M, Yoshida K, Fujiwara H, Takeda S, Araki Y. Quantitative measurement of a candidate serum biomarker peptide derived from α2-HS-glycoprotein, and a preliminary trial of multidimensional peptide analysis in females with pregnancy-induced hypertension. Ann Clin Biochem 2017; 55:287-295. [DOI: 10.1177/0004563217717748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Purpose We previously attempted to develop quantitative enzyme-linked immunosorbent assay (ELISA) systems for the PDA039/044/071 peptides, potential serum disease biomarkers (DBMs) of pregnancy-induced hypertension (PIH), primarily identified by a peptidomic approach (BLOTCHIP®-mass spectrometry (MS)). However, our methodology did not extend to PDA071 (cysteinyl α2-HS-glycoprotein341–367), due to difficulty to produce a specific antibody against the peptide. The aim of the present study was to establish an alternative PDA071 quantitation system using liquid chromatography-multiple reaction monitoring (LC-MRM)/MS, to explore the potential utility of PDA071 as a DBM for PIH. Methods We tested heat/acid denaturation methods in efforts to purify serum PDA071 and developed an LC-MRM/MS method allowing for specific quantitation thereof. We measured serum PDA071 concentrations, and these results were validated including by three-dimensional (3D) plotting against PDA039 (kininogen-1439–456)/044 (kininogen-1438–456) concentrations, followed by discriminant analysis. Results PDA071 was successfully extracted from serum using a heat denaturation method. Optimum conditions for quantitation via LC-MRM/MS were developed; the assayed serum PDA071 correlated well with the BLOTCHIP® assay values. Although the PDA071 alone did not significantly differ between patients and controls, 3D plotting of PDA039/044/071 peptide concentrations and construction of a Jackknife classification matrix were satisfactory in terms of PIH diagnostic precision. Conclusions Combination analysis using both PDA071 and PDA039/044 concentrations allowed PIH diagnostic accuracy to be attained, and our method will be valuable in future pathophysiological studies of hypertensive disorders of pregnancy.
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Affiliation(s)
- Kensuke Hamamura
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mitsuaki Yanagida
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
| | | | - Michio Banzai
- Department of Obstetrics and Gynecology,
Yamagata Saisei Hospital, Yamagata, Japan
| | - Hiroshi Yoshitake
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
| | - Daisuke Nonaka
- Membrane Protein and Ligand Analysis Center,
Protosera Inc., Hyogo, Japan
| | - Kenji Tanaka
- Membrane Protein and Ligand Analysis Center,
Protosera Inc., Hyogo, Japan
| | - Mayumi Sakuraba
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
| | - Yasuka Miyakuni
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology,
Juntendo University Urayasu Hospital, Chiba, Japan
| | - Kenji Takamori
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
| | - Michio Nojima
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology,
Juntendo University Urayasu Hospital, Chiba, Japan
| | - Koyo Yoshida
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology,
Juntendo University Urayasu Hospital, Chiba, Japan
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology,
Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshihiko Araki
- Institute for Environmental and
Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba,
Japan
- Department of Obstetrics and Gynecology,
Juntendo University Graduate School of Medicine, Tokyo, Japan
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17
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Yu Y, Prassas I, Muytjens CM, Diamandis EP. Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis. J Proteomics 2017; 155:40-48. [DOI: 10.1016/j.jprot.2017.01.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
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18
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HONG XY, LI SM, WANG Y. Analysis of Urine Peptidome and Post-translation Modifications by Nano Liquid Chromatography-High Resolution Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60931-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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Cheon DH, Nam EJ, Park KH, Woo SJ, Lee HJ, Kim HC, Yang EG, Lee C, Lee JE. Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry. J Proteome Res 2015; 15:229-44. [DOI: 10.1021/acs.jproteome.5b00773] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dong Huey Cheon
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Interdisciplinary
Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Republic of Korea
| | - Eun Ji Nam
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Kyu Hyung Park
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Se Joon Woo
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Hye Jin Lee
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Hee Cheol Kim
- Department
of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Eun Gyeong Yang
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Cheolju Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Ji Eun Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
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20
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Abstract
Plasma hormone peptides, including GLP-1, GIP, Glucagon, and OXM, possess multiple physiological roles and potential therapeutic and diagnostic utility as biomarkers in the research of metabolic disorders. These peptides are subject to proteolytic degradation causing preanalytical variations. Stabilization for accurate quantitation of these active peptides in ex vivo blood specimens is essential for drug and biomarker development. We investigated the protease-driven instability of these peptides in conventional serum, plasma, anticoagulated whole blood, as well as whole blood and plasma stabilized with protease inhibitors. The peptide was monitored by both time-course Matrix-Assisted Laser Desorption Ionization Time-to-Flight Mass Spectrometry (MALDI –TOF MS) and Ab-based assay (ELISA or RIA). MS enabled the identification of proteolytic fragments. In non-stabilized blood samples, the results clearly indicated that dipeptidyl peptidase-IV (DPP-IV) removed the N-terminal two amino acid residues from GLP-1, GIP and OXM(1-37) and not-yet identified peptidase(s) cleave(s) the full-length OXM(1-37) and its fragments. DPP-IV also continued to remove two additional N-terminal residues of processed OXM(3–37) to yield OXM(5–37). Importantly, both DPP-IV and other peptidase(s) activities were inhibited efficiently by the protease inhibitors included in the BD P800* tube. There was preservation of GLP-1, GIP, OXM and glucagon in the P800 plasma samples with half-lives > 96, 96, 72, and 45 hours at room temperature (RT), respectively. In the BD P700* plasma samples, the stabilization of GLP-1 was also achieved with half-life > 96 hours at RT. The stabilization of these variable peptides increased their utility in drug and/or biomarker development. While stability results of GLP-1 obtained with Ab-based assay were consistent with those obtained by MS analysis, the Ab-based results of GIP, Glucagon, and OXM did not reflect the time-dependent degradations revealed by MS analysis. Therefore, we recommended characterizing the degradation of the peptide using the MS-based method when investigating the stability of a specific peptide.
