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Amiri-Dashatan N, Koushki M, Abbaszadeh HA, Rostami-Nejad M, Rezaei-Tavirani M. Proteomics Applications in Health: Biomarker and Drug Discovery and Food Industry. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2018; 17:1523-1536. [PMID: 30568709 PMCID: PMC6269565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Advancing in genome sequencing has greatly propelled the understanding of the living world; however, it is insufficient for full description of a biological system. Focusing on proteomics has emerged as another large-scale platform for improving the understanding of biology. Proteomic experiments can be used for different aspects of clinical and health sciences such as food technology, biomarker discovery and drug target identification. Since proteins are main constituents of foods, proteomic technology can monitor and characterize protein content of foods and their change during production process. The proteomic biomarker discovery is advanced in various diseases such as cancer, cardiovascular diseases, AIDS, and renal diseases which provide non-invasive methods by the use of body fluids such as urine and serum. Proteomics is also used in drug target identification using different approaches such as chemical proteomics and protein interaction networks. The development and application of proteomics has increased tremendously over the last decade. Advances in proteomics methods offer many promising new directions of studying in clinical fields. In this regard, we want to discuss proteomics technology application in food investigations, drug, and biomarker discovery.
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Affiliation(s)
- Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Koushki
- Department of Biochemistry, Medicine Faculty, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hojjat-Allah Abbaszadeh
- Hearing Disorders Research Center.Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Rostami-Nejad
- Research Institute for Gastroenterology and Liver Diseases, Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Atay S, Wilkey DW, Milhem M, Merchant M, Godwin AK. Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers. Mol Cell Proteomics 2017; 17:495-515. [PMID: 29242380 DOI: 10.1074/mcp.ra117.000267] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/21/2017] [Indexed: 12/13/2022] Open
Abstract
Developing tumors continuously release nano-sized vesicles that represent circulating "fingerprints" of the tumor's identity. In gastrointestinal stromal tumor (GIST), we have previously reported that these tumors release "oncosomes" carrying the constitutively activated tyrosine kinase (TK) receptor KIT. Despite the clinical utility of TK inhibitors, such as imatinib mesylate (IM), recurrence and metastasis are clinical problems that urge the need to identify new tumor-derived molecules. To this aim, we performed the first high quality proteomic study of GIST-derived exosomes (GDEs) and identified 1,060 proteins composing the core GDE proteome (cGDEp). The cGDEp was enriched in diagnostic markers (e.g. KIT, CD34, ANO1, PROM1, PRKCQ, and ENG), as well as proteins encoded by genes previously reported expressed in GIST (e.g. DPP4, FHL1, CDH11, and KCTD12). Many of these proteins were validated using cell lines, patient-derived KIT+ exosomes, and GIST tissues. We further show that in vitro and in vivo-derived GDE, carry proteins associated with IM response, such as Sprouty homolog 4 (SPRY4), surfeit 4 (SURF4), ALIX, and the cGMP-dependent 3',5'-cyclic phosphodiesterase 2A (PDE2A). Additionally, we report that the total exosome levels and exosome-associated KIT and SPRY4 protein levels have therapeutic values. In fact, molecular characterization of in vivo-derived KIT+ exosomes indicate significant sorting of p-KITTyr719, total KIT, and SPRY4 after IM-treatment of metastatic patients as compared with the pre-IM levels. Our data suggest that analysis of circulating exosomes levels and molecular markers of IM response in GIST patients with primary and metastatic disease is suitable to develop liquid based biopsies for the diagnosis, prognosis, and monitoring of response to treatment of these tumors. In summary, these findings provide the first insight into the proteome of GIST-derived oncosomes and offers a unique opportunity to further understand their oncogenic elements which contribute to tumorigenesis and drug resistance. Data are available via ProteomeXchange with identifier PXD007997.
