Regulatory T cells are the main cell population involved in the prevention or suppression of unwanted overt inflammatory processes. At the intestinal surface, which is chronically exposed to stimuli from both microbes and diet, peripheral Foxp3+ T cells (pTregs) are thought to prevent the development of inflammatory bowel diseases and food allergies. Surprisingly, very few Tregs are found in the most exposed layer of the intestinal mucosa: the single-cell layered epithelium. Yet, the understanding of immune regulatory processes at this layer is of utmost importance for a better comprehension of how pathological inflammatory processes arise, and for the development of novel intervention strategies. During the first four years of funding for this project we described environmental cues, transcription factors, and functional consequences related to the adaptation of CD4 T cells to the gut epithelium. We found that CD4 T cells belonging to different T helper lineages convert into CD8??+CD4+ intraepithelial lymphocytes (CD4-IELs) in a microbiota-, retinoic acid-, IFN-? and TGF-?- dependent manner. This unexpected T cell plasticity was also observed among total Tregs, which lose Foxp3 and convert to CD4-IELs upon migration to the epithelium, an effect attributed to the loss of the transcription factor ThPOK. Importantly, our work also suggested that pTregs and CD4-IELs perform complementary roles in the regulation of intestinal inflammation. Our preliminary repertoire analysis indicates strong TCR biases in both pTregs and CD4-IELs in the epithelium. However, the role of TCR stimulation for epithelial CD4 T cell residency and plasticity, the diversity of TCR repertoire and the nature of TCR ligands in epithelial CD4 T cell populations remain to be determined. We hypothesize that intra-epithelial adaptation of anti-inflammatory T cells is shaped by their TCR and by factors found in the epithelium, determining gut T cell functional specialization. Based on extensive published and unpublished data, this proposal undertakes several intertwined aspects of CD4 T cell adaptation to the gut epithelium, bringing together both conceptual and technological innovations. Using a combination of intersectional genetics, single-cell repertoire analyses and in vitro NFAT assays, we will define the TCR repertoire and ligands of epithelial CD4 T cells. Our unpublished data suggest a coordinated response involving multiple transcription factors that regulate Treg stability, tissue residency and CD4-IEL function. We will perform RNA-seq, ChIP-seq and ATAC-seq, combined with mouse genetics, to define the molecular machinery involved in the transcriptional changes observed in CD4 T cells that undergo epithelium-specific adaptation. Finally, we will define the role of continuous ThPOK and TCR expression in Treg suppressive function and whether CD4 T cell ?IEL differentiation? is important for immune regulation in the epithelium both at steady state and in models of intestinal inflammation. Hence, this proposal aims to characterize entirely novel immune regulatory pathways in the gut as well as to identify molecular mechanisms that determine plasticity of intestinal CD4 T cell lineages and their functional relevance.

Public Health Relevance

The proposed research has significant relevance to public health because it directly addresses possible cellular and molecular mechanisms involved in immune regulation in the gut tissue. By pursuing an understanding of the main components and interactions of the intestine/microbes/immune system network, this proposal may provide novel strategies for the development of mucosal vaccines and new therapeutic avenues for the treatment of inflammatory bowel diseases, celiac disease and food allergies.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Project (R01)
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Cellular and Molecular Immunology - B Study Section (CMIB)
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Perrin, Peter J
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Rockefeller University
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New York
United States
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Hoytema van Konijnenburg, David P; Reis, Bernardo S; Pedicord, Virginia A et al. (2017) Intestinal Epithelial and Intraepithelial T Cell Crosstalk Mediates a Dynamic Response to Infection. Cell 171:783-794.e13
Faria, Ana M C; Reis, Bernardo S; Mucida, Daniel (2017) Tissue adaptation: Implications for gut immunity and tolerance. J Exp Med 214:1211-1226
Sujino, Tomohisa; London, Mariya; Hoytema van Konijnenburg, David P et al. (2016) Tissue adaptation of regulatory and intraepithelial CD4? T cells controls gut inflammation. Science 352:1581-6
Rogoz, Aneta; Reis, Bernardo S; Karssemeijer, Roos A et al. (2015) A 3-D enteroid-based model to study T-cell and epithelial cell interaction. J Immunol Methods 421:89-95
Reis, Bernardo S; Lee, Kihyun; Fanok, Melania H et al. (2015) Leptin receptor signaling in T cells is required for Th17 differentiation. J Immunol 194:5253-60
Reis, Bernardo S; Hoytema van Konijnenburg, David P; Grivennikov, Sergei I et al. (2014) Transcription factor T-bet regulates intraepithelial lymphocyte functional maturation. Immunity 41:244-56
Esterházy, Daria; Mucida, Daniel (2014) Serum amyloid A proteins take retinol for a ride. Trends Immunol 35:505-6
Reis, Bernardo Sgarbi; Rogoz, Aneta; Costa-Pinto, Frederico Azevedo et al. (2013) Mutual expression of the transcription factors Runx3 and ThPOK regulates intestinal CD4? T cell immunity. Nat Immunol 14:271-80
Mucida, Daniel; Husain, Mohammad Mushtaq; Muroi, Sawako et al. (2013) Transcriptional reprogramming of mature CD4? helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes. Nat Immunol 14:281-9