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Affiliation(s)
- Jizu Yi
- BD Diagnostics, One Becton Drive, Franklin Lakes, NJ, United States of America
- * E-mail: (JY); (DC)
| | - David Warunek
- BD Diagnostics, One Becton Drive, Franklin Lakes, NJ, United States of America
| | - David Craft
- BD Diagnostics, One Becton Drive, Franklin Lakes, NJ, United States of America
- * E-mail: (JY); (DC)
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21
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Phenotype-Driven Plasma Biobanking Strategies and Methods. J Pers Med 2015; 5:140-52. [PMID: 26110578 PMCID: PMC4493492 DOI: 10.3390/jpm5020140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/05/2015] [Indexed: 12/22/2022] Open
Abstract
Biobank development and integration with clinical data from electronic medical record (EMR) databases have enabled recent strides in genomic research and personalized medicine. BioVU, Vanderbilt's DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions. Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt. This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care. Here, we describe the considerations and components involved in implementing a plasma biobank program from a feasibility assessment through pilot sample collection.
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22
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Husi H, Skipworth RJE, Cronshaw A, Stephens NA, Wackerhage H, Greig C, Fearon KCH, Ross JA. Programmed cell death 6 interacting protein (PDCD6IP) and Rabenosyn-5 (ZFYVE20) are potential urinary biomarkers for upper gastrointestinal cancer. Proteomics Clin Appl 2015; 9:586-96. [PMID: 25644331 DOI: 10.1002/prca.201400111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Cancer of the upper digestive tract (uGI) is a major contributor to cancer-related death worldwide. Due to a rise in occurrence, together with poor survival rates and a lack of diagnostic or prognostic clinical assays, there is a clear need to establish molecular biomarkers. EXPERIMENTAL DESIGN Initial assessment was performed on urine samples from 60 control and 60 uGI cancer patients using MS to establish a peak pattern or fingerprint model, which was validated by a further set of 59 samples. RESULTS We detected 86 cluster peaks by MS above frequency and detection thresholds. Statistical testing and model building resulted in a peak profiling model of five relevant peaks with 88% overall sensitivity and 91% specificity, and overall correctness of 90%. High-resolution MS of 40 samples in the 2-10 kDa range resulted in 646 identified proteins, and pattern matching identified four of the five model peaks within significant parameters, namely programmed cell death 6 interacting protein (PDCD6IP/Alix/AIP1), Rabenosyn-5 (ZFYVE20), protein S100A8, and protein S100A9, of which the first two were validated by Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE We demonstrate that MS analysis of human urine can identify lead biomarker candidates in uGI cancers, which makes this technique potentially useful in defining and consolidating biomarker patterns for uGI cancer screening.
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Affiliation(s)
- Holger Husi
- Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,School of Clinical Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Andrew Cronshaw
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Carolyn Greig
- School of Clinical Sciences, University of Edinburgh, Edinburgh, UK.,School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, UK
| | | | - James A Ross
- School of Clinical Sciences, University of Edinburgh, Edinburgh, UK
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23
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Samperi R, Capriotti AL, Cavaliere C, Colapicchioni V, Chiozzi RZ, Laganà A. Food Proteins and Peptides. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00006-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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24
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Quantitative evaluation of peptide-extraction methods by HPLC–triple-quad MS–MS. Anal Bioanal Chem 2014; 407:1595-605. [DOI: 10.1007/s00216-014-8389-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/25/2014] [Accepted: 12/02/2014] [Indexed: 12/23/2022]
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25
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Shahanavaj K, Gil-Bazo I, Castiglia M, Bronte G, Passiglia F, Carreca AP, del Pozo JL, Russo A, Peeters M, Rolfo C. Cancer and the microbiome: potential applications as new tumor biomarker. Expert Rev Anticancer Ther 2014; 15:317-30. [PMID: 25495037 DOI: 10.1586/14737140.2015.992785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbial communities that colonize in humans are collectively described as microbiome. According to conservative estimates, about 15% of all types of neoplasms are related to different infective agents. However, current knowledge is not sufficient to explain how the microbiome contributes to the growth and development of cancers. Large and thorough studies involving colonized, diverse and complex microbiome entities are required to identify microbiome as a potential cancer marker and to understand how the immune system is involved in response to pathogens. This article reviews the existing evidence supporting the enigmatic association of transformed microbiome with the development of cancer through the immunological modification. Ascertaining the connection between microbiome and immunological responses with risk of cancer may direct to explaining significant advances in the etiology of cancer, potentially disclosing a novel paradigm of research for the management and prevention of cancer.
