Understanding allergies : how infections affect the function of T helper cells

Allergic disorders are caused by a combination of hereditary and environmental factors. The hygiene hypothesis postulates that early-life microbial exposures impede the development of subsequent allergic diseases. However, unambiguous evidence that microbes reduce the development of allergic disorders is still lacking. Intestinal helminth parasites can alter immune responses to vaccines, other infections, allergens and autoantigens, implying effects on host immune responses in distal barrier tissues. To investigate how infections may affect the allergic immune response, we used so-called ‘wildling mice’ (laboratory mice that were colonized by a rich and diverse repertoire of microbes at barrier surfaces and come into contact with putative pathogens from birth), or C57BL/6 mice that were infected with the intestinal helminth H. polygyrus and analyzed allergic immune responses in these settings. In a clinical setting, we also analyzed T helper cells from nasal polyp samples of chronic rhinosinusitis patients.

In Paper I, we asked whether lifelong exposure to a rich microbial milieu had any effect on the allergic immune response of C57BL/6 mice. We found that wildlings were characterized by a large population of antigen-experienced T cells, including pro-allergic Th2 cells, that expanded primarily after weaning. In models of airway exposure to house dust mites, interleukin-33 or Alternaria alternata, wildlings developed strong allergic inflammation, which was characterized by eosinophil recruitment, goblet cell metaplasia and antigenspecific IgG1 and IgE responses. Wildlings developed robust de novo Th2 cell responses to incoming allergens, while pre-existing Th2 cells could also be recruited into the allergic immune response in a cytokine-driven and TCR-independent fashion. Thus, colonization of laboratory mice with a wild mouse microbiota does not dramatically dampen allergic immune responses across several models of airway allergen exposure.

In Papers II and III, we showed that H. polygyrus infection leads to the dissemination of Th2 cells into distal organs such as skin, lung and visceral adipose tissue. Long-lived Th2 cells in distal organs expressed CD69 mRNA and appeared to adopt gene expression features associated with the tissue from which they were isolated. Th2 cells in the lung responded vigorously to the alarmin recombination IL-33 and fungal extracts of Alternaria Alternata. Analysis of T cell receptor clonality demonstrated that distal organs were colonized by a range of Th2 cell clones that were dispersed throughout the mouse. Moreover, single-cell RNA-sequencing pinpointed cells with features of both Th1 and Th2 cells in the lung and visceral adipose tissue, suggesting that these cells may be capable of exerting multiple functions.

In Paper IV, we analyzed the transcriptomes of single T helper cells from nasal polyps of patients with chronic rhinosinusitis and validated these findings using multiparameter flow cytometry. Polyp tissue contained suppressive T regulatory (Treg) cells, Th2 cells, type 2 innate lymphoid cells, and three transcriptionally distinct subsets of cytotoxic CD4+ T cells (CD4+ CTL). GATA3 expression was a feature of polyp Treg cells, whereas Th2 cells highly expressed TCN1, CD200R, and HPGDS and were enriched for genes involved in lipid metabolism. Only a portion of polyp Th2 cells expressed the prostaglandin D2 receptor CRTH2, whereas a subpopulation of CD109+CRTH2− Th2 cells expressed mRNA for common inhibitor receptors including LAG3 and TIM3 and produced IL-10.

The work presented in the thesis improves our understanding of how heavy microbial exposures and helminth infections can alter the immune system and affect T helper cell responses in the context of allergy. The elucidation of gene signature and functionality of Th2 cells from patients with chronic rhinosinusitis expanded our knowledge of T helper cells not only in mouse models but also in human beings.

List of scientific papers

I. Ma, J., Urgard, E. §, Runge, S. §, Classon, C. H. §, Stark, J. M., Mathä, L., Cheng, L., Zedtwitz, S., Baleviciute, A., Alvarez, J., Hoyer, M., Li, M., Gernand, A. M., Huang, H., Vrtala, S., Boon, L., Bayaerts, R., Adner, M., Gonzalez, I. M., Du, J., Rosshart, P.#, Nylén, S.#, Coquet, J. M#. The wild mouse microbiota modulates responsiveness to allergen challenge. §,#Equal contribution. [Manuscript]

II. Classon, C. H., Li, M., Clavero, A. L., Ma, J., Feng, X., Tibbitt, C. A., Stark, J. M., Cardoso, R., Ringqvist, E., Boon, L., Villablanca, E. J., Rothfuchs, A. G., Eidsmo, L., Coquet, J. M., & Nylén, S. (2022). Intestinal helminth infection transforms the CD4+ T cell composition of the skin. Mucosal Immunology. 15(2), 257–267.
https://doi.org/10.1038/s41385-021-00473-9

III. Ma, J., Urgard, E., Tibbitt, C.A, Classon, C. H., Stark, J. M., Li, M., Sato, K., Murrell, B., Nylén, S., & Coquet, J. M. Intestinal helminth infection induces dissemination of long-lived Th2 cells with Th1 features to distal organs. [Manuscript]

IV. Ma, J.*, Tibbitt, C. A.*, Georén, S. K., Christian, M., Murrell, B., Cardell, L.-O., Bachert, C., & Coquet, J. M. (2021). Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps. Science Immunology. 6(62), eabg6356. *Equal contribution.
https://doi.org/10.1126/sciimmunol.abg6356