1
|
Liu Y, Wu Y, Wang Y, Zhang M, Li Z. Increased Levels of Serum Protein Complexes Are Associated with Type 2 Diabetes. Int J Med Sci 2018; 15:210-216. [PMID: 29483811 PMCID: PMC5820849 DOI: 10.7150/ijms.22517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/23/2017] [Indexed: 01/14/2023] Open
Abstract
Objective: To screen novel biomarkers in the levels of protein complexes for type 2 diabetes mellitus (T2DM). Methods: Serum immunoinflammation-related protein complexes (IIRPCs) and diabetes-related protein complexes (DRPCs) in 1537 serum samples including 504 healthy controls, 320 patients with prediabetes, and 713 patients with T2DM were analyzed using an optimized native polyacrylamide gel electrophoresis (native-PAGE). Results: Seven patterns of serum IIRPCs and four patterns of serum DRPCs were observed in the study population, respectively. Significant increase in the levels of serum IIRPCs in T2DM was detected relative to healthy controls. Change trends of serum DRPCs are as below: patients with T2DM>patients with prediabetes> healthy controls. Conclusion: Our findings suggest that increased levels of serum IIRPCs and DRPCs were associated with T2DM.
Collapse
Affiliation(s)
- Yujie Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, PR China
| | - Yunpeng Wu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, PR China
| | - Yanmin Wang
- Department of Clinical Laboratory, Heze Municipal Hospital, Shandong 274031, PR China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, PR China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, PR China
| |
Collapse
|
2
|
Song H, Xiong H, Che J, Xi QS, Huang L, Xiong HH, Zhang P. Gel-based chemical cross-linking analysis of 20S proteasome subunit-subunit interactions in breast cancer. ACTA ACUST UNITED AC 2016; 36:564-570. [PMID: 27465334 DOI: 10.1007/s11596-016-1626-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/29/2022]
Abstract
The ubiquitin-proteasome system plays a pivotal role in breast tumorigenesis by controlling transcription factors, thus promoting cell cycle growth, and degradation of tumor suppressor proteins. However, breast cancer patients have failed to benefit from proteasome inhibitor treatment partially due to proteasome heterogeneity, which is poorly understood in malignant breast neoplasm. Chemical crosslinking is an increasingly important tool for mapping protein three-dimensional structures and proteinprotein interactions. In the present study, two cross-linkers, bis (sulfosuccinimidyl) suberate (BS(3)) and its water-insoluble analog disuccinimidyl suberate (DSS), were used to map the subunit-subunit interactions in 20S proteasome core particle (CP) from MDA-MB-231 cells. Different types of gel electrophoresis technologies were used. In combination with chemical cross-linking and mass spectrometry, we applied these gel electrophoresis technologies to the study of the noncovalent interactions among 20S proteasome subunits. Firstly, the CP subunit isoforms were profiled. Subsequently, using native/SDSPAGE, it was observed that 0.5 mmol/L BS(3) was a relatively optimal cross-linking concentration for CP subunit-subunit interaction study. 2-DE analysis of the cross-linked CP revealed that α1 might preinteract with α2, and α3 might pre-interact with α4. Moreover, there were different subtypes of α1α2 and α3α4 due to proteasome heterogeneity. There was no significant difference in cross-linking pattern for CP subunits between BS(3) and DSS. Taken together, the gel-based characterization in combination with chemical cross-linking could serve as a tool for the study of subunit interactions within a multi-subunit protein complex. The heterogeneity of 20S proteasome subunit observed in breast cancer cells may provide some key information for proteasome inhibition strategy.
