Major research achievements
Pattern recognition is a corner stone of immunology. While this paradigm originally pertained to the recognition of microbial patterns, we have pursued 'viability' as a molecular pattern in the immune system. Life and death of individual cells are at the very core of multicellular existence: on one hand, regulated cell death is necessary for replacement of cells and for organogenesis, whereas death associated with infection signifies a serious threat to survival of the organism. Using this as a paradigmatic guideline, we have documented the consequences of cell death on antigen processing and presentation as well as on differentiation of T cells. Likewise, we have established how viability of the infectious agent serves as a unique pattern on its own, mobilizing the execution of cell death and enabling the immune system to gauge the threat level of microbial invasion. En route, we made major contributions to fields outside our own: we were the first to demonstrate how extracellular cues interpreted through cell surface receptors modulate the rate and consequences of phagosome maturation. We demonstrated phagosome autonomous behavior during simultaneous phagocytosis of microbes and dying cells, dictated by Toll-like receptor engagement specifically from phagosomes carrying microbial cargo. We identified a novel pathway for cross-presentation in dendritic cells that relies on regulated subcellular communication specifically between phagosomes and the endosomal recycling compartment. We designed a novel cancer immunotherapy approach whereby bacterial flagellin expression in tumor cells synergistically mobilizes two major pathways of innate immunity against tumors. We defined innate recognition of infected dying cells as the physiological trigger for differentiation of T helper 17 cells, a subset best suited for host defense against infections associated with cell death. We have revealed the transcriptional programs distinct to different tissue phagocytes responding to apoptosis in situ.
Specific Research Directions
The impact of Cell Death and Infection on Intestinal Homeostasis
Intestinal epithelial cells are renewed by apoptosis every 4-5 days making the intestine an ideal model tissue for studying innate immune recognition of apoptotic cells in tissues. We found that intestinal lamina propria phagocytes can sample and internalize dying intestinal epithelial cells. Our findings were counter to the common view that these cells were simply shed into the lumen without consequence. Transcriptional profiling revealed that intestinal phagocytes downregulate inflammatory genes and upregulate negative regulators of inflammation when they internalize apoptotic intestinal epithelial cells. Our findings identify the natural program of apoptosis within the intestinal epithelium as a prominent mechanism for enforcing intestinal homeostasis.
Notably, a number of phagocyte genes that were differentially modulated in response to dying cells overlapped with defined genetic susceptibility loci for Inflammatory Bowel Disease. These findings suggest that polymorphisms in these genes might alter the ability of phagocytes to respond appropriately to the immunosuppressive signals from apoptotic cells. By understanding the immune consequences of cell death within the intestinal epithelium, we can begin to implement therapeutic strategies aimed at enforcing the same immunosuppressive mechanisms that phagocytes use to maintain homeostasis within the gut.
Innate Detection and Immune Response to Microbial Viability
We were the first to demonstrate the ability of the innate immune system to detect the very essence of microbial infectivity, microbial viability itself, in the form of prokaryotic messenger RNA, which we found is present in live and lost from dead bacteria. We have termed the immune stimulatory signatures of microbial viability as vita-PAMPs to distinguish them from the molecular structures (PAMPs) that live and dead microbes share. We would like to know how detection of vita-PAMPs shapes the ensuing protective T cell and B cell responses. What other microbial derived molecules and metabolites serve as vita-PAMPs? How does the detection of vita-PAMPs impact the well characterized innate immune signaling pathways that have been studied in response to single microbial agonists? We believe these questions are important because they would significantly increase our understanding of the immune response to infection, and enable us to improve vaccine performance with signatures of microbial viability.
Control of Antigen Presentation by Toll-like Receptors
Our research here has led to pioneering discoveries that have impacted our understanding of the subcellular mechanisms mediating immunity and tolerance, and have also informed optimal strategies for vaccine design. Dendritic cells play center stage in these studies because they internalize extracellular components and present peptides derived from these to T cells, and either defend the host from infection or protect the host from autoimmunity. The decision on how to respond is made primarily according to the inflammatory content of the internalized material. We found that microbial structures engage Toll-like receptors, which then tailor the antigen processing and presentation machinery in dendritic cells to enable post-translational modifications and subcellular trafficking of key regulatory molecules. Our studies on antigen presentation intersect with signal transduction, protein trafficking between organelles, and T cell activation to define the regulation of these pathways and their impact on the organismal response to infection or cell death. Defining key regulatory players or checkpoints will enable their exploitation to enhance tolerance or improve immunity to infectious diseases and cancer.