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 FDA-approved treatment for peanut allergy (PA). Peanut-reactive (pr) CD4+ T cells are pivotal in PA pathogenesis as well as OIT-induced desensitization (DS). However, the underlying pr CD4+ T cell immune mechanisms leading to sustained unresponsiveness (SU) after OIT discontinuation remain largely unknown. We analyzed single-cell RNA and protein immunophenotypes and TCR repertoires of pr CD4+ T cells from a phase 2 peanut OIT trial cohort. We identify increased cytotoxicity-related phenotypes and Th1 CTL (cytotoxic T lymphocytes)-like cell clonal expansion during OIT in pr T effector memory cells, while Th2-related phenotypes and Th2a-like cell clonal expansion decreased. OIT participants who achieved SU had lower baseline Th2-related phenotypes, elevated cytotoxicity-related gene signatures in pr Teff cells post-OIT and higher CD39 expression in pr Tregs (T regulatory cells) after OIT withdrawal. These findings clarify OIT-induced CD4+ T cell tolerance mechanisms and can guide effective allergen-specific OIT strategies.