Collapse
Affiliation(s)
- Hai Song
- Department of Scientific Research and Teaching, Tangshan People's Hospital, Tangshan, 063001, China
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Che
- National Biological Experimental Teaching Demonstration Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qing-Song Xi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Liu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui-Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
3
|
Mammalian proteasome subtypes: Their diversity in structure and function. Arch Biochem Biophys 2015; 591:132-40. [PMID: 26724758 DOI: 10.1016/j.abb.2015.12.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/22/2015] [Indexed: 11/21/2022]
Abstract
The 20S proteasome is a multicatalytic proteinase catalysing the degradation of the majority of intracellular proteins. Thereby it is involved in almost all basic cellular processes, which is facilitated by its association with various regulator complexes so that it appears in different disguises like 26S proteasome, hybrid-proteasome and others. The 20S proteasome has a cylindrical structure built up by four stacked rings composed of α- and β-subunits. Since the three active site-containing β-subunits can all or in part be replaced by immuno-subunits, three main subpopulations exist, namely standard-, immuno- and intermediate-proteasomes. Due to posttranslational modifications or/and genetic variations all α- and β-subunits occur in multiple iso- or proteoforms. This leads to the fact that each of the three subpopulations is composed of a variety of 20S proteasome subtypes. This review summarizes the knowledge of proteasome subtypes in mammalian cells and tissues and their possible biological and medical relevancy.
Collapse
|
4
|
Baker TA, Bach HH, Gamelli RL, Love RB, Majetschak M. Proteasomes in lungs from organ donors and patients with end-stage pulmonary diseases. Physiol Res 2014; 63:311-9. [PMID: 24564596 DOI: 10.33549/physiolres.932607] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteasomes appear to be involved in the pathophysiology of various acute and chronic lung diseases. Information on the human lung proteasome in health and disease, however, is sparse. Therefore, we studied whether end-stage pulmonary diseases are associated with alterations in lung 20S/26S proteasome content, activity and 20S subunit composition. Biopsies were obtained from donor lungs (n=7) and explanted lungs from patients undergoing lung transplantation because of end stage chronic obstructive pulmonary disease (COPD; n=7), idiopathic pulmonary fibrosis (IPF, n=7) and pulmonary sarcoidosis (n=5). 20S/26S proteasomes in lung extracts were quantified by ELISA, chymotrypsin-like proteasome peptidase activities measured and 20S proteasome beta subunits analyzed by Western blot. As compared with donor lungs, proteasome content was increased in IPF and sarcoidosis, but not in COPD. The relative distribution of free 20S and 26S proteasomes was similar; 20S proteasome was predominant in all extracts. Proteasome peptidase activities in donor and diseased lungs were indistinguishable. All extracts contained a mixed composition of inducible 20S beta immuno-subunits and their constitutive counterparts; a disease associated distribution could not be identified. A higher content of lung proteasomes in IPF and pulmonary sarcoidosis may contribute to the pathophysiology of human fibrotic lung diseases.
Collapse
Affiliation(s)
- T A Baker
- Loyola University Chicago, Maywood, IL, USA.
