Peanut allergy oral immunotherapy drives single-cell multi-omic changes in peanut-reactive T cells associated with sustained unresponsiveness

Oral immunotherapy (OIT) is the only U.S. Food and Drud Administration-approved treatment for peanut allergy. Peanut-reactive (pr) CD4⁺ T cells are pivotal in peanut allergy pathogenesis and OIT-induced desensitization. However, the underlying pr CD4⁺ T cell immune mechanisms leading to sustained unresponsiveness after OIT discontinuation are largely unknown. We analyzed single-cell RNA and protein immunophenotypes and T cell receptor repertoires of pr CD4⁺ T cells from a phase 2 peanut OIT trial cohort. We identified increased cytotoxicity-related phenotypes and type 1 helper cytotoxic T lymphocyte-like cell clonal expansion during OIT, while type 2 helper T (T_H2) cell-related phenotypes and T_H2-like cell clonal expansion decreased. OIT participants achieving sustained unresponsiveness were distinguished by lower baseline T_H2-related phenotypes, elevated post-OIT cytotoxicity-related pr effector T cell gene signatures and higher CD39 expression in pr regulatory T cells. These findings clarify OIT-induced CD4⁺ T cell tolerance mechanisms and can guide effective allergen-specific OIT strategies.