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Affiliation(s)
- Khan Shahanavaj
- Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, UP, India
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26
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Xu Z, Wu C, Xie F, Slysz GW, Tolic N, Monroe ME, Petyuk VA, Payne SH, Fujimoto GM, Moore RJ, Fillmore TL, Schepmoes AA, Levine DA, Townsend RR, Davies SR, Li S, Ellis M, Boja E, Rivers R, Rodriguez H, Rodland KD, Liu T, Smith RD. Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes. J Proteome Res 2014; 14:422-33. [PMID: 25350482 PMCID: PMC4286152 DOI: 10.1021/pr500840w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high-throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with postexcision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics and provides insights not readily obtainable from such approaches.
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Affiliation(s)
- Zhe Xu
- Biological Sciences Division and ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
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27
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Fania C, Sogno I, Vasso M, Torretta E, Leone R, Bruno A, Consonni P, Albini A, Gelfi C. A PSA-guided approach for a better diagnosis of prostatic adenocarcinoma based on MALDI profiling and peptide identification. Clin Chim Acta 2014; 439:42-9. [PMID: 25312866 DOI: 10.1016/j.cca.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is the second cause of mortality in men worldwide. The prostate-specific antigen (PSA) test is routinely adopted in diagnosis; nevertheless more reliable biomarkers are continuously under investigation by monitoring the release of molecules into the bloodstream. The serum protein profiles appear to provide cancer-specific fingerprints that help to discriminate patients (especially with low PSA level) from controls, improving the performance of existing clinical tests. METHODS Samples from healthy controls and PCa patients with low (≤4 ng/mL) and high PSA (>4 ng/mL) levels were analyzed by MALDI profiling, and by a multi fractionation approach coupled to ESI-MS for peaks identification. RESULTS MALDI profiling achieved to detect 10 and 14 changed peaks (p-value <0.05), respectively, in PCa patients with low and high PSA versus controls. In particular, a peak identified as C3f fragment, resulted overexpressed in low PSA PCa patients. CONCLUSIONS PSA test, coupled to MALDI profiling, is able to detect changes, specifically related to PCa, in low molecular weight protein range. Furthermore, for the first time in prostate cancer research, the identification and quantification of the small peptide C3f appears to be relevant for the detection of false negatives, providing an additive diagnostic power to PSA (p<0.01) and suggesting its use in clinical tests.
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Affiliation(s)
- Chiara Fania
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy.
| | - Ilaria Sogno
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Michele Vasso
- Istituto di Bioimmagini e Fisiologia Molecolare (IBFM)-CNR, C.da Pietrapollastra-Pisciotto, Cefalù, Palermo 90015, Italy.
| | - Enrica Torretta
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy.
| | - Roberta Leone
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy.
| | - Antonino Bruno
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Paolo Consonni
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Adriana Albini
- IRCCS Tecnologie Avanzate e Modelli Assistenziali in Oncologia - Arcispedale Santa Maria Nuova, Viale Umberto I 50, Reggio Emilia 42123, Italy.
| | - Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy; Istituto di Bioimmagini e Fisiologia Molecolare (IBFM)-CNR, Via F.lli Cervi 93, Segrate, Milan 20090, Italy.
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Guerrero A, Dallas DC, Contreras S, Chee S, Parker EA, Sun X, Dimapasoc L, Barile D, German JB, Lebrilla CB. Mechanistic peptidomics: factors that dictate specificity in the formation of endogenous peptides in human milk. Mol Cell Proteomics 2014; 13:3343-51. [PMID: 25172956 DOI: 10.1074/mcp.m113.036194] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An extensive mass spectrometry analysis of the human milk peptidome has revealed almost 700 endogenous peptides from 30 different proteins. Two in-house computational tools were created and used to visualize and interpret the data through both alignment of the peptide quasi-molecular ion intensities and estimation of the differential enzyme participation. These results reveal that the endogenous proteolytic activity in the mammary gland is remarkably specific and well conserved. Certain proteins-not necessarily the most abundant ones-are digested by the proteases present in milk, yielding endogenous peptides from selected regions. Our results strongly suggest that factors such as the presence of specific proteases, the position and concentration of cleavage sites, and, more important, the intrinsic disorder of segments of the protein drive this proteolytic specificity in the mammary gland. As a consequence of this selective hydrolysis, proteins that typically need to be cleaved at specific positions in order to exert their activity are properly digested, and bioactive peptides encoded in certain protein sequences are released. Proteins that must remain intact in order to maintain their activity in the mammary gland or in the neonatal gastrointestinal tract are unaffected by the hydrolytic environment present in milk. These results provide insight into the intrinsic structural mechanisms that facilitate the selectivity of the endogenous milk protease activity and might be useful to those studying the peptidomes of other biofluids.
