A study on the role of T helper cells in allergic inflammation

Asthma is a chronic inflammatory disease of the airways affecting hundreds of millions of people worldwide. Central to the development of asthma and allergic airway inflammation are CD4 T cells, which upon activation through their T cell antigen receptor, differentiate into T helper (Th) cells with the potential to secrete distinct sets of cytokines. These cytokines have the ability to potentiate or regulate inflammation in all the organs of the body. In asthma, Th2 cells that produce IL-4, IL-5 and IL-13, have been heavily implicated in promoting pathogenesis in the lung. However, other T helper cell subsets, such as IL-17producing Th17 cells may also play a pathogenic role. Paper I established that peroxisome proliferator activated receptor gamma (PPAR- was an important factor for the differentiation of IL-5and IL-13-producing Th2 cells in a mouse model of allergic airway inflammation with the allergen, house dust mite (HDM). Mice lacking PPAR- in T cells did not develop Th2 cell-associated pathologies, including airway eosinophilia and goblet cell metaplasia. Further, these mice were unable to mount a protective immune response to infection with Heligmosomoides polygyrus. Mechanistically, PPAR- appeared to promote the expression of the IL-33 receptor on Th2 cells, which enhanced their pathogenic functions. Paper II used single-cell RNA sequencing (scRNA-seq) to resolve distinct subsets of T helper cells in the HDM model of asthma. Th2 cells were found to differentially express over 100 genes including known Th2 cell genes such as Gata3, Il13, Il1rl1 and Pparg (described in paper I) as well as many other genes not previously reported to have a specific role in promoting Th2 cell function. Th2 cells were enriched for genes associated with lipid metabolism, which when blocked, impaired Th2 cell-driven inflammation in the lung tissue and airways. scRNA-seq also resolved a population of Th cells responding to type-I interferons. Paper III established a novel mouse model using dog allergen extract instillations to induce airway inflammation, which was characterized by a mixed Th2/Th17 response. In characterizing this model it demonstrated that dog allergen extracts can induce high levels of airway eosinophilia and neutrophilia, airway hyperresponsiveness, goblet cell metaplasia and increased serum levels of IgE. scRNA-seq of T helper cells from the airways of dog allergen-exposed mice resolved several distinct subsets, providing a gene expression signature for responding Th17 cells and providing a largely overlapping gene signature for Th2 cells as that which was elucidated in paper II. Sublingual immunotherapy using recombinant dog allergens proved successful in ameliorating airway eosinophilia and the Th2 cell response to dog allergen challenge, but did not affect the Th17 cell response. The work presented in this thesis improves our understanding of the factors governing T helper cell differentiation and function in the context of allergic airway inflammation. It showcases that scRNA-seq is a powerful tool to study diverse T helper cell populations and sheds light on genes and cellular processes of relevance to specific subsets. Finally, the novel mouse model of dog allergies presents a tool with which to study airway inflammation driven both by Th2 and Th17 cells as well as an approach to treat dog allergies. LIST OF SCIENTIFIC PAPERS I. Chen, T. , Tibbitt, C.A. , Feng, X. , Stark, J.M. , Rohrbeck, L. , Rausch, L. , Sedimbi, S.K. , Karlsson, M.C. I. , Lambrecht, B.N. , Karlsson Hedestam, G.B. , Hendriks, R.W. , Chambers, B.J., Nylén, S. , and Coquet, J.M. (2017). PPAR-gamma promotes type 2 immune responses in allergy and nematode infection. Sci Immunol 2. II. Tibbitt, C.A. *, Stark, J.M. *, Martens, L. , Ma, J., Mold, J.E. , Deswarte, K. , Oliynyk, G. , Feng, X. , Lambrecht, B.N. , De Bleser, P., Nylén, S. Hammad H. , Arsenian Henriksson, M. , Saeys, Y. , and Coquet, J.M. (2019). SingleCell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells. Immunity 51, 169-184 e165. III. Stark, J.M. , Liu, J., Tibbitt, C.A. , Ma, J., Wintersand, A. , Adner, M. , Grönlund, H. , Gafvelin, G. , and Coquet, J.M. Dog allergens induce a dual neutrophilic and eosinophilic infiltrate hallmarked by vigorous TH2 and TH17 cell responses, Manuscript