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Zeng Y, Deng FY, Zhu W, Zhang L, He H, Xu C, Tian Q, Zhang JG, Zhang LS, Hu HG, Deng HW. Mass spectrometry based proteomics profiling of human monocytes. Protein Cell 2016; 8:123-133. [PMID: 27878450 PMCID: PMC5291777 DOI: 10.1007/s13238-016-0342-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022] Open
Abstract
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged. Biological functions of these monocyte-expressed genes were annotated and classified via Gene Ontology (GO) analysis. Furthermore, by extracting the overlapped genes from in vivo and in vitro datasets, a core gene list including 541 unique genes was generated. Based on the core gene list, further gene-disease associations, pathway and network analyses were performed. Data analyses based on multiple bioinformatics tools produced a large body of biologically meaningful information, and revealed a number of genes such as SAMHD1, G6PD, GPD2 and ENO1, which have been reported to be related to immune response, blood biology, bone remodeling, and cancer respectively. As a unique resource, this study can serve as a reference map for future in-depth research on monocytes biology and monocyte-involved human diseases.
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Affiliation(s)
- Yong Zeng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.,Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Fei-Yan Deng
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.,Laboratory of Proteins and Proteomics, Department of Epidemiology, Soochow University School of Public Health, Suzhou, 205123, China
| | - Wei Zhu
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lan Zhang
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Hao He
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Qing Tian
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Ji-Gang Zhang
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China. .,Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
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Alonso-Orgaz S, Moreno-Luna R, López JA, Gil-Dones F, Padial LR, Moreu J, de la Cuesta F, Barderas MG. Proteomic characterization of human coronary thrombus in patients with ST-segment elevation acute myocardial infarction. J Proteomics 2014; 109:368-81. [DOI: 10.1016/j.jprot.2014.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 01/04/2023]
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3
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Polkinghorne VR, Standeven KF, Schroeder V, Carter AM. Role of proteomic technologies in understanding risk of arterial thrombosis. Expert Rev Proteomics 2014; 6:539-50. [DOI: 10.1586/epr.09.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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4
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Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N, Chakraborty S. Comparative Proteomics Reveals a Role for Seed Storage Protein AmA1 in Cellular Growth, Development, and Nutrient Accumulation. J Proteome Res 2013; 12:4904-30. [DOI: 10.1021/pr4007987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalit Agrawal
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Kanika Narula
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Swaraj Basu
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Shubhendu Shekhar
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Sudip Ghosh
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Asis Datta
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
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5
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Shrivastava P, Bagchi T. Differential expression of alpha II spectrin in monocytes of tuberculosis patients. Int Immunopharmacol 2013; 17:759-62. [PMID: 24055022 DOI: 10.1016/j.intimp.2013.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/06/2013] [Accepted: 09/06/2013] [Indexed: 11/17/2022]
Abstract
Monocytes play a crucial role in immune response to tuberculosis. The present study focuses on identifying differences in the monocyte proteome profile of tuberculosis patients, household contacts and healthy controls. Differential protein expression was studied by two-dimensional (2D) gel electrophoresis. One of the spots consistently showed either lower intensity or was absent in patients and was identified as alpha II-spectrin. The decreased expression of αII-spectrin was further validated by quantitative PCR (qPCR) and western blot analysis. This study suggests the possible role of decreased levels of αII-spectrin in the pathology of tuberculosis.