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Affiliation(s)
- Andres Guerrero
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
| | - David C Dallas
- ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Stephanie Contreras
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Sabrina Chee
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Evan A Parker
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Xin Sun
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Lauren Dimapasoc
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Daniela Barile
- ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - J Bruce German
- ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616
| | - Carlito B Lebrilla
- From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
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Matysiak J, Hajduk J, Pietrzak Ł, Schmelzer CEH, Kokot ZJ. Shotgun proteome analysis of honeybee venom using targeted enrichment strategies. Toxicon 2014; 90:255-64. [PMID: 25173076 DOI: 10.1016/j.toxicon.2014.08.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 01/30/2023]
Abstract
The aim of this study was to explore the honeybee venom proteome applying a shotgun proteomics approach using different enrichment strategies (combinatorial peptide ligand libraries and solid phase extraction). The studies were conducted using nano-LC/MALDI-TOF/TOF-MS system. The MS analysis of peptide profiles (in the range of 900-4500 Da) and virtual gel-image of proteins from Lab-on-Chip assay (in the range of 10-250 kDa) confirm that use of targeted enrichment strategies increase detection of honeybee venom components. The gel-free shotgun strategy and sophisticated instrumentation led to a significant increase of the sensitivity and higher number of identified peptides in honeybee venom samples, comparing with the current literature. Moreover, 11 of 12 known honeybee venom allergens were acknowledged and 4 new, so far uncharacterized proteins were identified. In addition, similarity searches were performed in order to investigate biological relations and homology between newly identified proteins sequences from Apis mellifera and other Hymenoptera.
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Affiliation(s)
- Jan Matysiak
- Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland.
| | - Joanna Hajduk
- Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
| | - Łukasz Pietrzak
- Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
| | - Christian E H Schmelzer
- Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Zenon J Kokot
- Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
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Wang Y, Chen J, Chen L, Zheng P, Xu HB, Lu J, Zhong J, Lei Y, Zhou C, Ma Q, Li Y, Xie P. Urinary peptidomics identifies potential biomarkers for major depressive disorder. Psychiatry Res 2014; 217:25-33. [PMID: 24661976 DOI: 10.1016/j.psychres.2014.02.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/11/2014] [Accepted: 02/19/2014] [Indexed: 12/23/2022]
Abstract
Major depressive disorder (MDD) is a debilitating psychiatric illness with no available objective laboratory-based diagnostic test. In this study, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based peptidomics was applied to identify potential urinary diagnostic biomarkers for MDD. A training set of 42 first-episode drug-naive MDD patients and 28 age- and gender-matched healthy controls (HC) was used to develop a peptide diagnostic pattern. Then, the diagnostic efficacy of this pattern was assessed in an independent blinded test set consisting of 24 MDD patients and 13 age- and gender-matched HC. A combination of five potential biomarkers was identified, yielding a sensitivity of 91.7% and specificity of 84.6% in the test set. Moreover, the protein precursors of four of the five peptides were identified by tandem mass spectrometric analysis: serum albumin, apolipoprotein A-I, protein AMBP, and basement membrane-specific heparan sulfate proteoglycan core protein. Taken together, the peptide pattern may be valuable for establishing an objective laboratory-based diagnostic test for MDD.
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Affiliation(s)
- Ying Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jianjun Chen
- Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Liang Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Hong-Bo Xu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jia Lu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jiaju Zhong
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Yang Lei
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Chanjuan Zhou
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Yan Li
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China.
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Affiliation(s)
| | - Matthew Bogyo
- Departments of 1Chemical and Systems Biology,
- Microbiology and Immunology, and
- Pathology, Stanford University School of Medicine, Stanford, California 94305-5324;
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He J, Zeng ZC, Xiang ZL, Yang P. Mass spectrometry-based serum peptide profiling in hepatocellular carcinoma with bone metastasis. World J Gastroenterol 2014; 20:3025-3032. [PMID: 24659894 PMCID: PMC3961966 DOI: 10.3748/wjg.v20.i11.3025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/14/2013] [Accepted: 01/02/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the potential of serum peptides as a diagnostic tool for hepatocellular carcinoma (HCC) with bone metastasis.
METHODS: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used to characterize the serum peptide profile of HCC patients with bone metastasis. Serum samples from 138 HCC patients (66 cases with and 72 cases without bone metastasis) were randomly assigned into a training set (n = 76) and a test set (n = 62). Differential serum peptides were examined using ClinProt magnetic bead-based purification followed by MALDI-TOF-MS. The sequences of differentially expressed serum peptides were identified using liquid chromatography-mass spectrometry. A diagnostic model was established using a learning algorithm of radial basis function neural network verified by a single blind trial. Receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic power of the established model.
RESULTS: Ten peptide peaks were significantly different between HCC patients with or without bone metastasis (P < 0.001). Sequences of seven peptides with mass to charge ratios (m/z) of 1780.7, 1866.5, 2131.6, 2880.4, 1532.4, 2489.8, and 2234.3 were successfully identified. These seven peptides were derived from alpha-fetoprotein, prothrombin, serglycin, isoform 2 of inter-alpha-trypsin inhibitor heavy chain H4, isoform 1 of autophagy-related protein 16-2, and transthyretin and fibrinogen beta chains, respectively. The recognition rate and predictive power of a diagnostic model established on the basis of six significant peptides (m/z for these six peptides were 1535.4, 1780.7, 1866.5, 2131.6, 2880.4, and 2901.9) were 89.47% and 82.89%, respectively. The sensitivity and specificity of this model based upon a single blind trial were 85.29% and 85.71%, respectively. ROC analysis found that the AUC (area under the ROC curve) value was 0.911.
CONCLUSION: Our study suggested that serum peptides may serve as a diagnosis tool for HCC bone metastasis.
