Specifically, our group is interested in the following research areas:

Technology Development for Comprehensive and Quantitative Proteomic Analysis of ‘Real-time’ Cells

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 our 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.
Much of our research involves state-of-art mass spectrometers as described in Michael Hooker Proteomics Center