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Affiliation(s)
- Parul Shrivastava
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
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6
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Interindividual variation in the proteome of human peripheral blood mononuclear cells. PLoS One 2013; 8:e61933. [PMID: 23613975 PMCID: PMC3629925 DOI: 10.1371/journal.pone.0061933] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 03/15/2013] [Indexed: 01/12/2023] Open
Abstract
Peripheral blood mononuclear cells (PBMCs) are main actors in inflammatory processes and linked to many diseases, including rheumatoid arthritis, atherosclerosis, asthma, HIV and cancer. Moreover, they seem an interesting ‘surrogate tissue’ that can be used in biomarker discovery. In order to get a good experimental design for quantitative expression studies, the knowledge of the interindividual variation is an essential part. Therefore, PBMCs were isolated from 24 healthy volunteers (15 males, 9 females, ages 63–86) with no clinical signs of inflammation. The extracted proteins were separated using the two dimensional difference in gel electrophoresis technology (2D-DIGE), and the gel images were processed with the DeCyder 2D software. Protein spots present in at least 22 out of 24 healthy volunteers were selected for further statistical analysis. Determination of the coefficient of variation (CV) of the normalized spot volume values of these proteins, reveals that the total variation of the PBMC proteome varies between 12,99% to 148,45%, with a mean value of 28%. A supplemental look at the causes of technical variation showed that the isolation of PBMCs from whole blood is the factor which influences the experimental variance the most. This isolation should be handled with extra care and an additional washing step would be beneficial. Knowing the extent of variation, we show that at least 10 independent samples per group are needed to obtain statistical powerful data. This study demonstrates the importance of considering variance of a human population for a good experimental design for future protein profiling or biomarker studies.
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Castagna A, Polati R, Bossi AM, Girelli D. Monocyte/macrophage proteomics: recent findings and biomedical applications. Expert Rev Proteomics 2012; 9:201-15. [PMID: 22462790 DOI: 10.1586/epr.12.11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Macrophages, originating from the migration and differentiation of circulating monocytes into virtually all tissues, are extremely flexible and plastic cells that play vital homeostatic roles, but also contribute to the pathophysiology of many human diseases. For these reasons, they are intensively studied by different approaches, recently including proteomics. Macrophage cells can be taken from a range of different sources, including blood monocytes and macrophages from tissues. Macrophages can also be generated by in vitro culture from blood monocytes, and cell lines derived from this lineage can be used. Similarly, many different proteomic techniques can be used, ranging from classic approaches based on 2D gel electrophoresis to more recent high-throughput gel-free techniques essentially based on mass spectrometry. Here, we review the application of such techniques to the study of monocytes/macrophages, and summarize some results potentially relevant to two paradigmatic conditions - atherosclerosis and disorders of iron metabolism.
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Affiliation(s)
- Annalisa Castagna
- Department of Medicine, Unit of Internal Medicine, University of Verona, Policlinico G.B. Rossi, Piazzale L.A. Scuro 10, Verona, Italy
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Simula MP, Notarpietro A, Toffoli G, De Re V. 2-D gel electrophoresis: constructing 2D-gel proteome reference maps. Methods Mol Biol 2012; 815:163-173. [PMID: 22130991 DOI: 10.1007/978-1-61779-424-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) is the most popular and versatile method of protein separation among a rapidly growing array of proteomic technologies. Based on two independent biochemical characteristics of proteins, it combines isoelectric focusing, which separates proteins according to their isoelectric point (pI), and SDS-PAGE, which separates them further according to their molecular mass. An evolution of conventional 2-DE is represented by the 2D-Difference in Gel Electrophoresis (2D-DIGE) that allows sample multiplexing and achieving more accurate and sensitive quantitative proteomic determinations. The 2-DE separation permits the generation of protein maps of different cells or tissues and the study, by differential proteomics, of protein expression changes associated to the different states of a biological system. In order to identify the molecular bases of pathological processes, it is also useful to characterize the physiological protein homeostasis in healthy cells or tissues. On these grounds, the availability of detailed 2D reference maps could be very useful for proteomic studies. The protocol described in this chapter is based on the 2D-DIGE technology and has been applied to obtain the first 2-DE reference map of the human small intestine.
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Affiliation(s)
- Maria Paola Simula
- Experimental and Clinical Pharmacology Unit, CRO Centro di Riferimento Oncologico, IRCCS National Cancer Institute, via F. Gallini 2, Aviano-PN 33081, Italy.