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Sandanayake NS, Camuzeaux S, Sinclair J, Blyuss O, Andreola F, Chapman MH, Webster GJ, Smith RC, Timms JF, Pereira SP. Identification of potential serum peptide biomarkers of biliary tract cancer using MALDI MS profiling. BMC Clin Pathol 2014; 14:7. [PMID: 24495412 PMCID: PMC3923428 DOI: 10.1186/1472-6890-14-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 01/13/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The aim of this discovery study was the identification of peptide serum biomarkers for detecting biliary tract cancer (BTC) using samples from healthy volunteers and benign cases of biliary disease as control groups. This work was based on the hypothesis that cancer-specific exopeptidases exist and that their activities in serum can generate cancer-predictive peptide fragments from circulating proteins during coagulation. METHODS This case control study used a semi-automated platform incorporating polypeptide extraction linked to matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) to profile 92 patient serum samples. Predictive models were generated to test a validation serum set from BTC cases and healthy volunteers. RESULTS Several peptide peaks were found that could significantly differentiate BTC patients from healthy controls and benign biliary disease. A predictive model resulted in a sensitivity of 100% and a specificity of 93.8% in detecting BTC in the validation set, whilst another model gave a sensitivity of 79.5% and a specificity of 83.9% in discriminating BTC from benign biliary disease samples in the training set. Discriminatory peaks were identified by tandem MS as fragments of abundant clotting proteins. CONCLUSIONS Serum MALDI MS peptide signatures can accurately discriminate patients with BTC from healthy volunteers.
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Affiliation(s)
- Neomal S Sandanayake
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, University College London, London, UK.,Cancer Proteomics Laboratory, EGA Institute for Women's Health, University College London, London, UK.,Kolling Institute, University of Sydney, St Leonards, Australia
| | - Stephane Camuzeaux
- Cancer Proteomics Laboratory, EGA Institute for Women's Health, University College London, London, UK
| | - John Sinclair
- Cancer Proteomics Laboratory, EGA Institute for Women's Health, University College London, London, UK
| | - Oleg Blyuss
- Cancer Proteomics Laboratory, EGA Institute for Women's Health, University College London, London, UK
| | - Fausto Andreola
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, University College London, London, UK
| | - Michael H Chapman
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, University College London, London, UK.,Department of Gastroenterology, University College Hospitals NHS Foundation Trust, London, UK
| | - George J Webster
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, University College London, London, UK.,Department of Gastroenterology, University College Hospitals NHS Foundation Trust, London, UK
| | - Ross C Smith
- Kolling Institute, University of Sydney, St Leonards, Australia
| | - John F Timms
- Cancer Proteomics Laboratory, EGA Institute for Women's Health, University College London, London, UK
| | - Stephen P Pereira
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, University College London, London, UK.,Department of Gastroenterology, University College Hospitals NHS Foundation Trust, London, UK
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Guo N, Wen Q, Li ZJ, Xu RC, Peng FF, Yu XQ. Optimization and evaluation of magnetic bead separation combined with matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS) for proteins profiling of peritoneal dialysis effluent. Int J Mol Sci 2014; 15:1162-75. [PMID: 24441570 PMCID: PMC3907861 DOI: 10.3390/ijms15011162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/04/2014] [Accepted: 01/10/2014] [Indexed: 11/23/2022] Open
Abstract
Peritoneal dialysis effluent (PDE) potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but this approach has not been used in the PDE analysis. In this study, we developed a strategy for screening PDE proteins <15 kDa and applied this technique to identify potential biomarkers for peritonitis. We examined four kinds of magnetic beads, including a carbon series (C3, C8), weak cation exchange (WCX) and immobilized metal-affinity chromatography (IMAC-Cu) beads. Samples processed with IMAC-Cu magnetic beads consistently showed more MS signals across all beads within the measured mass range. Moreover, there was no difference in the number and morphology of MS signals between concentrated and unconcentrated samples. The PDE peptidome pattern, based on a panel of 15 peaks, accurately recognized peritonitis PD patients from peritonitis-free patients with sensitivity of 90.5% and specificity of 94.7% respectively. Therefore, IMAC-Cu magnetic beads and unconcentrated samples can be used as a fast and cost-effective approach for sample preparation prior to more in-depth discovery of predictive biomarkers of disease in patients on dialysis.
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Affiliation(s)
- Na Guo
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
| | - Qiong Wen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
| | - Zhi-Jian Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
| | - Ri-Cong Xu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
| | - Fen-Fen Peng
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
| | - Xue-Qing Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58th Zhongshan Road II, Guangzhou 510080, China.
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Findeisen P, Peccerella T, Neumaier M, Schadendorf D. Proteomics for biomarker discovery in malignant melanoma. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/17469872.3.2.209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tammen H, Peck A, Budde P, Zucht HD. Peptidomics analysis of human blood specimens for biomarker discovery. Expert Rev Mol Diagn 2014; 7:605-13. [PMID: 17892366 DOI: 10.1586/14737159.7.5.605] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review addresses the concepts, limitations and perspectives for the application of peptidomics science and technologies to discover putative biomarkers in blood specimens. Peptidomics can be defined as the comprehensive multiplex analysis of endogenous peptides contained within a biological sample under defined conditions to describe the multitude of native peptides in a biological compartment. In addition to the discovery of disease associated biomarkers, an emerging field in peptidomics is the analysis of peptides to describe in vivo effects of protease inhibitors. The development and application of peptidomics technologies represent an arena of biomarker research that has the potential for adding significant clinical value.
