Bio

Professional Education


  • Bachelor of Engineering, Beijing Institute Of Technology (2014)
  • Doctor of Philosophy, Peking University (2019)

Stanford Advisors


Research & Scholarship

Current Research and Scholarly Interests


Chemical Proteomics with spatial and temporal resolution

Publications

All Publications


  • S-glycosylation-based cysteine profiling reveals regulation of glycolysis by itaconate. Nature chemical biology Qin, W., Qin, K., Zhang, Y., Jia, W., Chen, Y., Cheng, B., Peng, L., Chen, N., Liu, Y., Zhou, W., Wang, Y. L., Chen, X., Wang, C. 2019

    Abstract

    Itaconate has been recently recognized as an anti-inflammatory metabolite involved in the pathogen-macrophage interface. Due to its weak electrophilicity, itaconate could modify cysteines of the protein KEAP1 and glutathione, which contribute to its anti-inflammatory effect. However, the substrates of itaconate modification in macrophages have not been systematically profiled, which largely impedes the understanding of its roles in immune responses. Here, we developed a specific thiol-reactive probe, 1-OH-Az, for quantitative chemoproteomic profiling of cysteine modifications by itaconate, and provided a global portrait of its proteome reactivity. We found that itaconate covalently modifies key glycolytic enzymes and impairs glycolytic flux mainly through inhibition of fructose-bisphosphate aldolase A (ALDOA). Moreover, itaconate attenuates the inflammatory response in stimulated macrophages by impairing the glycolysis. Our study provides a valuable resource of protein targets of itaconate in macrophages and establishes a negative-feedback link between glycolysis and itaconate, elucidating new functional insights for this anti-inflammatory metabolite.

    View details for DOI 10.1038/s41589-019-0323-5

    View details for PubMedID 31332308

  • Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Qin, W., Qin, K., Fan, X., Peng, L., Hong, W., Zhu, Y., Lv, P., Du, Y., Huang, R., Han, M., Cheng, B., Liu, Y., Zhou, W., Wang, C., Chen, X. 2018; 57 (7): 1817?20

    Abstract

    The unexpected, non-enzymatic S-glycosylation of cysteine residues in various proteins by per-O-acetylated monosaccharides is described. This artificial S-glycosylation greatly compromises the specificity and validity of metabolic glycan labeling in living cells by per-O-acetylated azido and alkynyl sugars, which has been overlooked in the field for decades. It is demonstrated that the use of unacetylated unnatural sugars can avoid the artifact formation and a corrected list of O-GlcNAcylated proteins and O-GlcNAc sites in HeLa cells has been assembled by using N-azidoacetylgalactosamine (GalNAz).

    View details for DOI 10.1002/anie.201711710

    View details for Web of Science ID 000424212300009

    View details for PubMedID 29237092

  • Quantitative time-resolved chemoproteomics reveals that stable O-GlcNAc regulates box C/D snoRNP biogenesis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Qin, W., Lv, P., Fan, X., Quan, B., Zhu, Y., Qin, K., Chen, Y., Wang, C., Chen, X. 2017; 114 (33): E6749?E6758

    Abstract

    O-linked GlcNAcylation (O-GlcNAcylation), a ubiquitous posttranslational modification on intracellular proteins, is dynamically regulated in cells. To analyze the turnover dynamics of O-GlcNAcylated proteins, we developed a quantitative time-resolved O-linked GlcNAc proteomics (qTOP) strategy based on metabolic pulse-chase labeling with an O-GlcNAc chemical reporter and stable isotope labeling with amino acids in cell culture (SILAC). Applying qTOP, we quantified the turnover rates of 533 O-GlcNAcylated proteins in NIH 3T3 cells and discovered that about 14% exhibited minimal removal of O-GlcNAc or degradation of protein backbones. The stability of those hyperstable O-GlcNAcylated proteins was more sensitive to O-GlcNAcylation inhibition compared with the more dynamic populations. Among the hyperstable population were three core proteins of box C/D small nucleolar ribonucleoprotein complexes (snoRNPs): fibrillarin (FBL), nucleolar protein 5A (NOP56), and nucleolar protein 5 (NOP58). We showed that O-GlcNAcylation stabilized these proteins and was essential for snoRNP assembly. Blocking O-GlcNAcylation on FBL altered the 2'-O-methylation of rRNAs and impaired cancer cell proliferation and tumor formation in vivo.

