Chengpin Shen

Fudan University, Shanghai, Shanghai Shi, China

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Publications (6)18.6 Total impact

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    ABSTRACT: In the analysis of proteins in human umbilical vein endothelial cells (HUVEC) treated with dimethyl sulfoxide (DMSO) and NEDD8-activating enzyme inhibitor (MLN4924, MLN), the Progenesis LC-MS software (Nonlinear Dynamics Ltd) was applied to liquid chromatography spectrum alignment, while spectrum similarities were figured out among several experiments of the same sample, and also among different samples. After double enzymolysis, the sample was added with digested QconCAT standard proteins. They were separated by HPLC-MS/MS, followed by spectrum alignment and data analysis. This established experiment flow offered a better identification result of more than 8 000 proteins, while the original result was about 7 000 proteins, ensuring a relatively high identification efficiency. On the basis of relative quantification with spectrum count, the described procedure can analyze the differential expression of proteins induced by DMSO and MLN. The similarities of total ion chromatograms after alignment were also compared. This method was proved to be quick and easy, with the advantages of high throughput and high sensitivity.
    04/2014; 32(4):349-54.
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    ABSTRACT: Secretomics is receiving more and more considerable attention due to the key roles of secreted proteins in cancer. Most of the potential biomarkers for clinical diagnosis and treatment of cancer are secreted proteins. However, the low concentration of secreted proteins and contaminants released from dead cells are a great challenge to secretomic profiling studies. Although some bioinformatics tools such as SecretomeP and SignalP can help to annotate or predict secreted proteins, they also cause false positive or negative rates of identification especially for nonclassical secreted proteins. Therefore, an iTRAQ based quantitative proteomics strategy was set up in this work and applied in the secretomics study of metastatic HCC cell lines. A total of 94 proteins were identified as secreted and 31 of them were newly found in our data. Compared with the known secreted proteins participating in inter-cellular signalling, most of the newly identified secreted proteins were metabolic enzymes, such as PKM2 and EHHADH, whose functions focused on the synthesis/metabolism of glucose, fatty acids and amino acids. Exploring their secretion would help to further study their bio-functions in conditioned media and the effects on the interactions of cancer cells and the microenvironment. Differences between the secretomes of the two metastatic HCC cell lines were also explored in the same experiment. This strategy showed its superiority in accurately identifying secreted proteins as well as monitoring their variation under different biological conditions.
    The Analyst 06/2013; · 4.23 Impact Factor
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    ABSTRACT: Proteolysis affects every protein at some point in its life cycle. Many biomarkers of disease or cancer are stable proteolytic fragments in biological fluids. There is great interest and a challenge in proteolytically modified protein study to identify physiologic protease-substrate relationships and find potential biomarkers. In this study, two human hepatocellular carcinoma (HCC) cell lines with different metastasis potential, MHCC97L, and HCCLM6, were researched with a high-throughput and sensitive PROTOMAP platform. In total 391 proteins were found to be proteolytically processed and many of them were cleaved into persistent fragments instead of completely degraded. Fragments related to 161 proteins had different expressions in these two cell lines. Through analyzing these significantly changed fragments with bio-informatic tools, several bio-functions such as tumor cell migration and anti-apoptosis were enriched. A proteolysis network was also built up, of which the CAPN2 centered subnetwork, including SPTBN1, ATP5B, and VIM, was more active in highly metastatic HCC cell line. Interestingly, proteolytic modifications of CD44 and FN1 were found to affect their secretion. This work suggests that proteolysis plays an important role in human HCC metastasis.
    Proteomics 05/2012; 12(12):1917-27. · 4.43 Impact Factor
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    ABSTRACT: Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media, which are rich in salts and other compounds that interfere with most proteomics techniques, presents a problem for secretome studies. Ultrafiltration, precipitation, and dialysis are three major extraction methods that can be used to overcome this problem. The present study for the first time, compared the merits and shortcomings of these three methods, without bias. Centrifugal ultrafiltration provided the best extraction efficiency, and precipitation provided the highest number of identifiable proteins. The three methods yielded closely related, but different, information on the secretome; thus, they should be considered complementary or, at least, supplementary methods. Three hundred and sixty unique proteins were identified, including 211 potential secreted proteins. Compared with previous studies, this study also identified 42 new secreted proteins. The present study not only offers a reference for the selection of secretome extraction methods, but also expands the secretome database for the investigation of hepatocellular carcinoma.
    Science China. Life sciences 01/2011; 54(1):34-8. · 2.02 Impact Factor
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    ABSTRACT: A new mass spectrometry based analysis strategy has been established here for high-molecular-weight (HMW) proteome research. First, a 2-hydroxyethyl agarose/polyacrylamide (HEAG/PAM) electrophoresis gel was designed for the first time to realize an easy-handling separation method with high spatial resolution for HMW proteins, good reproducibility and mass spectrometry-compatible silver staining. Second, ZnO-polymethyl methacrylate (ZnO-PMMA) nanobeads were applied here for enriching and desalting the peptides from the HMW proteins. Third, the peptides were analyzed by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) with the presence of the ZnO-PMMA nanobeads, and their MS signals were enhanced markedly. The success rate of identification for HMW proteins was significantly increased due to high enriching efficiency and salt tolerance capability as well as signal enhancing capability of the ZnO-PMMA nanobeads. We believe that this analysis strategy will inspire and accelerate the HMW proteome studies.
    Talanta 09/2010; 82(4):1594-8. · 3.50 Impact Factor
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    ABSTRACT: Given the importance of secreted proteins as a source for early detection and diagnosis of disease, secreted proteins have been arousing considerable attention. However, the analysis of secreted proteins represents a challenge for current proteomic techniques. One of the difficulties in secretomic study is to concentrate proteins from large volume of growth media, particularly, the low abundant and low molecular weight proteins (molecular weight <30 kDa). Herein, we describe a novel strategy for harvesting secretory proteins. In this approach, proteins secreted from the human hepatocellular carcinoma cell line were enriched by zeolite LTL nanocrystals, followed by 1-D SDS-PAGE for protein fractionation and then by LC-ESI-MS/MS for protein identification. In total, 1474 unique proteins were confidently identified, including 505 low molecular weight proteins, and covered a broad range of pI and molecular weight. Furthermore, this study not only offered an efficient and powerful method for the enrichment of secretory proteins but also allowed in-depth study of secretome of hepatocellular carcinoma cells. The reported work is expected to represent one of the most comprehensive secretomic analyses so far.
    Proteomics 09/2009; 9(21):4881-8. · 4.43 Impact Factor