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Affiliation(s)
- Harald Tammen
- Digilab BioVisioN GmbH, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
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38
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Clement CC, Santambrogio L. The lymph self-antigen repertoire. Front Immunol 2013; 4:424. [PMID: 24379811 PMCID: PMC3864156 DOI: 10.3389/fimmu.2013.00424] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/20/2013] [Indexed: 01/26/2023] Open
Abstract
The lymphatic fluid originates from the interstitial fluid which bathes every parenchymal organ and reflects the “omic” composition of the tissue from which it originates in its physiological or pathological signature. Several recent proteomic analyses have mapped the proteome-degradome and peptidome of this immunologically relevant fluid pointing to the lymph as an important source of tissue-derived self-antigens. A vast array of lymph-circulating peptides have been mapped deriving from a variety of processing pathways including caspases, cathepsins, MMPs, ADAMs, kallikreins, calpains, and granzymes, among others. These self peptides can be directly loaded on circulatory dendritic cells and expand the self-antigenic repertoire available for central and peripheral tolerance.
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Affiliation(s)
- Cristina C Clement
- Department of Pathology, Albert Einstein College of Medicine , New York, NY , USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine , New York, NY , USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
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He G, Kuang J, Koomen J, Kobayashi R, Khokhar AR, Siddik ZH. Recruitment of trimeric proliferating cell nuclear antigen by G1-phase cyclin-dependent kinases following DNA damage with platinum-based antitumour agents. Br J Cancer 2013; 109:2378-88. [PMID: 24104967 PMCID: PMC3817341 DOI: 10.1038/bjc.2013.613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/11/2013] [Accepted: 09/16/2013] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In cycling tumour cells, the binary cyclin-dependent kinase Cdk4/cyclin D or Cdk2/cyclin E complex is inhibited by p21 following DNA damage to induce G1 cell-cycle arrest. However, it is not known whether other proteins are also recruited within Cdk complexes, or their role, and this was investigated. METHODS Ovarian A2780 tumour cells were exposed to the platinum-based antitumour agent 1R,2R-diaminocyclohexane(trans-diacetato)(dichloro)platinum(IV) (DAP), which preferentially induces G1 arrest in a p21-dependent manner. The Cdk complexes were analysed by gel filtration chromatography, immunoblot and mass spectrometry. RESULTS The active forms of Cdk4 and Cdk2 complexes in control tumour cells have a molecular size of ~140 kDa, which increased to ~290 kDa when inhibited following G1 checkpoint activation by DAP. Proteomic analysis identified Cdk, cyclin, p21 and proliferating cell nuclear antigen (PCNA) in the inhibited complex, and biochemical studies provided unequivocal evidence that the increase in ~150 kDa of the inhibited complex is consistent with p21-dependent recruitment of PCNA as a trimer, likely bound to three molecules of p21. Although p21 alone was sufficient to inhibit the Cdk complex, PCNA was critical for stabilising p21. CONCLUSION G1 Cdk complexes inhibited by p21 also recruit PCNA, which inhibits degradation and, thereby, prolongs activity of p21 within the complex.
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Affiliation(s)
- G He
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Unit 1950, 1515 Holcombe Boulevard, Houston, TX, USA
| | - J Kuang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Unit 1950, 1515 Holcombe Boulevard, Houston, TX, USA
| | - J Koomen
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R Kobayashi
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - A R Khokhar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Unit 1950, 1515 Holcombe Boulevard, Houston, TX, USA
| | - Z H Siddik
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Unit 1950, 1515 Holcombe Boulevard, Houston, TX, USA
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Li Y, Li Y, Chen T, Kuklina AS, Bernard P, Esteva FJ, Shen H, Ferrari M, Hu Y. Circulating proteolytic products of carboxypeptidase N for early detection of breast cancer. Clin Chem 2013; 60:233-42. [PMID: 24146311 DOI: 10.1373/clinchem.2013.211953] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Carboxypeptidase N (CPN) is important in regulating vasoactive peptide hormones, growth factors, and cytokines by specifically cleaving their C-terminal basic residues. We investigated whether circulating peptides specifically cleaved by CPN in the tumor microenvironment can be stage-specific indicators of breast cancer. METHODS CPN activity was measured using an ex vivo peptide cleavage assay by incubating synthesized C3f peptide (His6-C3f_S1304-R1320-His6) in interstitial fluids of breast tumors and adjacent normal breast tissues in mice with orthotopic implantation of the human cell line MDA-MB-231. The nature and extent of peptide cleavage by CPN was investigated by fragment profiling using nanopore fractionation and mass spectrometry. The fragment profiles in interstitial fluid correlated with concentrations of CPN-catalyzed peptides in blood samples taken from the tumor-bearing mice, healthy women, and breast cancer patients. CPN expression in the same set of samples was further examined by immunohistochemistry and immunoblotting. RESULTS We showed that generation of C3f_R1310-L1319 specifically correlated with the CPN expression level. In both the mouse and clinical patient samples, CPN was clearly increased in tumor tissues compared with normal breast tissue, whereas corresponding CPN abundance in blood remained constant. Concentrations of 6 CPN-catalyzed peptides predominantly increased in sera taken from the mice (n = 8) at 2 weeks after orthotopic implantation. Six homologous peptides displayed significantly higher expression in the patients' plasma as early as the first pathologic stage of breast cancer. CONCLUSIONS Circulating CPN-catalyzed peptide concentrations reflect the CPN activity in tumors. These biomarkers show strong potential for the noninvasive and early diagnosis of breast cancer.
