Beijing Proteome Research Center

Beijing, China

Beijing Proteome Research Center

Beijing, China
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Gupta V.,Scripps Research Institute | Yang J.,Beijing Proteome Research Center | Liebler D.C.,Vanderbilt University | Carroll K.S.,Scripps Research Institute
Journal of the American Chemical Society | Year: 2017

Targeted covalent inhibitors have emerged as a powerful approach in the drug discovery pipeline. Key to this process is the identification of signaling pathways (or receptors) specific to (or overexpressed in) disease cells. In this context, fragment-based ligand discovery (FBLD) has significantly expanded our view of the ligandable proteome and affords tool compounds for biological inquiry. To date, such covalent ligand discovery has almost exclusively employed cysteine-reactive small-molecule fragments. However, functional cysteine residues in proteins are often redox-sensitive and can undergo oxidation in cells. Such reactions are particularly relevant in diseases, like cancer, which are linked to excessive production of reactive oxygen species. Once oxidized, the sulfur atom of cysteine is much less reactive toward electrophilic groups used in the traditional FBLD paradigm. To address this limitation, we recently developed a novel library of diverse carbon-based nucleophile fragments that react selectively with cysteine sulfenic acid formed in proteins via oxidation or hydrolysis reactions. Here, we report analysis of sulfenic acid-reactive C-nucleophile fragments screened against a colon cancer cell proteome. Covalent ligands were identified for >1280 S-sulfenylated cysteines present in "druggable" proteins and orphan targets, revealing disparate reactivity profiles and target preferences. Among the unique ligand-protein interactions identified was that of a pyrrolidinedione nucleophile that reacted preferentially with protein tyrosine phosphatases. Fragment-based covalent ligand discovery with C-nucleophiles affords an expansive snapshot of the ligandable "redoxome" with significant implications for covalent inhibitor pharmacology and also affords new chemical tools to investigate redox-regulation of protein function. © 2017 American Chemical Society.

Zhang Y.,Peking University | Ye Y.,Peking University | Shen D.,Peking University | Jiang K.,Peking University | And 6 more authors.
Cancer Science | Year: 2010

To search for potential protein markers of colorectal cancer (CRC), the changes in protein expression levels between microdissected tumor cells and normal mucosa epithelia were analyzed by an acetylation stable isotopic labeling method coupled with linear quadrupole ion trap fourier transform mass spectrometry (LTQ-FTMS). In total, 137 proteins were up-regulated or down-regulated significantly in cancer by at least two-fold. Based on gene ontology analysis, the largest part of differential proteins were unknown for both subcellular localization and biological process. In particular, the significant up-regulation of transgelin-2 (TAGLN2) in CRC was validated by Western blot analysis and further evaluated by immunohistochemistry in paired tumor and normal mucosa samples from 120 consecutive CRC patients, 20 adenomas, and eight synchronous hepatic metastases of CRC. TAGLN2 expression was frequently observed in cancer cells, precancerous lesions, and hepatic metastases, whereas in normal epithelia expression was rarely observed. The overexpression of TAGLN2 was associated with lymph node and distant metastasis, advanced clinical stage (P < 0. .001), and shorter overall survival in CRCs. Cox regression analysis indicated that high tumor-TAGLN2 expression represents an independent prognostic factor. Consequently, over-expression of TAGLN2 may serve as a new biomarker for predicting progression and prognosis of CRC. © 2009 Japanese Cancer Association.

PubMed | Beijing Proteome Research Center and Peking University
Type: | Journal: Proteomics. Clinical applications | Year: 2017

To analysis proteins in the tissue of pterygia, and to investigate their potential roles in pterygia, using the comparative proteomic technique of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) coupled with offline 2DLC-MS/MS, Western-bolt.The tissues of pterygia and healthy conjunctiva were collected from 10 pterygia patients (6 females, 4 males; average age was 52 years old; average course of disease was 6 years) in our hospital from September, 2015 to March, 2016. iTRAQ was used to analyze proteins in the patients pterygia and healthy conjunctiva. Proteins with a fold change of >2. 0 or <0. 5 were considered to be significantly differentially expressed (with corrected p-values of <0. 1). The identified proteins were subjected to subsequent gene ontology analysis using the DAVID database. Then we confirmed the targeted proteins with western-blot.156 proteins that expressed differently between the pterygia and healthy conjunctiva were identified using iTRAQ analysis. Of these proteins, 18 were down-regulated, and 138 were up-regulated. On the basis of biological processes in gene ontology, the identified proteins were mainly involved in cellular process, metabolic proces, developmental process, location, cellular component organization, Among these proteins, matrix Metalloproteinase 10(MMP-10) and CD34 may have potential roles in the pathogenesis of pterygia. Then we confirmed with Westen-bolt that MMP10 and CD34 were up-regulated in pterygia.This study is the first to identify 156 proteins associated with pterygia with iTRAQ technology. Data in our study will aid in providing a better understanding of pterygia. This article is protected by copyright. All rights reserved.