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Affiliation(s)
- Safinur Atay
- From the ‡Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160;
| | - Daniel W Wilkey
- §University of Louisville Room 209, Donald Baxter Research Building, 570 S. Preston Street, Louisville, Kentucky 40202
| | - Mohammed Milhem
- ¶Division of Hematology, Oncology, Blood and Marrow Transplantation 200 Hawkins Drive, C32 GH Iowa City, Iowa 52242
| | - Michael Merchant
- §University of Louisville Room 209, Donald Baxter Research Building, 570 S. Preston Street, Louisville, Kentucky 40202
| | - Andrew K Godwin
- From the ‡Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160.,‖University of Kansas Cancer Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160
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Peljhan S, Jakop T, Šček D, Skvarča V, Goričar B, Žabar R, Mencin N. HPLC fingerprinting approach for raw material assessment and unit operation tracking for IVIG production from Cohn I+II+III fraction. Electrophoresis 2017; 38:2880-2885. [DOI: 10.1002/elps.201700212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 01/05/2023]
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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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Hasan F, Vidanapathirana P, Das S, Fernand VE, Siraj N, Losso JN, Warner IM. Ionic liquids as buffer additives in ionic liquid-polyacrylamide gel electrophoresis separation of mixtures of low and high molecular weight proteins. RSC Adv 2015. [DOI: 10.1039/c5ra11559k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Three novel ionic liquids (ILs) [CnPBr] (n= 4, 6, 8) have been synthesized and were used as buffer additives in IL-PAGE separation of mixture of acidic proteins.
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Affiliation(s)
- Farhana Hasan
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | | | - Susmita Das
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | - Vivian E. Fernand
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
- Department of Chemistry and Physics
| | - Noureen Siraj
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | - Jack N. Losso
- Department of Food Science
- Louisiana State University
- Baton Rouge
- USA
| | - Isiah M. Warner
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
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Yang Y, Ma L, Guan W, Wang Y, DU Y, Ga Q, Ge RL. Differential plasma proteome analysis in patients with high-altitude pulmonary edema at the acute and recovery phases. Exp Ther Med 2014; 7:1160-1166. [PMID: 24940404 PMCID: PMC3991535 DOI: 10.3892/etm.2014.1548] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/17/2014] [Indexed: 11/22/2022] Open
Abstract
This study aimed to investigate the differential expression of plasma proteins in patients suffering from high-altitude pulmonary edema (HAPE) at different phases. A complete proteomic analysis was performed using two-dimensional gel electrophoresis followed by mass spectrometry in three patients with HAPE at the acute stage and recovery phase. Comparisons between the expression patterns of the patients with HAPE at the two different phases led to the identification of eight protein spots with a >1.5-fold difference in expression between the acute and recovery phases. These differentially expressed proteins were apolipoproteins, serum amyloid P component, complement components and others. Apolipoprotein A-I (Apo A-I), serum amyloid P component and fibrinogen were overexpressed in the patients with HAPE in the acute stage compared with their expression levels in the recovery phase. However, Apo A-IV and antithrombin-III were overexpressed in the patients with HAPE in the recovery phase compared with their expression levels in the acute stage. The results indicate that the differential plasma proteome in patients with HAPE may be associated with the occurrence of HAPE, and the expression changes of Apo A-I and A-IV may offer further understanding of HAPE to aid its prognosis, diagnosis and treatment.