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Affiliation(s)
- Yaojun Li
- Department of Nanomedicine, The Methodist Hospital Research Institute, Houston, TX
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Santambrogio L, Stern LJ. Carrying yourself: self antigen composition of the lymphatic fluid. Lymphat Res Biol 2013; 11:149-54. [PMID: 24024574 DOI: 10.1089/lrb.2013.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Advances in proteomics methodology and instrumentation have allowed detailed characterization of the composition of lymph. Far from being a simple ultrafiltrate of blood plasma, lymph has been shown to carry a rich repertoire of proteins and peptides reflecting the tissue of origin and its physiological state. Peptides derived from lymph can be loaded on the MHCII proteins, particularly those present on immature and/or inactivated antigen presenting cells, and may play an important role in maintenance of peripheral tolerance.
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Affiliation(s)
- Laura Santambrogio
- 1 Department of Pathology, Microbiology and Immunology, Albert Einstein College of Medicine , New York, New York
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42
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Hong WX, Liu W, Zhang Y, Huang P, Yang X, Ren X, Ye J, Huang H, Tang H, Zhou G, Huang X, Zhuang Z, Liu J. Identification of serum biomarkers for occupational medicamentosa-like dermatitis induced by trichloroethylene using mass spectrometry. Toxicol Appl Pharmacol 2013; 273:121-9. [PMID: 23994554 DOI: 10.1016/j.taap.2013.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 01/03/2023]
Abstract
Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become a serious occupational health hazard. In the present study, we collected fasting blood samples from patients with OMLDT (n=18) and healthy volunteers (n=33) to explore serum peptidome patterns. Peptides in sera were purified using weak cation exchange magnetic beads (MB-WCX), and analyzed by matrix-assisted laser desorption ionization time-of-flight-mass spectrometry (MALDI-TOF-MS) and ClinProTools bioinformatics software. The intensities of thirty protein/peptide peaks were significantly different between the healthy control and OMLDT patients. A pattern of three peaks (m/z 2106.3, 2134.5, and 3263.67) was selected for supervised neural network (SNN) model building to separate the OMLDT patients from the healthy controls with a sensitivity of 95.5% and a specificity of 73.8%. Furthermore, two peptide peaks of m/z 4091.61 and 4281.69 were identified as fragments of ATP-binding cassette transporter family A member 12 (ABCA12), and cationic trypsinogen (PRRS1), respectively. Our findings not only show that specific proteomic fingerprints in the sera of OMLDT patients can be served as a differentiated tool of OMLDT patients with high sensitivity and high specificity, but also reveal the novel correlation between OMLDT with ABC transports and PRRS1, which will be of potential value for clinical and mechanistic studies of OMLDT.
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Affiliation(s)
- Wen-Xu Hong
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
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Hu X, Wetsel RA, Ramos TN, Mueller-Ortiz SL, Schoeb TR, Barnum SR. Carboxypeptidase N-deficient mice present with polymorphic disease phenotypes on induction of experimental autoimmune encephalomyelitis. Immunobiology 2013; 219:104-8. [PMID: 24028840 DOI: 10.1016/j.imbio.2013.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/08/2013] [Accepted: 08/16/2013] [Indexed: 10/26/2022]
Abstract
Carboxypeptidase N (CPN) is a member of the carboxypeptidase family of enzymes that cleave carboxy-terminal lysine and arginine residues from a large number of biologically active peptides and proteins. These enzymes are best known for their roles in modulating the activity of kinins, complement anaphylatoxins and coagulation proteins. Although CPN makes important contributions to acute inflammatory events, little is known about its role in autoimmune disease. In this study we used CPN(-/-) mice in experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis. Unexpectedly, we observed several EAE disease phenotypes in CPN(-/-) mice compared to wild type mice. The majority of CPN(-/-) mice died within five to seven days after disease induction, before displaying clinical signs of disease. The remaining mice presented with either mild EAE or did not develop EAE. In addition, CPN(-/-) mice injected with complete or incomplete Freund's adjuvant died within the same time frame and in similar numbers as those induced for EAE. Overall, the course of EAE in CPN(-/-) mice was significantly delayed and attenuated compared to wild type mice. Spinal cord histopathology in CPN(-/-) mice revealed meningeal, but not parenchymal leukocyte infiltration, and minimal demyelination. Our results indicate that CPN plays an important role in EAE development and progression and suggests that multiple CPN ligands contribute to the disease phenotypes we observed.
