Development of Commensal-Specific T cell Studies

PROJECT SUMMARY The gastrointestinal tract is colonized by a complex community of commensal bacteria living in harmony with the host. It is now well known that the composition of this microbiome and its interaction with the immune system can have a profound impact on health and disease, not only in the gut environment but throughout the whole body. As such, commensal dysbiosis in the gut is linked to not only inflammatory bowel diseases (IBD), but also several types of autoimmunity, metabolic diseases, and cancer. Unraveling the complex dynamic between the microbiome and the immune system is thus a major goal for the field of immunology and a direct pathway to the development of better treatments for a wide range of diseases. A key to understanding adaptive immune responses to commensal bacteria lies with the development of better tools to study T cells with specificity for a given bacterial antigen. This has been an ongoing challenge for the field, and many studies have relied on heavily manipulated models that, while informative, may only be revealing biology that occurs under special circumstances, or worse, may be misleading due to experimental artifacts. To help remedy this problem, our lab has developed the use of peptide:MHC tetramers that can directly identify commensal antigen-specific T cells within endogenous polyclonal T cell repertoires, thereby providing data of the highest physiological relevance. However, the widespread use of tetramers has been stymied by the extremely low frequencies of these antigen-specific T cells in lymphoid and gut tissues under most biological conditions. A worthy compromise to this conundrum may be to combine the use of tetramers with other known methods of minimally manipulating T cell repertoires in mice to improve antigen- specific T cell frequencies while preserving as much authentic biology as possible. The overall goal of this project is to develop a robust, physiologically relevant in vivo experimental system to study T cells with specificity for commensal bacteria of the gastrointestinal tract. We hypothesize that a combined use of single chain TCR (scTCR) transgenes, retrogenic bone marrow chimeric mice, and peptide:MHC tetramer reagents will provide an outstanding opportunity to achieve this. We will establish this powerful and important tool for the field by developing and evaluating 1) scTCR retrogenic mice with biased T cell repertoires to facilitate the study of commensal antigen-specific T cells, and 2) a scTCR retrogenic mixed bone marrow chimera system to study the role of candidate genes in their development.