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Affiliation(s)
- Yingzhong Yang
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
| | - Lan Ma
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
| | - Wei Guan
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China ; Department of Respiratory Medicine, Qinghai University Affiliated Hospital, Xining, Qinghai 810001, P.R. China
| | - Yaping Wang
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
| | - Yang DU
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
| | - Qin Ga
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
| | - Ri-Li Ge
- Research Center for High Altitude Medical Sciences, Qinghai University School of Medicine, Xining, Qinghai 810001, P.R. China
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Prudent M, Tissot JD, Lion N. Proteomics of blood and derived products: what’s next? Expert Rev Proteomics 2014; 8:717-37. [DOI: 10.1586/epr.11.58] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ortiz A, Richa L, Defer C, Dernis D, Huart JJ, Tokarski C, Rolando C. Proteomics applied to transfusion plasma: the beginning of the story. Vox Sang 2013; 104:275-91. [PMID: 23438183 DOI: 10.1111/j.1423-0410.2012.01663.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
'Safe blood' is and has always been the major concern in transfusion medicine. Plasma can undergo virus inactivation treatments based on physicochemical, photochemical or thermal methodologies for pathogen inactivation. The validation of these treatments is essentially based on clottability assays and clotting factors' titration; however, their impact on plasma proteins at the molecular level has not yet been evaluated. Proteomics appears as particularly adapted to identify, to localize and, consequently, to correlate these modifications to the biological activity change. At the crossroads of biology and analytical sciences, proteomics is the large-scale study of proteins in tissues, physiological fluids or cells at a given moment and in a precise environment. The proteomic strategy is based on a set of methodologies involving separative techniques like mono- and bidimensional gel electrophoresis and chromatography, analytical techniques, especially mass spectrometry, and bioinformatics. Even if plasma has been extensively studied since the very beginning of proteomics, its application to transfusion medicine has just begun. In the first part of this review, we present the principles of proteomics analysis. Then, we propose a state of the art of proteomics applied to plasma analysis. Finally, the use of proteomics for the evaluation of the impact of storage conditions and pathogen inactivation treatments applied to transfusion plasma and for the evaluation of therapeutic protein fractionated is discussed.
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Affiliation(s)
- A Ortiz
- USR CNRS 3290, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique (MSAP), Université de Lille 1, Sciences et Technologie, Villeneuve d'Ascq, France
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9
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Proteome alterations in response to aristolochic acids in experimental animal model. J Proteomics 2012; 76 Spec No.:79-90. [PMID: 22796065 DOI: 10.1016/j.jprot.2012.06.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/26/2012] [Accepted: 06/29/2012] [Indexed: 11/23/2022]
Abstract
Strong indications have been presented that dietary poisoning with aristolochic acids (AA) is responsible for Endemic Nephropathy (EN) and AA associated cancer of the upper urinary tract (UUTC). Our recent investigation showed drastic urinary proteome changes in AA treated mice. This study was designed to identify proteome changes associated with AA nephrotoxicity in experimental animal model. The DBA and C57BL mice, which differ in AA sensitivity, were exposed to AA for 4 days. The strategy for urinary, plasma and kidney tissue proteome study of AA exposed and control mice integrated gel-based and in-solution tryptic digestion combined with LC-ESI-MS/MS. To maximize proteome coverage, plasma fractionation scheme was developed and MS compatible sequential tissue extraction procedure was established. Proteomic analyses of urinary, plasma and kidney tissue tryptic digests resulted in identification of several cytoskeletal proteins, as well as proteins involved in kidney development and inflammatory response, that are differentially expressed in both AA exposed and control mice. These proteins are consistent with renal pathogenesis of endotoxicity and cancer. This proteomic strategy could be effectively translated for unbiased discovery of potential biomarkers for EN and associated UUTC in humans. At the same time, these results highlight the significance of AA exposure with EN. This article is part of a Special Issue entitled: Integrated omics.
