Endotype dependent loss of tolerance in cow milk allergies is driven by antigen-specific CD4+ T cell outgrowth and gut microbial dysbiosis

Cow milk allergy (CMA) is one of the most common infant food allergies, presenting in IgE- and non-IgE-mediated forms. Currently, the allergen-reactive CD4+ T cell inflammatory responses that distinguish CMA endotypes are not well characterized. In this study, we isolated allergen-reactive conventional (Tcon) and regulatory (Treg) CD4+ T cells from IgE and non-IgE mediated pediatric CMA patients and performed an in-depth cellular and molecular characterization of the composition and function of both T helper (TH) and TH-like subsets. Bacteria present in the gut microbiota were also analysed to assess potential differences between CMA endotypes, and associations between TH and TH-like subsets were mapped against the composition of gut bacterial species. Our findings show that alterations in the balance between allergen-reactive Tcon and Treg cells underlies the development of food allergen sensitization in both IgE- and non-IgE-mediated forms of CMA. Additionally, differences in the composition of TH and TH-like subsets, as well as in the bacterial species present, showed significant associations with the development of specific CMA endotypes. Together, these findings provide a rational explanation for the distinct immunopathologies observed in endotype-specific immune responses against a common allergen and offer insights into the development of therapeutic strategies for distinct CMA endotypes.