Single-cell profiling of peanut-responsive T cells in patients with peanut allergy reveals heterogeneous effector T H 2 subsets

• Published in: Journal of allergy and clinical immunology Vol. 141; no. 6; p. 2107
• Main Authors: Chiang, David, Chen, Xintong, Jones, Stacie M, Wood, Robert A, Sicherer, Scott H, Burks, A Wesley, Leung, Donald Y M, Agashe, Charuta, Grishin, Alexander, Dawson, Peter, Davidson, Wendy F, Newman, Leah, Sebra, Robert, Merad, Miriam, Sampson, Hugh A, Losic, Bojan, Berin, M Cecilia
• Format: Journal Article
• Language: English
• Published: United States Elsevier Limited 01.06.2018
• Subjects: Adult; Antigens; CD4 antigen; CD40L protein; Cloning; Cytokines; Demographics; Experiments; Female; Flow cytometry; Food allergies; Gene expression; Growth factors; Helper cells; Human subjects; Humans; Immunoglobulin E; Immunological tolerance; Immunotherapy; Interleukin 1; Interleukin 13; Interleukin 2; Interleukin 4; Interleukin 5; Interleukin 9; Lymphocytes T; Male; Pathogenesis; Peanut Hypersensitivity - immunology; Peripheral blood; Phenotypic variations; Randomized Controlled Trials as Topic; Ribonucleic acid; RNA; T cell receptors; T-Lymphocyte Subsets - immunology; Th2 Cells - immunology; Young Adult; Food allergy; peanut allergy; regulatory T; tolerance; T(H)2
• ISSN: 0091-6749; 1097-6825
• DOI: 10.1016/j.jaci.2017.11.060

The contribution of phenotypic variation of peanut-specific T cells to clinical allergy or tolerance to peanut is not well understood. Our objective was to comprehensively phenotype peanut-specific T cells in the peripheral blood of subjects with and without peanut allergy (PA). We obtained samples from patients with PA, including a cohort undergoing baseline peanut challenges for an immunotherapy trial (Consortium of Food Allergy Research [CoFAR] 6). Subjects were confirmed as having PA, or if they passed a 1-g peanut challenge, they were termed high-threshold subjects. Healthy control (HC) subjects were also recruited. Peanut-responsive T cells were identified based on CD154 expression after 6 to 18 hours of stimulation with peanut extract. Cells were analyzed by using flow cytometry and single-cell RNA sequencing. Patients with PA had tissue- and follicle-homing peanut-responsive CD4 T cells with a heterogeneous pattern of T 2 differentiation, whereas control subjects had undetectable T-cell responses to peanut. The PA group had a delayed and IL-2-dependent upregulation of CD154 on cells expressing regulatory T (Treg) cell markers, which was absent in HC or high-threshold subjects. Depletion of Treg cells enhanced cytokine production in HC subjects and patients with PA in vitro, but cytokines associated with highly differentiated T 2 cells were more resistant to Treg cell suppression in patients with PA. Analysis of gene expression by means of single-cell RNA sequencing identified T cells with highly correlated expression of IL4, IL5, IL9, IL13, and the IL-25 receptor IL17RB. These results demonstrate the presence of highly differentiated T 2 cells producing T 2-associated cytokines with functions beyond IgE class-switching in patients with PA. A multifunctional T 2 response was more evident than a Treg cell deficit among peanut-responsive T cells.