Publications
Microscale Immune Studies Laboratory
The overarching goal is to develop novel technologies to elucidate molecular mechanisms of the innate immune response in host cells to pathogens such as bacteria and viruses including the mechanisms used by pathogens to subvert/suppress/obfuscate the immune response to cause their harmful effects. Innate immunity is our first line of defense against a pathogenic bacteria or virus. A comprehensive 'system-level' understanding of innate immunity pathways such as toll-like receptor (TLR) pathways is the key to deciphering mechanisms of pathogenesis and can lead to improvements in early diagnosis or developing improved therapeutics. Current methods for studying signaling focus on measurements of a limited number of components in a pathway and hence, fail to provide a systems-level understanding. We have developed a systems biology approach to decipher TLR4 pathways in macrophage cell lines in response to exposure to pathogenic bacteria and their lipopolysaccharide (LPS). Our approach integrates biological reagents, a microfluidic cell handling and analysis platform, high-resolution imaging and computational modeling to provide spatially- and temporally-resolved measurement of TLR-network components. The Integrated microfluidic platform is capable of imaging single cells to obtain dynamic translocation data as well as high-throughput acquisition of quantitative protein expression and phosphorylation information of selected cell populations. The platform consists of multiple modules such as single-cell array, cell sorter, and phosphoflow chip to provide confocal imaging, cell sorting, flow cytomtery and phosphorylation assays. The single-cell array module contains fluidic constrictions designed to trap and hold single host cells. Up to 100 single cells can be trapped and monitored for hours, enabling detailed statistically-significant measurements. The module was used to analyze translocation behavior of transcription factor NF-kB in macrophages upon activation by E. coli and Y. pestis LPS. The chip revealed an oscillation pattern in translocation of NF-kB indicating the presence of a negative feedback loop involving IKK. Activation of NF-kB is preceded by phosphorylation of many kinases and to correlate the kinase activity with translocation, we performed flow cytometric assays in the PhosphoChip module. Phopshorylated forms of p38. ERK and RelA were measured in macrophage cells challenged with LPS and showed a dynamic response where phosphorylation increases with time reaching a maximum at {approx}30-60min. To allow further downstream analysis on selected cells, we also implemented an optical-trapping based sorting of cells. This has allowed us to sort macrophages infected with bacteria from uninfected cells with the goal of obtaining data only on the infected (the desired) population. The various microfluidic chip modules and the accessories required to operate them such as pumps, heaters, electronic control and optical detectors are being assembled in a bench-top, semi-automated device. The data generated is being utilized to refine existing TLR pathway model by adding kinetic rate constants and concentration information. The microfluidic platform allows high-resolution imaging as well as quantitative proteomic measurements with high sensitivity (<pM) and time-resolution ({approx}15 s) in the same population of cells, a feat not achievable by current techniques. Furthermore, our systems approach combining the microfluidic platform and high-resolution imaging with the associated computational models and biological reagents will significantly improve our ability to study cell-signaling involved in host-pathogen interactions and other diseases such as cancer. The advances made in this project have been presented at numerous national and international conferences and are documented in many peer-reviewed publications as listed. Finer details of many of the component technologies are described in these publications. The chapters to follow in this report are also adapted from other manuscripts that are accepted for publication, submitted or in preparation to be submitted to peer-reviewed journals.