    View details for DOI 10.1073/pnas.1702688114

    View details for Web of Science ID 000407610400006

    View details for PubMedID 28760965

    View details for PubMedCentralID PMC5565422

  • Quantitative Profiling of Protein Carbonylations in Ferroptosis by an Aniline-Derived Probe JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Chen, Y., Liu, Y., Lan, T., Qin, W., Zhu, Y., Qin, K., Gao, J., Wang, H., Hou, X., Chen, N., Angeli, J., Conrad, M., Wang, C. 2018; 140 (13): 4712?20

    Abstract

    Ferroptosis is a regulated form of necrotic cell death implicated in carcinogenesis and neurodegeneration that is driven by phospholipid peroxidation. Lipid-derived electrophiles (LDEs) generated during this process can covalently modify proteins ("carbonylation") and affect their functions. Here we report the development of a quantitative chemoproteomic method to profile carbonylations in ferroptosis by an aniline-derived probe. Using the method, we established a global portrait of protein carbonylations in ferroptosis with >400 endogenously modified proteins and for the first time, identified >20 residue sites with endogenous LDE modifications in ferroptotic cells. Specifically, we discovered and validated a novel cysteine site of modification on voltage-dependent anion-selective channel protein 2 (VDAC2) that might play an important role in sensitizing LDE signals and mediating ferroptosis. Our results will contribute to the understanding of ferroptotic signaling and pathogenesis and provide potential biomarkers for ferroptosis detection.

    View details for DOI 10.1021/jacs.8b01462

    View details for Web of Science ID 000429508600037

    View details for PubMedID 29569437

  • Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker. ACS chemical biology Qin, K., Zhu, Y., Qin, W., Gao, J., Shao, X., Wang, Y. L., Zhou, W., Wang, C., Chen, X. 2018; 13 (8): 1983?89

    Abstract

    Large-scale quantification of protein O-linked ?- N-acetylglucosamine (O-GlcNAc) modification in a site-specific manner remains a key challenge in studying O-GlcNAc biology. Herein, we developed an isotope-tagged cleavable linker (isoTCL) strategy, which enabled isotopic labeling of O-GlcNAc through bioorthogonal conjugation of affinity tags. We demonstrated the application of the isoTCL in mapping and quantification of O-GlcNAcylation sites in HeLa cells. Furthermore, we investigated the O-GlcNAcylation sensitivity to the sugar donor by quantifying the levels of modification under different concentrations of the O-GlcNAc labeling probe in a site-specific manner. In addition, we applied isoTCL to compare the O-GlcNAcylation stoichiometry levels of more than 100 modification sites between placenta samples from male and female mice and confirmed site-specifically that female placenta has a higher O-GlcNAcylation than its male counterpart. The isoTCL platform provides a powerful tool for quantitative profiling of O-GlcNAc modification.

    View details for DOI 10.1021/acschembio.8b00414

    View details for PubMedID 30059200

  • Chemoproteomic profiling of protein modifications by lipid-derived electrophiles CURRENT OPINION IN CHEMICAL BIOLOGY Chen, Y., Qin, W., Wang, C. 2016; 30: 37?45

    Abstract

    Lipid-derived electrophiles (LDEs) are a group of endogenous reactive metabolites generated as products of lipid peroxidation when cells are under oxidative stress. LDEs are able to covalently modify nucleophilic residues in proteins to alter their structures and activities, either resulting in irreversible functional damage or triggering aberrant signaling pathways. Traditional biochemical methods have revealed individual protein targets modified by LDEs, however, deciphering the toxicity and/or signaling roles of LDEs requires systematic studies of these modifications in a high-throughput fashion. Here we survey recent progress in developing chemical proteomic strategies to globally profile protein-LDE interactions directly from complex proteomes. These powerful chemoproteomic methods have yielded a rich inventory of proteins and residue sites that are sensitive to LDE modification, serving as valuable resources to investigate mechanisms of their cellular toxicity at the molecular level.

    View details for DOI 10.1016/j.cbpa.2015.10.029

    View details for Web of Science ID 000370099500007

    View details for PubMedID 26625013

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