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Poduri A, Bahl A, Talwar KK, Khullar M. Proteomic analysis of circulating human monocytes in coronary artery disease. Mol Cell Biochem 2011; 360:181-8. [PMID: 21938407 DOI: 10.1007/s11010-011-1055-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/08/2011] [Indexed: 01/19/2023]
Abstract
Monocytes play an important role in inflammation and atherosclerosis; however, the molecular details underlying these diverse functions are not completely understood. Proteomic analysis of monocytes can provide new insights into their biological role in coronary artery disease (CAD). Twenty angiographically confirmed male, CAD patients (≥50% stenosis) attending cardiology clinic of Nehru Hospital, PGIMER, Chandigarh, and who were not receiving any lipid lowering therapy and 20 TMT negative subjects who served as controls were enrolled in the study. Circulating monocytes isolated from overnight fasting blood samples were analyzed by 2D gel electrophoresis (pH 4-7), and differentially expressed protein spots were subjected to mass spectrometry and identification of proteins. We observed 333 ± 40 protein spots in monocytes from patients and 312 ± 20 in controls; out of which 63 protein spots showed altered intensity in CAD patients. Thirteen spots showed fivefold increased and two protein spots showed fivefold decreased expression in CAD group as compared to control group, respectively. Two proteins showing decreased expression in monocytes from CAD patients were identified as: (i) glutathione transferase and (ii) heat shock protein 70 KDa. Proteins showing increased expression in CAD patients were identified as: (i) vimentin, (ii) mannose binding lectin receptor protein, and (iii) S100A8 calcium-binding protein. The results of our study offer identification of several proteins in monocytes which can provide new perspectives in role of monocytes in pathogenesis of atherosclerosis.
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Affiliation(s)
- Aruna Poduri
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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10
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Mithoe SC, Menke FLH. Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation. PHYTOCHEMISTRY 2011; 72:997-1006. [PMID: 21315387 DOI: 10.1016/j.phytochem.2010.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/25/2010] [Accepted: 12/06/2010] [Indexed: 05/14/2023]
Abstract
Plants and animal cells use intricate signaling pathways to respond to a diverse array of stimuli. These stimuli include signals from environment, such as biotic and abiotic stress signals, as well as cell-to-cell signaling required for pattern formation during development. The transduction of the signal often relies on the post-translational modification (PTM) of proteins. Protein phosphorylation in eukaryotic cells is considered to be a central mechanism for regulation and cellular signaling. The classic view is that phosphorylation of serine (Ser) and threonine (Thr) residues is more abundant, whereas tyrosine (Tyr) phosphorylation is less frequent. This review provides an overview of the progress in the plant phosphoproteomics field and how this progress has lead to a re-evaluation of the relative contribution of tyrosine phosphorylation to the plant phosphoproteome. In relation to this appreciated contribution of tyrosine phosphorylation we also discuss some of the recent progress on the role of tyrosine phosphorylation in plant signal transduction.
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Affiliation(s)
- Sharon C Mithoe
- Department of Biology, Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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11
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Chen X, Zhang W, Zhang B, Zhou J, Wang Y, Yang Q, Ke Y, He H. Phosphoproteins regulated by heat stress in rice leaves. Proteome Sci 2011; 9:37. [PMID: 21718517 PMCID: PMC3150237 DOI: 10.1186/1477-5956-9-37] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 06/30/2011] [Indexed: 12/23/2022] Open
Abstract
Background High temperature is a critical abiotic stress that reduces crop yield and quality. Rice (Oryza sativa L.) plants remodel their proteomes in response to high temperature stress. Moreover, phosphorylation is the most common form of protein post-translational modification (PTM). However, the differential expression of phosphoproteins induced by heat in rice remains unexplored. Methods Phosphoprotein in the leaves of rice under heat stress were displayed using two-dimensional electrophoresis (2-DE) and Pro-Q Diamond dye. Differentially expressed phosphoproteins were identified by MALDI-TOF-TOF-MS/MS and confirmed by Western blotting. Results Ten heat-phosphoproteins were identified from twelve protein spots, including ribulose bisphos-phate carboxylase large chain, 2-Cys peroxiredoxin BAS1, putative mRNA binding protein, Os01g0791600 protein, OSJNBa0076N16.12 protein, putative H(+)-transporting ATP synthase, ATP synthase subunit beta and three putative uncharacterized proteins. The identification of ATP synthase subunit beta was further validated by Western-blotting. Four phosphorylation site predictors were also used to predict the phosphorylation sites and the specific kinases for these 10 phosphoproteins. Conclusion Heat stress induced the dephosphorylation of RuBisCo and the phosphorylation of ATP-β, which decreased the activities of RuBisCo and ATP synthase. The observed dephosphorylation of the mRNA binding protein and 2-Cys peroxiredoxin may be involved in the transduction of heat-stress signaling, but the functional importance of other phosphoproteins, such as H+-ATPase, remains unknown.
