CD4 T cells play a central role in orchestrating adaptive immune responses. After being activated through their T cell receptor (TCR) in a particular cytokine milieu, naive CD4 T cells differentiate into distinct T helper (Th) lineages, including Th1, Th2 and Th17 cells that produce interferon (IFN)-gamma;, interleukin (IL)-4 and IL-17, respectively, as their signature effector cytokines. These cells are indispensable for different types of immunity to various microorganisms: Th1 cells are important for protective immune responses to intracellular viral and bacterial infection;Th2 cells for expelling extracellular parasites such as helminths;and Th17 cells for controlling extracellular bacteria and fungi. Additional CD4 T cells include follicular T cells (Tfh) and regulatory T cells (Treg). Tfh cells are critical for promoting antibody responses, whereas Treg cells, which consist of natural-occurring regulatory T cells (nTregs) and inducible regulatory T cells (iTregs), are responsible for maintaining immune tolerance and lymphocyte homeostasis. Inappropriate Th responses to pathogens may lead to chronic infection and/or tissue damage to the host. Similarly, unnecessary activation of Th1, Th17 or Th2 cells by harmless environmental- or self-antigens can cause organ-specific autoimmune diseases or allergic inflammatory diseases. The activation, differentiation and expansion of Th cells are tightly regulated by specific transcription factors that are induced and/or activated by a combination of cytokines. During Th1 cell differentiation, IFNgamma and IL-12 are responsible for inducing T-bet gene expression and Stat4 phosphorylation, respectively;both T-bet and Stat4 are critical for Th1 cells to produce IFNgamma. Similarly, GATA-3 expression and Stat5 activation induced by IL-4 and IL-2, respectively, are the two key elements for Th2 cell differentiation and functions. RORgammat/Stat3, Foxp3/Stat5, and Bcl-6/Stat3 are the crucial counterparts during differentiation of Th17, Treg and Tfh cells, respectively. However, these so-called master regulators, although necessary, may not be sufficient to induce a specific Th cell phenotype. Many other transcription factors, forming a network with these key factors, also act in the process of T cell differentiation. In addition, for these known transcription factors, how they regulate lineage-specific gene expression and/or epigenetic modifications through their binding to cis-regulatory elements are still elusive. Therefore, identifying the components of transcriptional regulatory network and investigating mechanisms of their actions are essential for understanding the differentiation processes into distinct Th cell lineages. During the past year, Unit scientists reported a T-bet-ZsGreen reporter (TBGR) mouse strain, in which GFP faithfully reflects T-bet expression. After cross-breeding TBGR with a number of mouse strains deficient in key Th1 factors, such as Stat4, IFNgammaRI and T-bet, alone or in combination, we studied the regulation and functions of T-bet in vivo in responses to T. gondii infection. These mice are also being used for investigating T-bet regulation and functions in other immune cells such as innate lymphoid cells. In order to isolate and study T cell and ILC subsets based on their expression of key transcription factor, we have recently generated a new mouse model in which T-bet expression is indicated by a blue fluorescent protein (AmCyan). This mouse strain has been bred with other transcription factor reporter mice. The mice have also been transferred to our collaborators for studying other immune cell subsets. To better understand the transcriptional regulatory network in T cell differentiation, we have profiled the gene expression patterns of distinct T cell subsets at various differentiating time points in vitro via RNAseq (in collaboration with Keji Zhao's group). The datasets not only guide us in our future studies but also serve as a useful resource for the whole immunology research community. We have analyzed the datasets focusing on long intergenic non-coding RNAs (LincRNAs);all the data have been deposited to GEO and ready for publication. We expect that future analysis of the lincRNAs that are identified in our study will reveal their important functions in T cell development, differentiation and immune response. In addition, our dataset will serve as an important resource for studying transcriptional regulatory networks during T cell development and differentiation by comparing the dynamic expression of protein-coding genes including transcription factors, cytokines, chemokines, cytokine receptors, chemokine receptors, other cell surface molecules, and signaling molecules. Innate lymphoid cells (ILCs) play critical roles during innate immune responses to pathogens and lymphoid organ development. IL-7Ra+ ILC subsets, similar to T helper (Th) cell subsets, produce distinctive effector cytokines. However, the molecular control of IL-7Ra+ ILC development and maintenance has yet to be dissected. We found that GATA3 is indispensable for the development of all IL-7Ra+ ILC subsets. Consistent with this defect, Gata3 conditional deficient mice have no lymph nodes and are susceptible to Citrobactor rodentium infection (infection was done in collaboration with Yasmine Belkaid's group). Genome-wide gene analyses indicate that GATA3 regulates a similar set of cytokines and receptors in ILC2s and Th2 cells and is critical for the maintenance of ILC2s. Thus, GATA3 plays parallel roles in establishing and regulating both adaptive and innate lymphocytes. This finding reveals a common basic principle of ILC and T cell development controlled by transcription factor GATA3.

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