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| Xian Chen, Ph.D.
Associate Professor |  |
Research Interests
Dr. Chen is the faculty director of the UNC-Duke Proteomics Center at the University of North Carolina in Chapel Hill and holds the positions of Associate professor in the Department of Biochemistry and Biophysics, and a member in the Program of Molecular Biology&Biotechnology, and in Lineberger Comprehensive Cancer Center. His primary interests lie in both developing and applying novel mass spectrometry (MS)-based proteomics methodologies for high throughput identification, quantification, and characterization of the pathologically relevant changes in protein expression, post-translational modifications (PTMs), and protein-protein interactions.
Technology Development for Comprehensive and Quantitative Proteomic Analysis
In the past years, our researches have been focused on developing and using real-time applications of cutting edge technologies of proteomics to investigate systematically the molecular mechanisms of pathogenesis of various human diseases such as leukemia, Mycobacterium tuberculosis, immune disorders, etc. In this regard we have been establishing multiple proteomics platforms in a pipeline capable of conducting a multi-angle dissection of the regulatory mechanisms of the cellular changes under pathological circumstances related to signal transduction and cellular regulation. In 1999, we introduced a proteomic technique named as Amino Acid-Coded mass Tagging (AACT) or as SILAC given by others that has now been proved very useful for large-scale proteomic analysis of the challenging issues including quantitative changes in proteome and in PTMs, de novo sequencing for data-dependent protein identification, and dual-tagging quantitative approach for profiling protein-protein interactions. Currently we are continuing the efforts on improving the sensitivity and accuracy of MS-based proteomics for characterizing low-abundance proteins and PTMs by integrating our newly developed nanoreactor to microscale multi-dimensional separation scheme.
Investigation of Systems Regulation in Toll-like Receptor (TLR)-mediated Pathogenesis
One of the current projects in my laboratory focuses on developing systems immunology approaches that are capable of performing the pathway/network-based analysis of various signal transdution pathways that instruct systemic immune responses. For example, the innate immunity stimulated via toll-like receptors (TLRs) alerts the host and defends against the invasion of pathogenic microorganisms by the production of proinflammatory cytokines, however, the excessive production of these cytokines can cause severe immunopathology including bacterial septic shock, toxic-shock syndrome, immunodeficiencies, atherosclerosis, etc. where TLR signaling affects in part their development and progression. Here we aim at dissecting on a broad-scale the components and temporal functional links in those signal tranduction and intracellular pathways that regulate and coordinate the immune balance between protecting individuals against infection and eradicating immune disorders. To address these concerns, we have developed a unbiased systems strategy, which is not fully rely on pre-convinced notion or hypothesis, by integrating the capabilities of whole-species comparative proteomic analysis, the zoom-in profiling of pathway-scale protein-protein interactions, and the genome-scale functional analysis for novel target characterization. For the first time, our preliminary data from a systems investigation of bacteria (LPS)-stimulated living macrophages (host) indicated that the global picture for TLR-mediated signal transduction is largely incomplete, suggesting that there are many undiscovered signal proteins participating in these pathways to modulate the signals. In fact, our systems approach has simultaneously identified and characterized many proteins previously unknown in the LPS-induced signaling pathway including a timely inhibitory regulator of the signaling. As our systems approach provides the mechanistic understanding of how and when the signaling for overall cytokine production will be activated or shut down in a timely manner, we will be able to identify potential therapeutic targets in the signaling pathways to control more effectively and precisely the excessive inflammatory response associated with immune disorders.
Proteomic-based Mechanistic Investigation of Stress-induced Cellular Responses/Effects in Cancer Pathogenesis
Understanding the biological consequences of human exposures to low-dose radiation or trace chemicals is becoming increasingly important as greater exposures to these stresses occur from new man-made sources and space travel. However, it is difficult to estimate the health risks from these stresses in humans that involve possibly not only neoplastic diseases but also somatic mutations related to other illnesses including birth defects and ocular maladies. The disease progression possibly results from low-dose stress effects that depend on several variables, and most of them are not possible to correct for in any epidemiologic study, largely due to the lack of systems investigation on the molecular mechanisms underlying the induction and transmission of the effects of oxidative, bystander, adaptive and genomic instability. Using a robust proteomic technology platform capable of carrying out both proteome-wide and pathway-scale analyses in both a simple pure culture of fibroblasts or epithelials and an advanced culture system, the goal of our project is to investigate systematically the stress effects on cells in real time by directly analyzing the end point products, that is, the unique change of protein expression at low dose radiation. Taken together, the systems results from both global and complex-specific proteomics and computational network analysis, our integrated platform will be able to identify the makeup components (the regulated proteins in low-dose radiation) on a large-scale and map the networks of possible connections among them to reveal functional pathways.