Ding Y.,Zhejiang Chinese Medical University | Lu B.,Zhejiang Chinese Medical University | Chen D.,Academy of Military Medical science | Meng L.,Zhejiang Chinese Medical University | And 2 more authors.
Proteomics | Year: 2010

Irritable bowel syndrome (IBS) is one of the most common functional disorders of the gastrointestinal tract. It is characterized by abdominal pain and changes in bowel habits. Various studies have investigated the pathophysiologic processes underlying IBS, but the mechanism remains poorly understood. In the present study, we established an IBS model and identified differentially expressed proteins in colon tissue of IBS rats compared with healthy controls by 2-D gel electrophoresis, MALDI-TOF-MS, and Western blot analysis. Our results showed that 13 of the 1396 protein spots on 2-D gel were differently expressed between the IBS and control groups. Ontological analysis of these proteins revealed primary roles in catalytic activity (protein disulfide-isomerase A3, glyoxalase I, cathepsin S, α-enolase), structural support (cytokeratin 8), antioxidant activity (peroxiredoxin-6), protein binding (transgelin, serpin peptidase inhibitor B5), and signal transduction (40S ribosomal protein SA). Protein disulfide-isomerase A3 and cytokeratin 8 overexpression in IBS were confirmed by Western blot. The findings indicate that multiple proteins are involved in IBS processes that influence intestinal tract immunity, inflammation, and nerve regulation. Our study provides useful candidate genes and proteins for further investigation. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA.

Yan Y.,Hefei University of Technology | Jiang W.,Hefei University of Technology | Liu L.,Hefei University of Technology | Wang X.,Hefei University of Technology | And 5 more authors.
Cell | Year: 2015

Inflammasomes are involved in diverse inflammatory diseases, so the activation of inflammasomes needs to be tightly controlled to prevent excessive inflammation. However, the endogenous regulatory mechanisms of inflammasome activation are still unclear. Here, we report that the neurotransmitter dopamine (DA) inhibits NLRP3 inflammasome activation via dopamine D1 receptor (DRD1). DRD1 signaling negatively regulates NLRP3 inflammasome via a second messenger cyclic adenosine monophosphate (cAMP), which binds to NLRP3 and promotes its ubiquitination and degradation via the E3 ubiquitin ligase MARCH7. Importantly, in vivo data show that DA and DRD1 signaling prevent NLRP3 inflammasome-dependent inflammation, including neurotoxin-induced neuroinflammation, LPS-induced systemic inflammation, and monosodium urate crystal (MSU)-induced peritoneal inflammation. Taken together, our results reveal an endogenous mechanism of inflammasome regulation and suggest DRD1 as a potential target for the treatment of NLRP3 inflammasome-driven diseases. © 2015 Elsevier Inc. All rights reserved.

Yang J.,Beijing Proteome Research Center | Carroll K.S.,Scripps Research Institute | Liebler D.C.,Vanderbilt University
Molecular and Cellular Proteomics | Year: 2016

Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO2H), S-sulfonylation (-SO3H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Su S.,Harbin Medical University | Liu P.,Harbin Medical University | Zhang H.,Harbin Medical University | Li Z.,Harbin Medical University | And 3 more authors.
Investigative Ophthalmology and Visual Science | Year: 2011

Purpose. To identify proteomic differences between age-related nuclear cataracts (ARNCs) and normal lens nuclei. Methods. Total solubilized proteins from ARNC lens nuclei with different grades were compared with normal controls by 2-D differential in-gel electrophoresis (2-D DIGE). Proteins with different abundances were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses determined the compositions of high molecular weight (HMW; >200 kDa) aggregates found in ARNC lens nuclei. Western blot analysis was used to verify the changes in αA-crystallin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) levels. Results. The 2-D differential in-gel electrophoresis results showed that nine proteins were significantly less abundant in lens nuclei from ARNC patients than in control lens nuclei. Six proteins (αA-, βA3-, βA4-, βB1-, and γD-crystallin and putative uncharacterized protein DKFZp434A0627 from the CRYGS family) tended to decrease as the cataract grade increased, while the other three proteins (αB-crystallin, GAPDH, and retinal dehydrogenase 1) did not show such a tendency. SDS-PAGE showed decreased protein levels at ∼20 kDa in ARNC lenses but significantly increased levels at HMW (>200 kDa). Liquid chromatography tandem mass spectrometry analysis showed that the HMW aggregates derived largely from crystallins also contained filensin, phakinin, and carbonyl reductase 1. Of all the components, αA-crystallin accounted for the highest fraction. αA-, αB-, and γD-crystallin and DKFZp434A0627 were more prone to aggregate than other crystallins. Conclusions. The results show that crystallins, especially αA-crystallin, aggregate irreversibly during ARNC development. Some enzymes (GAPDH, retinal dehydrogenase 1, and carbonyl reductase 1) may be involved in and/or accelerate this process. © 2011 The Association for Research in Vision and Ophthalmology, Inc.