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Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen and angiogenin interact with common host proteins, including annexin A2, which is essential for survival of latently infected cells. J Virol 2011; 86:1589-607. [PMID: 22130534 DOI: 10.1128/jvi.05754-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) infection and latency-associated nuclear antigen (LANA-1) upregulate the multifunctional protein angiogenin (ANG). Our studies demonstrate that silencing ANG or inhibiting its nuclear translocation downregulates KSHV LANA-1 expression and ANG is necessary for KSHV latency, anti-apoptosis and angiogenesis (Sadagopan et al., J. Virol. 83:3342-3364, 2009; Sadagopan et al., J Virol. 85:2666-2685, 2011). Here we show that LANA-1 interacts with ANG and colocalizes in latently infected endothelial telomerase-immortalized human umbilical vein endothelial (TIVE-LTC) cells. Mass spectrometric analyses of TIVE-LTC proteins immunoprecipitated by anti-LANA-1 and ANG antibodies identified 28 common cellular proteins such as ribosomal proteins, structural proteins, tRNA synthetases, metabolic pathway enzymes, chaperons, transcription factors, antioxidants, and ubiquitin proteosome proteins. LANA-1 and ANG interaction with one of the proteins, annexin A2, was validated. Annexin A2 has been shown to play roles in cell proliferation, apoptosis, plasmin generation, exocytosis, endocytosis, and cytoskeleton reorganization. It is also known to associate with glycolytic enzyme 3-phosphoglyceratekinase in the primer recognition protein (PRP) complex that interacts with DNA polymerase α in the lagging strand of DNA during replication. A higher level of annexin A2 is expressed in KSHV+ but not in Epstein-Barr virus (EBV)+ B-lymphoma cell lines. Annexin A2 colocalized with several LANA-1 punctate spots in KSHV+ body cavity B-cell lymphoma (BCBL-1) cells. In triple-staining analyses, we observed annexin A2-ANG-LANA-1, annexin A2-ANG, and ANG-LANA-1 colocalizations. Annexin A2 appeared as punctate nuclear dots in LANA-1-positive TIVE-LTC cells. In LANA-1-negative TIVE-LTC cells, annexin A2 was detected predominately in the cytoplasm, with some nuclear spots, and colocalization with ANG was observed mostly in the cytoplasm. Annexin A2 coimmunoprecipitated with LANA-1 and ANG in TIVE-LTC and BCBL-1 cells and with ANG in 293T cells independent of LANA-1. This suggested that annexin A2 forms a complex with LANA-1 and ANG as well as a separate complex with ANG. Silencing annexin A2 in BCBL-1 cells resulted in significant cell death, downregulation of cell cycle-associated Cdk6 and of cyclin D, E, and A proteins, and downregulation of LANA-1 and ANG expression. No effect was seen in KSHV⁻ lymphoma (BJAB and Ramos) and 293T cells. These studies suggest that LANA-1 association with annexin A2/ANG could be more important than ANG association with annexin A2, and KSHV probably uses annexin A2 to maintain the viability and cell cycle regulation of latently infected cells. Since the identified LANA-1- and ANG-interacting common cellular proteins are hitherto unknown to KSHV and ANG biology, this offers a starting point for further analysis of their roles in KSHV biology, which may lead to identification of potential therapeutic targets to control KSHV latency and associated malignancies.
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Zhang T, Gai Q, Qu F, Zhang Y. Ionic liquid-assisted SDS-PAGE to improve human serum protein separation. Electrophoresis 2011; 32:2904-10. [DOI: 10.1002/elps.201100184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/14/2011] [Accepted: 05/16/2011] [Indexed: 12/23/2022]
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Gaso-Sokac D, Kovac S, Clifton J, Josic D. Therapeutic plasma proteins--application of proteomics in process optimization, validation, and analysis of the final product. Electrophoresis 2011; 32:1104-17. [PMID: 21544836 DOI: 10.1002/elps.201000641] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An overview is given on the application of proteomic technology in the monitoring of different steps during the production of therapeutic proteins from human plasma. Recent advances in this technology enable the use of proteomics as an advantageous tool for the validation of already existing processes, the development and fine tuning of new production steps, the characterization and quality control of final products, the detection of both harmful impurities and modifications of the therapeutic protein and the auditing of batch-to-batch variations. Further, use of proteomics for preclinical testing of new products, which can be either recombinant or plasma-derived, is also discussed.
