Title: Transcriptomic and Gene Set Enrichment Analysis of Peanut stimulated CD4+ T cells during Peanut Oral Immunotherapy
Abstract: Early studies suggest that oral immunotherapy (OIT) decreases Th2 cytokine production, a possible mechanism for desensitization. However, data remains limited on the differences between individuals who develop transient desensitization (TD) versus sustained unresponsiveness (SU), a longer-lasting protection after OIT. We performed bulk RNA-sequencing on peanut-stimulated CD154+ CD4+ T cells from longitudinal samples of 22 participants over the course of a peanut OIT trial (5 SU, 6 TD, 6 treatment failures, and 5 on placebo). We conducted differential expression analysis comparing end of maintenance to baseline timepoints and analyzed the results using gene set enrichment analysis (GSEA) with an FDR of q<0.05. GSEA revealed differential enrichment of 18 Th1, 7 Th2, and 13 Th17 gene sets among OIT-treated participants, as compared to placebo. All Th2 and Th17 gene sets and 13/18 Th1 gene sets demonstrated enhancement at baseline compared to maintenance, and examination of these signatures demonstrated that these Th1, Th17, and Th2 signatures were more predominantly enhanced in the TD and treatment failure groups, as compared to the SU group. These data support the hypothesis that OIT shifts T helper cell phenotypes away from Th1, Th2, and Th17 signatures, and that these shifts occur predominantly in TD and treatment failures, but not in SU participants. These early differences may prove useful in predicting responses to OIT and discovering mechanisms to improve the efficacy of OIT.