| | | | | | | | | |
Collapse
|
5
|
Wang Y, Song G, Wang Y, Qiu L, Qin X, Liu H, Li F, Wang X, Li F, Guo S, Zhang Y, Li Z. Elevated Serum Levels of Circulating Immunoinflammation-Related Protein Complexes Are Associated with Cancer. J Proteome Res 2013; 13:710-9. [DOI: 10.1021/pr4008255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yanying Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Gaoguang Song
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Yanmin Wang
- Department
of Clinical Laboratory, Heze Municipal Hospital, Shandong 274031, P. R. China
| | - Ling Qiu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P. R. China
| | - Xuzhen Qin
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P. R. China
| | - Hui Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Fang Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Xiaodong Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Fenjie Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Shuai Guo
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Yaping Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| |
Collapse
|
6
|
Chen G, Wang Y, Qiu L, Qin X, Liu H, Wang X, Wang Y, Song G, Li F, Guo Y, Li F, Guo S, Li Z. Human IgG Fc-glycosylation profiling reveals associations with age, sex, female sex hormones and thyroid cancer. J Proteomics 2012; 75:2824-34. [DOI: 10.1016/j.jprot.2012.02.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/27/2012] [Accepted: 02/01/2012] [Indexed: 10/28/2022]
|
7
|
Wang X, Li F, Song G, Guo S, Liu H, Chen G, Li Z. Broad-spectrum four-dimensional orthogonal electrophoresis: a novel comprehensively feasible system for protein complexomics investigation. Mol Cell Proteomics 2012; 11:786-99. [PMID: 22375076 DOI: 10.1074/mcp.m111.012450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major challenge of "protein complexomics" is to separate intact protein complexes or interactional proteins without dissociation or denaturation from complex biological samples and to characterize structural subunits of protein complexes. To address these issues, we developed a novel approach termed "broad-spectrum four-dimensional orthogonal electrophoresis (BS4-DE) system," which is composed of a nondenaturing part I and denaturing part II. Here we developed a mild acidic-native-PAGE to constitute part I, together with native-thin-layer-IEF and basic-native-PAGE, widening the range of BS4-DE system application for extremely basic proteins with the range of pI from about 8 to 11 (there are obviously 1000 kinds of proteins in this interval), and also speculated on the mechanism of separating. We first proposed ammonium hydroxide-ultrasonic protein extractive strategy as a seamless connection between part I and part II, and also speculated on the extractive mechanism. More than 4000 protein complexes could be theoretically solved by this system. Using this approach, we focus on blood rich in protein complexes which make it challenging to sera/plasma proteome study. Our results indicated that the BS4-DE system could be applied to blood protein complexomics investigation, providing a comprehensively feasible approach for disease proteomics.
Collapse
Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | | | | | | | | | | | | |
Collapse
|
8
|
Separation and identification of HSP-associated protein complexes from pancreatic cancer cell lines using 2D CN/SDS-PAGE coupled with mass spectrometry. J Biomed Biotechnol 2011; 2011:193052. [PMID: 22028587 PMCID: PMC3199120 DOI: 10.1155/2011/193052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 01/08/2023] Open
Abstract
Protein complexes are a cornerstone of many biological processes and together they form various types of molecular machinery. A broad understanding of these protein complexes is crucial for revealing and building models of protein function and regulation. Pancreatic cancer is a highly lethal disease which is difficult to diagnose at early stage and even more difficult to cure. In this study, we applied a gradient clear native gel system combined with subsequent second-dimensional SDS-PAGE to separate protein complexes from cell lysates of SW1990 and PANC-1 pancreatic cancer cell lines with different degrees of differentiation. Ten heat-shock-protein- (HSP-) associated protein complexes were separated and identified, and the differentially expressed proteins related to cancers were also found, such as HSP60, protein disulfide-isomerase A4 (ERp72), and transitional endoplasmic reticulum ATPase (TER ATPase).
Collapse
|
9
|
Wang X, Zhao Z, Luo Y, Chen G, Li Z. Gel-based proteomics analysis of the heterogeneity of 20S proteasomes from four human pancreatic cancer cell lines. Proteomics Clin Appl 2011; 5:484-92. [PMID: 21751412 DOI: 10.1002/prca.201000149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 05/11/2011] [Accepted: 05/30/2011] [Indexed: 11/06/2022]
Abstract
PURPOSE The 20S proteasome is a multicatalytic protein complex, which plays a major role in intracellular protein degradation. In mammalian cells, it consists of 28 subunits arranged in four stacked rings (α1-7β1-7β1-7α1-7). The aim of this study is to characterize and compare subunit composition and heterogeneity (or subtypes) of the 20S proteasome from four human pancreatic cancer cell lines. EXPERIMENTAL DESIGN To study subunit compositions and heterogeneity of 20S proteasome from human pancreatic cancer cell lines, in the present study, 20S proteasome from four different pancreatic cancer cell lines (SW1990, a human exocrine adenocarcinoma, derived from spleen metastasis; PANC-1, a human ductal carcinoma in situ; BxPC-3, a human ductal carcinoma in situ; and CFPAC-1, a human ductal adenocarcinoma, derived from liver metastasis) were subjected to a gel-based proteomics analysis, respectively. RESULTS It was found that the differences in the subunit compositions and subtypes of the 20S proteasomes among four pancreatic cancer cell lines exist. Gel-based proteomics analysis showed that more than 60 subunits spots were separated and identified by MS. Our study revealed the presence of various isoforms for each of the subunits and different subtypes of the 20S proteasome. The significant differences among four cell lines are the relative abundances of immunoproteasome subunits, β1i and β2i, indicating that different subtypes of immunoproteasome among four cell lines exist. CONCLUSIONS AND CLINICAL RELEVANCE The 20S proteasome from four human pancreatic cancer cell lines was characterized. The different expression levels of immunoproteasome subunits, β1i and β2i, indicate that the 20S proteasome may have different subtypes among four cell lines, which may be related to cancer cell property and be useful for the establishment of personalized therapy using proteasome inhibitors in future.