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Affiliation(s)
- Dajana Gaso-Sokac
- Department of Chemistry, J. J. Strossmayer Univeristy, Osijek, Croatia
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14
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Protéomique et médecine transfusionnelle. Transfus Clin Biol 2011; 18:79-96. [DOI: 10.1016/j.tracli.2011.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/17/2011] [Indexed: 01/02/2023]
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15
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Clifton J, Huang F, Rucevic M, Cao L, Hixson D, Josic D. Protease inhibitors as possible pitfalls in proteomic analyses of complex biological samples. J Proteomics 2011; 74:935-41. [PMID: 21333769 DOI: 10.1016/j.jprot.2011.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 01/27/2011] [Accepted: 02/09/2011] [Indexed: 11/16/2022]
Abstract
Sample preparation, especially protein and peptide fractionation prior to identification by mass spectrometry (MS), is typically applied to reduce sample complexity. The second key element in this process is proteolytic digestion, which is performed most often with trypsin. Optimization of this step is an important factor in order to achieve both speed and better performance of proteomic analysis, and tryptic digestion prior to the MS analysis has been a topic of many studies. To date, only a few studies have paid attention to the negative interaction between the proteolytic enzyme and sample components, and sample losses caused by these interactions. In this study, we demonstrated impaired activity after "in solution" tryptic digestion of plasma proteins caused by a potent trypsin inhibitor family, inter-alpha inhibitor proteins. Sample boiling followed by gel electrophoretic separation and "in-gel" digestion drastically improved both the number of identified proteins and the sequence coverage in subsequent LC-ESI-MS/MS. The present investigations show that a thorough validation is necessary when "in solution" digestion followed by LC-MS analysis of complex biological samples is performed. The parallel use of two or more different mass spectrometers can also yield additional information and contribute to further method validation.
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Affiliation(s)
- James Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, USA
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16
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Peng J, Su Y, Shi Q, Chen W, Jiang Z. Protein fouling resistant membrane prepared by amphiphilic pegylated polyethersulfone. BIORESOURCE TECHNOLOGY 2011; 102:2289-2295. [PMID: 21051225 DOI: 10.1016/j.biortech.2010.10.045] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 10/10/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
A mild and facile grafting of poly(ether glycol) methyl ether methacrylate (PEGMA) monomers onto polyethersulfone (PES) was carried out. Then, the PES-g-PEGMA membranes with integrally anisotropic morphology were fabricated through the coupling of non-solvent induced phase inversion and surface segregation. Compared with PES control membrane, the surface hydrophilicity of PES-g-PEGMA membranes was remarkably enhanced due to the drastic enrichment of poly(ethylene glycol) (PEG) segments on the membrane surface; protein adsorption was significantly inhibited due to the hydrogen bonding interactions between hydrophilic groups and water molecules. Ultrafiltration experiments were used to assess the permeability and protein fouling resistance of the PES-g-PEGMA membranes. It was found that the PES-g-PEGMA membranes with higher surface coverage of PEG segments displayed stronger antibiofouling property. Moreover, the stable antibiofouling property for PES-g-PEGMA membranes was acquired due to covalent bonding interactions between hydrophilic PEGMA side chains and PES main chains.
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Affiliation(s)
- Jinming Peng
- Key Laboratory for Green Chemical Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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Brgles M, Clifton J, Walsh R, Huang F, Rucevic M, Cao L, Hixson D, Müller E, Josic D. Selectivity of monolithic supports under overloading conditions and their use for separation of human plasma and isolation of low abundance proteins. J Chromatogr A 2010; 1218:2389-95. [PMID: 21186030 DOI: 10.1016/j.chroma.2010.11.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/19/2010] [Accepted: 11/25/2010] [Indexed: 01/06/2023]
Abstract
Human serum albumin (HSA) and immunoglobulin G (IgG) represent over 75% of all proteins present in human plasma. These two proteins frequently interfere with detection, determination and purification of low abundance proteins that can be potential biomarkers and biomarker candidates for various diseases. Some low abundance plasma proteins such as clotting factors and inhibitors are also important therapeutic agents. In this paper, the characterization of ion-exchange monolithic supports under overloading conditions was performed by use of sample displacement chromatography (SDC). If these supports were used for separation of human plasma, the composition of bound and eluted proteins in both anion- and cation-exchange mode is dependent on column loading. Under overloading conditions, the weakly bound proteins such as HSA in anion-exchange and IgG in cation-exchange mode are displaced by stronger binding proteins, and this phenomenon was not dependent on column size. Consequently, small monolithic columns with a column volume of 100 and 200 μL are ideal supports for high-throughput screening in order to develop new methods for separation of complex mixtures, and for sample preparation in proteomic technology.
