Inflammation is the body’s essential response to infection and injury; however, chronic inflammation is a component of many prevalent human diseases – including atherosclerosis, rheumatoid arthritis, cancer and Alzheimer’s disease. We currently have two main areas of research in the lab, broadly focused on understanding and intervening in inflammation.
Protein Complexes and Signal Integration in Inflammation. One area of research is to understand gene regulatory mechanisms and regulatory networks controlling inflammation. A particular focus is the role of multi-protein DNA-bound complexes as a means to integrate signals and achieve specificity in gene regulation. We are employing cutting-edge techniques such as protein binding microarrays (PBMs), genome-wide chromatin immunoprecipitation (ChIP-seq), and gene expression analysis (RNA-seq) to examine transcriptional synergy and signal integration at both the molecular and genomic levels. While many small-scale studies have highlighted the importance of regulatory mechanisms such as cooperative transcription factor binding, synergistic cofactor recruitment, and DNA-based allostery in protein complex assembly, these have not been examined at a genome-wide scale. By integrating detailed characterizations of protein-DNA binding using the high-throughput PBM technology, with genomic ‘maps’ from ChIP-seq and RNA-seq, we aim to examine these important features at a systems-level. Furthermore, by incorporating DNA-level detail into gene regulatory maps, we will be able to more accurately model the impact of human genomic variations, such as SNP data, on inflammation and ultimately the onset and progression of chronic inflammation. We have several current projects in this area.
(i) We are studying the impact of the architectural proteins HGMA1a, HMGA1b and HMGA2 on NF-κB-dependent gene regulation. We are studying the cooperative interactions between HMGA proteins and NF-κB dimers to understand how interaction with architectural factors enhances transcription, and provides NF-κB dimer specificity in the inflammatory response.
(ii) Irf3 and NF-κB are critical transcriptional regulators of the Toll-like receptor 3 (TLR3)- and TLR4-mediated response to pathogens. We are studying NF-κB-Irf3 complexes to understand the link between DNA sequence, NF-κB-Irf3 interactions, and gene expression in TLR signaling and response to pathogens.
(iii) C/EBPb and NF-kB. We are investigating the role of NF-kB-C/EBPb synergy as a mechanism for integrating cytokine signaling in inflammation.
Synthetic Biology to Control Inflammation: A second area of research in the lab is focused on engineering macrophages for therapeutic purposes. Macrophages play a central role in the regulation of inflammation and homeostasis throughout the body. Macrophages are also integral to aspects of disease such as plaque formation in atherosclerosis, tumorigenesis and metastatsis in cancer, and insulin resistance in diabetes. Therefore, manipulation of macrophage function, using the emerging tools of synthetic biology, provides an exciting and potentially powerful means to affect disease biology for therapeutic purposes. A current project in the lab is to design simple synthetic circuits in macrophages that will respond to inflammatory and environmental signals and turn on specific transgenes. We envision that ultimately cells could be engineered to migrate to specific locations in the body and turn on genes to suppress or alter inflammation for therapeutic purposes.