PROJECT SUMMARY Disease associated with allergies such as asthma are a rising health problem with no current curative solutions. CD4+ helper T cells (TH) that respond to common allergens play an important role in driving airway inflammation in asthma. To better understand the diversity of T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells from asthmatics and non-asthmatics, with and without HDM allergy. From our analysis, besides canonical clusters of cells such as TH2, TH17, and TH1, we identified a novel subset of allergen-reactive TH cells characterized by an IFN responsive gene signature that we called THIFNR cells (Seumois et al. Science Immunology, 2020). Proportions of THIFNR cells were significantly increased in nonallergic individuals compared to allergic patients, suggesting an allergen-specific host specific response even in non-allergic individuals. Moreover, the exclusive presence of the allergen-reactive TH2 cells in the allergic patients suggests a protective role (anti-TH2 response) of the THIFNR cells in the non- allergic patients with exposure to allergen. This potential protective role was reinforced by our in vitro studies showing that TNF-related apoptosis-inducing ligand (TRAIL) produced by THIFNR cells directly inhibits T cell activation triggered by TCR engagement. In follow-up studies, we found THIFNR cells among viral-reactive TH cells directed towards Flu or SARS-CoV2, suggesting a broader role of those cells in immune responses. Also, we found THIFNR cells as a stable TH subset in a large cohort of healthy individuals. Because of the recent discovery of THIFNR cells, very little is known about their origins, differentiation, phenotype, and function. We hypothesize that these THIFNR HDM-reactive T cells could play a role through TRAIL engagement in dampening TH2 inflammation in allergy and asthma. In Aim 1, we will define the functional properties of THIFNR cells. We will perform co-culture experiments to test the ability of THIFNR cells to inhibit proliferation and function of TH2 cells in a TRAIL-dependent manner. In Aim 2 we will determine optimal conditions to induce differentiation of THIFNR cells in vitro and compare their functional properties with those generated in vivo. Finally, in Aim 3, we will determine if HDM-reactive THIFNR cells show persistence and plasticity in vivo. We will perform single-cell TCR sequencing of HDM-reactive THIFNR cells and other memory CD4+ T cell subsets isolated from longitudinally collected blood samples of HDM allergic and non-allergic subjects. By comparing TCR repertoire in longitudinal samples, we will assess persistence of THIFNR cells in vivo. Overall, functional studies in this R21 program will provide important insights into this novel CD4+ T cell subset; and form the basis of a future R01 application to conduct studies translating findings to the clinic.

PROJECT NARRATIVE WHO estimated that 20% of the world’s population suffer from respiratory allergies and derived diseases such as allergic rhinitis and asthma. However, there is still no clear answer to the question: “why do only some people develop allergy?”, underscoring the need to revisit our understanding of immune mechanisms of allergy. Using novel genomics unbiased tools, we discovered a new type of T cells, we called THIFNR cells, that, complementary to Tregulatory cells, may play an important role in preventing pathogenic inflammation in allergy and asthma. This grant aims to advance our understanding of the role of this novel subset in controlling allergic immune responses. Our work will provide novel mechanistic insights that may lead to the development of better therapeutic options for patients with allergic diseases.