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Affiliation(s)
- Xinhai Chen
- Key Laboratory of Ministry of Education for Genetic, Breeding and Multiple Utilization of Crops, Fuzhou 350002, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenfeng Zhang
- Key Laboratory of Ministry of Education for Genetic, Breeding and Multiple Utilization of Crops, Fuzhou 350002, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baoqian Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiechao Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongfei Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiaobin Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqin Ke
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaqin He
- Key Laboratory of Ministry of Education for Genetic, Breeding and Multiple Utilization of Crops, Fuzhou 350002, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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12
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Identification and validation of SRC and phospho-SRC family proteins in circulating mononuclear cells as novel biomarkers for pancreatic cancer. Transl Oncol 2011; 4:83-91. [PMID: 21461171 DOI: 10.1593/tlo.10202] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 12/16/2010] [Accepted: 12/30/2010] [Indexed: 01/21/2023] Open
Abstract
There is an urgent need to develop novel markers of pancreatic cancer to facilitate early diagnosis. Pancreatic carcinoma is characterized by marked stroma formation with a high number of infiltrating tumor-associated macrophages (TAMs) that originate from circulating mononuclear cells (MNCs). We hypothesized that differential analysis of protein expression and phosphorylation in circulating MNCs from healthy nude mice and nude mice bearing orthotopic human pancreatic cancer would identify a surrogate marker of pancreatic cancer. These differences were analyzed by two-dimensional gel electrophoresis followed by Western blot analysis using antibody against phosphorylated tyrosine proteins (pY). Protein and phosphorylated protein spots of interest were identified by mass spectrometry and validated by Western blot analysis as candidate markers for pancreatic cancer. We found that the expression and phosphorylation of Src family proteins were significantly higher in circulating MNCs from mice bearing pancreatic cancer than in circulating MNCs from healthy mice. TAMs in mice with pancreatic tumors also had higher Src family protein expression and phosphorylation than resident macrophages in the pancreas of healthy mice. The expression and phosphorylation of Src family proteins were correlated with tumor weight; however, increased Src expression and phosphorylation also occurred in MNCs from mice with chronic pancreatitis. This is the first report to explore novel pancreatic tumor markers in circulating MNCs. Although the specificity of the marker for pancreatic cancer was low, it could be used to monitor the disease or to select high-risk patients with chronic pancreatitis.