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Affiliation(s)
- Xianzhen Hu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rick A Wetsel
- Brown Foundation Institute of Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Theresa N Ramos
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stacey L Mueller-Ortiz
- Brown Foundation Institute of Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Trenton R Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Scott R Barnum
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Asante V, Mortier J, Schlüter H, Koksch B. Impact of fluorination on proteolytic stability of peptides in human blood plasma. Bioorg Med Chem 2013; 21:3542-6. [DOI: 10.1016/j.bmc.2013.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
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An extensive targeted proteomic analysis of disease-related protein biomarkers in urine from healthy donors. PLoS One 2013; 8:e63368. [PMID: 23723977 PMCID: PMC3665773 DOI: 10.1371/journal.pone.0063368] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/02/2013] [Indexed: 02/02/2023] Open
Abstract
The analysis of protein biomarkers in urine is expected to lead to advances in a variety of clinical settings. Several characteristics of urine including a low-protein matrix, ease of testing and a demonstrated proteomic stability offer distinct advantages over current widely used biofluids, serum and plasma. Improvements in our understanding of the urine proteome and in methods used in its evaluation will facilitate the clinical development of urinary protein biomarkers. Multiplexed bead-based immunoassays were utilized to evaluate 211 proteins in urines from 103 healthy donors. An additional 25 healthy donors provided serial urine samples over the course of two days in order to assess temporal variation in selected biomarkers. Nearly one-third of the evaluated biomarkers were detected in urine at levels greater than 1ng/ml, representing a diverse panel of proteins with respect to structure, function and biological role. The presence of several biomarkers in urine was confirmed by western blot. Several methods of data normalization were employed to assess impact on biomarker variability. A complex pattern of correlations with urine creatinine, albumin and beta-2-microglobulin was observed indicating the presence of highly specific mechanisms of renal filtration. Further investigation of the urinary protein biomarkers identified in this preliminary study along with a consideration of the underlying proteomic trends suggested by these findings should lead to an improved capability to identify candidate biomarkers for clinical development.
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Pesek J, Krüger T, Krieg N, Schiel M, Norgauer J, Großkreutz J, Rhode H. Native chromatographic sample preparation of serum, plasma and cerebrospinal fluid does not comprise a risk for proteolytic biomarker loss. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 923-924:102-9. [DOI: 10.1016/j.jchromb.2013.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 01/04/2023]
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Biberoglu K, Schopfer LM, Saxena A, Tacal O, Lockridge O. Polyproline tetramer organizing peptides in fetal bovine serum acetylcholinesterase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:745-53. [PMID: 23352838 DOI: 10.1016/j.bbapap.2013.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/26/2012] [Accepted: 01/14/2013] [Indexed: 11/28/2022]
Abstract
Acetylcholinesterase (AChE) in the serum of fetal cow is a tetramer. The related enzyme, butyrylcholinesterase (BChE), in the sera of humans and horse requires polyproline peptides for assembly into tetramers. Our goal was to determine whether soluble tetrameric AChE includes tetramer organizing peptides in its structure. Fetal bovine serum AChE was denatured by boiling to release non-covalently bound peptides. Bulk protein was separated from peptides by filtration and by high performance liquid chromatography. Peptide mass and amino acid sequence of the released peptides were determined by MALDI-TOF-TOF and LTQ-Orbitrap mass spectrometry. Twenty polyproline peptides, divided into 5 families, were identified. The longest peptide contained 25 consecutive prolines and no other amino acid. Other polyproline peptides included one non-proline amino acid, for example serine at the C-terminus of 20 prolines. A search of the mammalian proteome database suggested that this assortment of polyproline peptides originated from at least 5 different precursor proteins, none of which were the ColQ or PRiMA of membrane-anchored AChE. To date, AChE and BChE are the only proteins known that include polyproline tetramer organizing peptides in their tetrameric structure.
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Affiliation(s)
- Kevser Biberoglu
- Department of Biochemistry, Hacettepe University, Ankara, Turkey.
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48
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Kolesinska B, Podwysocka DJ, Rueping MA, Seebach D, Kamena F, Walde P, Sauer M, Windschiegl B, Meyer-Ács M, Vor der Brüggen M, Giehring S. Permeation through Phospholipid Bilayers, Skin-Cell Penetration, Plasma Stability, and CD Spectra ofα- andβ-Oligoproline Derivatives. Chem Biodivers 2013; 10:1-38. [DOI: 10.1002/cbdv.201200393] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Indexed: 11/06/2022]
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Darley MM, Ramos TN, Wetsel RA, Barnum SR. Deletion of carboxypeptidase N delays onset of experimental cerebral malaria. Parasite Immunol 2013; 34:444-7. [PMID: 22708514 DOI: 10.1111/j.1365-3024.2012.01376.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complement contributes to inflammation during pathogen infections; however, less is known regarding its role during malaria and in the severest form of the disease, cerebral malaria. Recent studies have shown that deletion of the complement anaphylatoxins receptors, C3aR and C5aR, does not alter disease susceptibility in experimental cerebral malaria (ECM). This does not, however, preclude C3a- and C5a-mediated contributions to inflammation in ECM and raises the possibility that carboxypeptidase regulation of anaphylatoxin activity rapidly over rides their functions. To address this question, we performed ECM using carboxypeptidase N-deficient (CPN(-/-)) mice. Unexpectedly, we found that CPN(-/-) mice survived longer than wild-type mice, but they were fully susceptible to ECM. CD4(+) and CD8(+) T cell infiltration was not reduced at the peak of disease in CPN(-/-) mice, and there was no corresponding reduction in pro-inflammatory cytokine production. Our results indicate that carboxypeptidases contribute to the pathogenesis of ECM and that studies examining the contribution of other carboxypeptidase families and family members may provide greater insight into the role these enzymes play in malaria.
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Affiliation(s)
- M M Darley
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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50
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Analysis of human serum phosphopeptidome by a focused database searching strategy. J Proteomics 2013; 78:389-97. [DOI: 10.1016/j.jprot.2012.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/17/2012] [Accepted: 10/08/2012] [Indexed: 12/20/2022]
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