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Liumbruno G, D’Alessandro A, Grazzini G, Zolla L. How has proteomics informed transfusion biology so far? Crit Rev Oncol Hematol 2010; 76:153-72. [DOI: 10.1016/j.critrevonc.2010.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 12/22/2009] [Accepted: 01/07/2010] [Indexed: 01/06/2023] Open
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The role of proteomics in plasma fractionation and quality control of plasma-derived therapeutic proteins. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2010; 8 Suppl 3:s86-91. [PMID: 20606756 PMCID: PMC2897198 DOI: 10.2450/2010.014s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Clifton JG, Huang F, Kovac S, Yang X, Hixson DC, Josic D. Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates. Electrophoresis 2010; 30:3636-46. [PMID: 19768705 DOI: 10.1002/elps.200900270] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteomic methods were used to identify the levels of impurities in three commercial plasma-derived clotting factor VIII-von Willebrand factor (FVIII/VWF) concentrates. In all three concentrates, significant amounts of other plasma proteins were found. In Octanate and Haemoctin, two concentrates developed in the 1990s, the major impurities identified were inter-alpha inhibitor proteins, fibrinogen and fibronectin. These two concentrates were also found to contain additional components such as clotting factor II (prothrombin) that are known activators of FVIII. In Wilate, a recently developed FVIII/VWF concentrate, the amount of these impurities was significantly reduced. Batch-to-batch variations and differences between three investigated products were detected using iTRAQ, an isotope labeling technique for comparative MS, demonstrating the potential value of this technique for quality control analysis. The importance of thorough proteomic investigations of therapeutic FVIII/VWF preparations from human plasma is also discussed.
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Affiliation(s)
- James G Clifton
- Proteomics Core, COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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Clifton J, Huang F, Gaso-Sokac D, Brilliant K, Hixson D, Josic D. Use of proteomics for validation of the isolation process of clotting factor IX from human plasma. J Proteomics 2009; 73:678-88. [PMID: 19819359 DOI: 10.1016/j.jprot.2009.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/24/2009] [Accepted: 09/28/2009] [Indexed: 12/25/2022]
Abstract
The use of proteomic techniques in the monitoring of different production steps of plasma-derived clotting factor IX (pd F IX) was demonstrated. The first step, solid-phase extraction with a weak anion-exchange resin, fractionates the bulk of human serum albumin (HSA), immunoglobulin G, and other non-binding proteins from F IX. The proteins that strongly bind to the anion-exchange resin are eluted by higher salt concentrations. In the second step, anion-exchange chromatography, residual HSA, some proteases and other contaminating proteins are separated. In the last chromatographic step, affinity chromatography with immobilized heparin, the majority of the residual impurities are removed. However, some contaminating proteins still remain in the eluate from the affinity column. The next step in the production process, virus filtration, is also an efficient step for the removal of residual impurities, mainly high molecular weight proteins, such as vitronectin and inter-alpha inhibitor proteins. In each production step, the active component, pd F IX and contaminating proteins are monitored by biochemical and immunochemical methods and by LC-MS/MS and their removal documented. Our methodology is very helpful for further process optimization, rapid identification of target proteins with relatively low abundance, and for the design of subsequent steps for their removal or purification.
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Affiliation(s)
- James Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, USA
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