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Otani M, Taniguchi T, Sakai A, Seta J, Kadoyama K, Nakamura-Hirota T, Matsuyama S, Sano K, Takano M. Phosphoproteome Profiling Using a Fluorescent Phosphosensor Dye in Two-Dimensional Polyacrylamide Gel Electrophoresis. Appl Biochem Biotechnol 2011; 164:804-18. [DOI: 10.1007/s12010-011-9175-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 01/18/2011] [Indexed: 10/18/2022]
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14
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Ye X, Johann DJ, Hakami RM, Xiao Z, Meng Z, Ulrich RG, Issaq HJ, Veenstra TD, Blonder J. Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS. J Proteomics 2009; 73:112-22. [PMID: 19709643 PMCID: PMC3159575 DOI: 10.1016/j.jprot.2009.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 08/17/2009] [Accepted: 08/18/2009] [Indexed: 12/24/2022]
Abstract
Proteomic profiling of membrane proteins is of vital importance in the search for disease biomarkers and drug development. However, the slow pace in this field has resulted mainly from the difficulty to analyze membrane proteins by mass spectrometry (MS). The objective of this investigation was to explore and optimize solubilization of membrane proteins for shotgun membrane proteomics of the CD14 human monocytes by examining different systems that rely on: i) an organic solvent (methanol) ii) an acid-labile detergent 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate (PPS), iii) a combination of both agents (methanol+PPS). Solubilization efficiency of different buffers was first compared using bacteriorhodopsin as a model membrane protein. Selected approaches were then applied on a membrane subproteome isolated from a highly enriched human monocyte population that was approximately 98% positive for CD14 expression as determined by FACS analysis. A methanol-based buffer yielded 194 proteins of which 93 (48%) were mapped as integral membrane proteins. The combination of methanol and acid-cleavable detergent gave similar results; 203 identified proteins of which 93 (46%) were mapped integral membrane proteins. However, employing PPS 216 proteins were identified of which 75 (35%) were mapped as integral membrane proteins. These results indicate that methanol alone or in combination with PPS yielded significantly higher membrane protein identification/enrichment than the PPS alone.
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Affiliation(s)
- Xiaoying Ye
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., NCI at Frederick, Frederick, Maryland 21702-1201, USA
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15
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Haudek VJ, Slany A, Gundacker NC, Wimmer H, Drach J, Gerner C. Proteome Maps of the Main Human Peripheral Blood Constituents. J Proteome Res 2009; 8:3834-43. [DOI: 10.1021/pr801085g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Verena J. Haudek
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
| | - Astrid Slany
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
| | - Nina C. Gundacker
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
| | - Helge Wimmer
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
| | - Johannes Drach
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
| | - Christopher Gerner
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria, Section Biomedical Laboratory Science, University of Applied Science, Vienna, Austria, and Department of Medicine I, Department of Clinical Oncology, Medical University of Vienna, Austria
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16
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Simula MP, Cannizzaro R, Marin MD, Pavan A, Toffoli G, Canzonieri V, De Re V. Two-dimensional gel proteome reference map of human small intestine. Proteome Sci 2009; 7:10. [PMID: 19298663 PMCID: PMC2667413 DOI: 10.1186/1477-5956-7-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 03/19/2009] [Indexed: 01/13/2023] Open
Abstract
Background The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D) reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals without duodenal illness, to create a protein database. This approach, may be useful for comparing similar protein samples in different laboratories and for the molecular characterization of intestinal pathologies without recurring to the use of surgical material. Results The enrolled population comprised five selected samples (3 males and 2 females, aged 19 to 42), taken from 20 adult subjects, on their first visit at the gastroenterology unit for a suspected celiac disease, who did not turn to be affected by any duodenal pathology after gastrointestinal and histological evaluations. Proteins extracted from the five duodenal mucosal specimens were singly separated by 2D gel electrophoresis. After image analysis of each 2D gel, 179 protein spots, representing 145 unique proteins, from 218 spots tested, were successfully identified by MALDI-TOF ms analysis. Normalized volumes, for each protein, have been reported for every gel. Proteins have been grouped according to their biological/metabolic functions. Conclusion This study represents to date the first detailed and reproducible 2D protein map of human duodenum. Spots identifications, reported in a database, will be helpful to identify the variability in protein expression levels, in isoforms expression, or in post-translational modifications associated to pathology or to a therapy.
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Affiliation(s)
- Maria Paola Simula
- CRO Centro di Riferimento Oncologico, IRCCS National Cancer Institute, Aviano, PN, Italy.