Su S.,Harbin Medical University | Leng F.,Harbin Medical University | Guan L.,Harbin Medical University | Zhang L.,Harbin Medical University | And 4 more authors.
Investigative ophthalmology & visual science | Year: 2014

PURPOSE: To identify differential changes in proteins and metabolites underlying "fast" type 1 (T1DC) and "slow" type 2 (T2DC) diabetic cataract (DC) formation in rat.METHODS: Rat models of types 1 and 2 diabetes consisted of streptozotocin injection without and with high-fat diet, respectively. Cataract progression was examined weekly. At week 6, total protein changes were comparatively and quantitatively assessed by two-dimensional differential in-gel electrophoresis (2-D DIGE) coupled with mass spectrometry, and relevant metabolic changes were examined. Differences in high molecular weight (HMW) crystallin species between diabetic and control lenses were similarly identified.RESULTS: Cataracts were morphologically different and progressed more slowly in T2DC versus T1DC. αA-crystallin, βB2-crystallin, and βA4-crystallin were significantly decreased in both DC types versus control. αB-crystallin was increased while βB1-crystallin was markedly decreased in T2DC. In T1DC, γB-crystallin and γS-crystallin fragmentation were increased. High-fat diet by itself had little impact, except for lowering γS-crystallin fragmentation. Despite significantly decreased opacity, a greater decrease in intermediate filaments (IFs) and more HMW crystallin species were observed in T2DC versus T1DC. However, aldose reductase expression and activity and sorbitol levels were increased to a greater extent in T1DC, while reduced glutathione (GSH) and reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) levels were decreased to a greater extent and adenosine triphosphate (ATP) level was much lower in T1DC versus T2DC.CONCLUSIONS: The results suggest that osmotic damage, GSH loss, and decreased ATP production might be important pathological mechanisms in T1DC formation, whereas crystallin modification and cross-linking/aggregation as well as IF degradation may play more crucial roles in T2DC formation. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Yao X.N.,Beijing Proteome Research Center
Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology | Year: 2010

AIM: Preparation of monoclonal antibody (mAb) against GP73 protein. METHODS: The N-terminal peptide (AAAERGAVELK) of GP73 protein was displayed on T7 phage, the recombinant phage was amplified and used as the immunogen to immunize mouse to produce antibody. The titer of the antiserum and the positive hybridoma clones which secreted the mAb against GP73 protein were detected by ELISA. The mAb specificity was assayed by ELISA and Western blot. RESULTS: The high specificity mAb against GP73 protein was selected from the mouse immunized with the recombinant T7 phages displaying the epitope of GP73 by cell fusion and screening. CONCLUSION: The appropriate protein epitope displayed on T7 phage could be used as alternative antigen to immunize animals to make specific antibody against the corresponding native protein.

He F.C.,Beijing Proteome Research Center
Science China Life Sciences | Year: 2013

When our knowledge of a field accumulates to a certain level, we are bound to see the rise of one or more great scientists. They will make a series of grand discoveries/breakthroughs and push the discipline into an 'age of grand discoveries'. Mathematics, geography, physics and chemistry have all experienced their ages of grand discoveries; and in life sciences, the age of grand discoveries has appeared countless times since the 16th century. Thanks to the ever-changing development of molecular biology over the past 50 years, contemporary life science is once again approaching its breaking point and the trigger for this is most likely to be 'lifeomics'. At the end of the 20th century, genomics wrote out the 'script of life'; proteomics decoded the script; and RNAomics, glycomics and metabolomics came into bloom. These 'omics', with their unique epistemology and methodology, quickly became the thrust of life sciences, pushing the discipline to new high. Lifeomics, which encompasses all omics, has taken shape and is now signalling the dawn of a new era, the age of grand discoveries. © 2013 The Author(s).

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