Collapse
Affiliation(s)
- Xinli Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P. R. China
| | | | | | | | | |
Collapse
|
10
|
Wang X, Chen G, Zhao Z, Wang X, Li Z. Proteomics-based Characterization of Protein Complexes from Human Pancreatic Cancer Cell Line. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
11
|
Cecconi D, Palmieri M, Donadelli M. Proteomics in pancreatic cancer research. Proteomics 2011; 11:816-28. [PMID: 21229586 DOI: 10.1002/pmic.201000401] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/12/2010] [Accepted: 08/25/2010] [Indexed: 12/13/2022]
Abstract
In this review, we give an overview of the actual role of proteomic technologies in the study of pancreatic cancers (PCs). We describe PC proteomics on the basis of sample origins, i.e. tissues, body fluids, and PC cell lines. As regards PC tissues, we report the identification of a number of candidate biomarkers of precursor lesions that may allow early diagnosis of this neoplasia. Moreover, we describe cytoskeletal and hypoxia-regulated proteins that confirm the involvement of cytoskeleton modifications and metabolism adaptations in carcinogenesis. We also discuss the most important biomarkers identified by proteomic analysis involved in local invasion and distant metastasis, and in the cross-talk between pancreatic tumor and the surrounding stroma. Furthermore, we report novel candidate biomarkers identified in serum, plasma, and pancreatic juice of cancer patients compared with cancer-free controls. Proteomic alterations in PC cell line models as compared to normal controls and studies on cell lines treated with drugs or new agents to understand their mechanism of pharmacological action or the onset of drug resistance are also presented. Finally, we discuss the recent improvements obtained in classical 2-DE and high-throughput proteomic strategies able to allow the overcoming of relevant proteomic drawbacks.
Collapse
Affiliation(s)
- Daniela Cecconi
- Department of Biotechnology, University of Verona, Verona, Italy.
| | | | | |
Collapse
|
12
|
Wang X, Chen G, Liu H, Zhao Z, Li Z. Four-Dimensional Orthogonal Electrophoresis System for Screening Protein Complexes and Protein−Protein Interactions Combined with Mass Spectrometry. J Proteome Res 2010; 9:5325-34. [DOI: 10.1021/pr100581x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Guoqiang Chen
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Hui Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhiyun Zhao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhili Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| |
Collapse
|
13
|
Chen G, Liu H, Wang X, Li Z. In vitro methylation by methanol: proteomic screening and prevalence investigation. Anal Chim Acta 2009; 661:67-75. [PMID: 20113717 DOI: 10.1016/j.aca.2009.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/21/2009] [Accepted: 12/10/2009] [Indexed: 11/17/2022]
Abstract
It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were 17 proteolytic peptides with 20 modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, as well as the precautious guide for the use of methanol in proteomic study.
Collapse
Affiliation(s)
- Guoqiang Chen
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | | | | | | |
Collapse
|