Publications
Chen X, Fei Z, Smith LM, Bradbury EM and Majidi V: Stable isotope-assisted MALDI-TOF mass spectrometry allows accurate determination of base compositions of PCR products. Analytical Chemistry 71:3118-3125, 1999.
Chen X, Smith LMB and Bradbury EM: Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Analytical Chemistry 72:1134-1143, 2000.
Abdi F, Bradbury EM, Dogget N, and Chen X: Validation of DNA Sequences Using Mass Spectrometry Coupled with Nucleotide Mass Tagging. Genome Research 12:1135-1141, 2002.
Gu S, Pan S, Bradbury EM, and Chen X: Use of Deuterium-Labeled Lysine for Efficient Protein Identification and Peptide de novo Sequencing. Analytical Chemistry 74:5774-5785, 2002.
Engen JR, Bradbury EM, and Chen X: Using stable-isotope labeled proteins for hydrogen exchange studies in complex mixtures. Analytical Chemistry 74:1680-1686, 2002.
Zhu H, Hunter T, Pan S, Bradbury EM, Yau P and Chen X: Residue-specific Mass Signatures for the Efficient Identification of Protein Modifications by Mass Spectrometry. Analytical Chemistry 74:1687-1694, 2002.
Rothfork JM, Timmins G, Harris MN, Chen X, Lusis AJ, Otto M, Cheung AL, and Gresham HD: Inactivation of a bacterial virulence pheromone by phagocyte-derived oxidants: New role for the NADPH oxidase in host defense. The Proceedings of the National Academy of Sciences USA 101(38) 13867-13872, 2004.
Harris MN, Ozpolat B, Abdi F, Gu S, Muwuenyega K, Lopez-Berestein G*, and Chen X: Comparative Proteomic Analyses of ATRA Induced Acute Promyelocytic Leukemia (APL) Cells Reveals A Systematic Post-Transcriptional Control in APL. Blood 104(5):1314-1323, 2004. (Also see editorial comments by S. Collins on 104(5) 1234-1235).
Gu S, Liu Z, Pan S, Jiang Z, Lu H, Amit O, Yu J, Hu CA, Chen X: Global Investigation of p53-Induced Apoptosis Through Quantitative Profiling Regulatory Proteins Using Comparative Amino Acid-Coded Tagging Proteomics. Molecular and Cellular Proteomics 3(10)998-1008, 2004.
Wang T, Gu S, Ronni T, Du Y-C, and Chen X: An in vivo Dual-tagging Proteomic Approach in Studying Signaling Pathways in Immune Response. Journal of Proteome Research 4:941-949, 2005.
Mawuenyega KG, Forst CV, Dobos KM, Belisle JT, Bradbury A, Chen J, Bradbury EM, and Chen X: Mycobacterium Tuberculosis Functional Network Analysis by Global Subcellular Protein Profiling. Molecular Biology of the Cell 16, 396-404, 2005.
Liu Z, Lu H, Shi H, Du Y, Yu J, Chen X, Liu KJJ, and Hu CA: PUMA Over-Expression Induces ROS Generation and Stathmin Degradation in Colorectal Cancer Cells. Cancer Research 65(5),1647-1654, 2005.
Xian Chen: Amino Acid-Coded Magging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells. The Proteomics Protocols Handbook, Methods in Molecular Biology/Methods in Molecular Medicine Book Series, Edited by John M. Walker, Humana Press, 2005.
Wang T, Ronni T, Gu S, Sun S, Yin H, and Chen X: Fliih Negatively Modulates the MyD88-dependent Signaling Pathway. Journal of Immunology 176:1355-1362, 2006.
Du Y-C, Gu S, Zhou J, Wang T, Cai H, MacInnes MA, Bradbury EM, and Chen X: The Dynamic Alterations of H2AX Complex during DNA Repair Detected by a Proteomic Approach Reveal the Critical Roles of Ca2+/Calmodulin in the Ionizing Radiation Induced Cell Cycle Arrest. Molecular and Cellular Proteomics 5:1033-1044, 2006.
Shui W, Fan J, Yang P, Zhai J, Lei J, Yan Y, Zhao D*, and Chen X: Novel Nanopore-based Proteolytic Reactor for Sensitive and Comprehensive Proteomic Analyses. Analytical Chemistry 78:4811-4819, 2006.
E-mail: xian_chen@med.unc.edu
Telephone: 919-843-5310
Address: 402A Mary Ellen Jones Building , NC