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Vergara D, Chiriacò F, Acierno R, Maffia M. Proteomic map of peripheral blood mononuclear cells. Proteomics 2008; 8:2045-51. [PMID: 18491318 DOI: 10.1002/pmic.200700726] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the field of proteomics extensive efforts have been focused on the knowledge of proteins expressed by different cell types. In particular, enormous progress has been done in the characterization of blood cellular components. In this work, we have established a public 2-DE database for human peripheral blood mononuclear cells (PBMCs) proteins. Two hundred and forty-six spots corresponding to 174 different proteins have been identified on 2-DE gels from PBMCs isolated from six healthy individuals. All the identified proteins have been classified in thirteen categories on the basis of their differential functions or cellular localization and annotated at the http://physiology.unile.it/proteomics. The role of several proteins has been discussed in relation to their biological function. We intend to show the potentiality of PBMCs to investigate the proteomics changes possibly associated with a large number of pathologies such as autoimmune, neurodegenerative and cancer diseases.
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Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Proteome of monocyte priming by lipopolysaccharide, including changes in interleukin-1beta and leukocyte elastase inhibitor. Proteome Sci 2008; 6:13. [PMID: 18492268 PMCID: PMC2413206 DOI: 10.1186/1477-5956-6-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/20/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Monocytes can be primed in vitro by lipopolysaccharide (LPS) for release of cytokines, for enhanced killing of cancer cells, and for enhanced release of microbicidal oxygen radicals like superoxide and peroxide. We investigated the proteins involved in regulating priming, using 2D gel proteomics. RESULTS Monocytes from 4 normal donors were cultured for 16 h in chemically defined medium in Teflon bags +/- LPS and +/- 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), a serine protease inhibitor. LPS-primed monocytes released inflammatory cytokines, and produced increased amounts of superoxide. AEBSF blocked priming for enhanced superoxide, but did not affect cytokine release, showing that AEBSF was not toxic. After staining large-format 2D gels with Sypro ruby, we compared the monocyte proteome under the four conditions for each donor. We found 30 protein spots that differed significantly in response to LPS or AEBSF, and these proteins were identified by ion trap mass spectrometry. CONCLUSION We identified 19 separate proteins that changed in response to LPS or AEBSF, including ATP synthase, coagulation factor XIII, ferritin, coronin, HN ribonuclear proteins, integrin alpha IIb, pyruvate kinase, ras suppressor protein, superoxide dismutase, transketolase, tropomyosin, vimentin, and others. Interestingly, in response to LPS, precursor proteins for interleukin-1beta appeared; and in response to AEBSF, there was an increase in elastase inhibitor. The increase in elastase inhibitor provides support for our hypothesis that priming requires an endogenous serine protease.
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Kang TH, Bae KH, Yu MJ, Kim WK, Hwang HR, Jung H, Lee PY, Kang S, Yoon TS, Park SG, Ryu SE, Lee SC. Phosphoproteomic analysis of neuronal cell death by glutamate-induced oxidative stress. Proteomics 2007; 7:2624-35. [PMID: 17610204 DOI: 10.1002/pmic.200601028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oxidative stress is one of the major causes of neuronal cell death in disorders such as perinatal hypoxia and ischemia. Protein phosphorylation is the most significant PTM of proteins and plays an important role in stress-induced signal transduction. Thus, the analysis of alternative protein phosphorylation states which occur during oxidative stress-induced cell death could provide valuable information regarding cell death. In this study, a reference phosphoproteome map of the mouse hippocampal cell line HT22 was constructed based on 125 spots that were identified by MALDI-TOF or LC-ESI-Q-TOF-MS analysis. In addition, proteins of HT22 cells at various stages of oxidative stress-induced cell death were separated by 2-DE and alterations in phosphoproteins were detected by Pro-Q Diamond staining. A total of 17 spots showing significant quantitative changes and seven newly appearing spots were identified after glutamate treatment. Splicing factor 2, peroxiredoxin 2, S100 calcium binding protein A11, and purine nucleoside phosphorylase were identified as up- or down-regulated proteins. CDC25A, caspase-8, and cyp51 protein appeared during oxidative stress-induced cell death. The data in this study from phosphoproteomic analysis provide a valuable resource for the understanding of HT22 cell death mechanisms mediated by oxidative stress.
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Affiliation(s)
- Tae Hyuk Kang
- Translational Research Center, KRIBB, Daejeon, South Korea
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