Professional Education

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

Stanford Advisors

Current Research and Scholarly Interests

Chemical Proteomics with spatial and temporal resolution

All Publications

  • Deciphering molecular interactions by proximity labeling. Nature methods Qin, W., Cho, K. F., Cavanagh, P. E., Ting, A. Y. 2021


    Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein 'baits', via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry or nucleic acid sequencing. Here we review the development of PL technologies and highlight studies that have applied PL to the discovery and analysis of molecular interactions. In particular, we focus on the use of PL for mapping protein-protein, protein-RNA and protein-DNA interactions in living cells and organisms.

    View details for DOI 10.1038/s41592-020-01010-5

    View details for PubMedID 33432242

  • Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nature communications Qin, W., Myers, S. A., Carey, D. K., Carr, S. A., Ting, A. Y. 2021; 12 (1): 4980


    Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes ("APEX-PS"). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments.

    View details for DOI 10.1038/s41467-021-25259-2

    View details for PubMedID 34404792

  • Chemoproteomic profiling of itaconation by bioorthogonal probes in inflammatory macrophages. Journal of the American Chemical Society Qin, W., Zhang, Y., Tang, H., Liu, D., Chen, Y., Liu, Y., Wang, C. 2020


    Itaconate is an anti-inflammatory metabolite involved in pathogen-macrophage interaction, but the mechanisms underlying its effect are not fully understood. Competitive cysteine profiling has been performed to interrogate itaconate's reactivity in cell lysates, however, methods for analyzing targets of itaconation directly in living macrophages are still lacking. Here we developed a specific bioorthogonal probe, itaconate-alkyne (ITalk), for quantitative and site-specific chemoproteomic profiling of itaconation in inflammatory macrophages. ITalk recapitulates the anti-inflammatory property of itaconate and enables biochemical evaluation and proteomic analysis of its direct targets. Our study delineates the widespread landscape of itaconate substrates, providing a versatile tool and comprehensive resource for investigating its function.

    View details for DOI 10.1021/jacs.9b11962

    View details for PubMedID 32496768

  • Chemoproteomic profiling of protein-metabolite interactions. Current opinion in chemical biology Qin, W., Yang, F., Wang, C. 2019; 54: 28-36


    Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational modifications or non-covalent binding interactions. Chemical proteomic strategies can help delineate global landscapes of cellular protein-metabolite interactions and provide molecular insights about their mechanisms of action. In this review, we summarized the recent progress in developments and applications of chemoproteomic strategies to profile protein-metabolite interactions.

    View details for DOI 10.1016/j.cbpa.2019.11.003

    View details for PubMedID 31812894

  • Chemoproteomic Profiling of O-GlcNAcylation in Caenorhabditis elegans. Biochemistry Qin, W., Xie, Z., Wang, J., Ou, G., Wang, C., Chen, X. 2019


    Genetic studies have revealed essential functions of O-linked N-acetylglucosamine (O-GlcNAc) modification in Caenorhabditis elegans. However, large-scale identification of O-GlcNAcylated proteins and mapping the modification sites in C. elegans remain relatively unexplored. By using a chemoproteomic strategy, we herein report the identification of 108 high-confidence O-GlcNAcylated proteins and 64 modification sites in C. elegans. Furthermore, quantitative proteomics upon altering O-GlcNAcylation show that the abundance of a large number of proteins are affected by O-GlcNAc. These proteins are involved in regulating reproduction and lifespan, which may correlate with the previously observed phenotypes in genetic studies. The data set in this study reveals the O-GlcNAc modification landscape in C. elegans and provides a valuable resource for dissecting the biological function of O-GlcNAcylation.

    View details for DOI 10.1021/acs.biochem.9b00622

    View details for PubMedID 31682414

  • 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


    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


    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


    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 chemoproteomics reveals O-GlcNAcylation of cystathionine γ-lyase (CSE) represses trophoblast syncytialization. Cell chemical biology Liu, J., Shao, X., Qin, W., Zhang, Y., Dang, F., Yang, Q., Yu, X., Li, Y. X., Chen, X., Wang, C., Wang, Y. L. 2021


    Emerging evidence indicates the involvement of O-GlcNAc modification in placental development and pregnant health through mechanisms that are not well understood. Herein, by applying the quantitative O-GlcNAc proteomics, we established a database of O-GlcNAcylated proteins in human placental trophoblasts. Hundreds of proteins that were dynamically O-GlcNAcylated during trophoblast differentiation were identified, among which cystathionine γ-lyase (CSE) exhibited the most significant change. Site-specific analysis by mass spectrometry revealed Ser138 as the core O-GlcNAc site in CSE, and its O-GlcNAcylation promoted the enzymatic activity to produce H2S, which in turn repressed trophoblast differentiation via inhibiting androgen receptor dimerization. Consistently, in preeclamptic placentas, remarkably enhanced CSE O-GlcNAcylation and H2S production were associated with restricted trophoblast differentiation. The findings establish a resource of O-GlcNAc dynamics in human placenta, and provide a deeper insight into the biological significance of O-GlcNAcylation in placental development as well as potential therapeutic targets for the relevant pregnant complications.

    View details for DOI 10.1016/j.chembiol.2021.01.024

    View details for PubMedID 33626323

  • Site-specific chemoproteomic profiling of targets of glyoxal. Future medicinal chemistry Chen, Y., Qin, W., Li, Z., Guo, Z., Liu, Y., Lan, T., Wang, C. 2019; 11 (23): 2979-2987


    Aim: Advanced glycation end products (AGE) are the biomarkers of aging and diabetes which are formed via reactions between glycating agents and biomacromolecules. However, no proteomic study has been reported to systematically investigate the protein substrates of AGEs. Results: In this paper, we used an aniline-based probe to capture the glyoxal-imine intermediate which is the transition sate of glyoxal-derived AGEs. Combined with the tandem orthogonal proteolysis activity-based protein profiling strategy, we successfully identified 962 lysines modified by glyoxal. Conclusion: Enzymes in glycolysis are heavily modified by glyoxal and our biochemical experiments showed that glyoxal can significantly inhibit the activity of GAPDH and glycolysis. These data indicated that AGEs modifications may contribute to pathological processes through impairing the glycolytic process.

    View details for DOI 10.4155/fmc-2019-0221

    View details for PubMedID 31663776

  • Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells. Nature communications Hao, Y., Fan, X., Shi, Y., Zhang, C., Sun, D. E., Qin, K., Qin, W., Zhou, W., Chen, X. 2019; 10 (1): 4065


    Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per-O-acetylated, which, however, can induce a long-overlooked side reaction, non-enzymatic S-glycosylation. Herein, we develop 1,3-di-esterified N-azidoacetylgalactosamine (GalNAz) as next-generation chemical reporters for metabolic glycan labeling. Both 1,3-di-O-acetylated GalNAz (1,3-Ac2GalNAz) and 1,3-di-O-propionylated GalNAz (1,3-Pr2GalNAz) exhibit high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying 1,3-Pr2GalNAz in mouse embryonic stem cells (mESCs), we identify ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We show that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase at serine 25, which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

    View details for DOI 10.1038/s41467-019-11942-y

    View details for PubMedID 31492838

    View details for PubMedCentralID PMC6731260

  • 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): 1983-1989


    Large-scale quantification of protein O-linked β- 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

  • 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


    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

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


    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