Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis
Ting Wen, … , Daniel Douek, Marc E. Rothenberg
Ting Wen, … , Daniel Douek, Marc E. Rothenberg
Published April 8, 2019
Citation Information: J Clin Invest. 2019;129(5):2014-2028. https://doi.org/10.1172/JCI125917.
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Research Article Immunology

Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis

Abstract

T cell heterogeneity is highly relevant to allergic disorders. We resolved the heterogeneity of human tissue CD3+ T cells during allergic inflammation, focusing on a tissue-specific allergic disease, eosinophilic esophagitis (EoE). We investigated 1088 single T cells derived from patients with a spectrum of disease activity. Eight disparate tissue T cell subtypes (designated T1–T8) were identified, with T7 and T8 enriched in the diseased tissue. The phenotypes of T7 and T8 resemble putative Treg (FOXP3+) and effector Th2-like (GATA3+) cells, respectively. Prodigious levels of IL-5 and IL-13 were confined to HPGDS+ CRTH2+IL-17RB+FFAR3+CD4+ T8 effector Th2 cells. EoE severity closely paralleled a lipid/fatty acid–induced activation node highlighted by the expression of the short-chain fatty acid receptor FFAR3. Ligands for FFAR3 induced Th2 cytokine production from human and murine T cells, including in an in vivo allergy model. Therefore, we elucidated the defining characteristics of tissue-residing CD3+ T cells in EoE, a specific enrichment of CD4+ Treg and effector Th2 cells, confinement of type 2 cytokine production to the CD4+ effector population, a highly likely role for FFAR3 in amplifying local Th2 responses in EoE, and a resource to further dissect tissue lymphocytes and allergic responses.

Authors

Ting Wen, Bruce J. Aronow, Yrina Rochman, Mark Rochman, Kiran KC, Phil J. Dexheimer, Philip Putnam, Vincent Mukkada, Heather Foote, Kira Rehn, Sam Darko, Daniel Douek, Marc E. Rothenberg

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Figure 8

FFAR3 induction and Th2-enhancing effects of butyrate.

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FFAR3 induction and Th2-enhancing effects of butyrate. (A) A magnified v...
(A) A magnified view in the upper panel emphasizing the IL5-correlating genes specifically present in the T8 cluster, with FFAR3 tracking with IL5 expression shown in the lower panel (orange, IL5 producers; blue, FFAR3+ T cells). (B) Upper panel: the single-cell expression patterns of FFAR3 across 3 disease activity states (N, normal; R, remission; A, active EoE), with each data point representing 1 of the 1088 tissue T cells. Lower panel: with 3 days of Th2 differentiation (anti–CD3-CD28 [activated] with or without IL-4), human blood CD4+ T cells isolated from patients with EoE upregulated FFAR3 transcript induced by αCD3-CD28 (activation) plus IL-4 but not αCD3-CD28 (activation) alone. (C) IL5 transcript production by human Jurkat cells following short-chain fatty acid exposures (C2, C3, and C4 each at 10 mM for 24 hours). (D) Jurkat cells express FFAR3 on the cell surface by immunofluorescence and FACS. Original magnification, ×400. (E) In a murine asthma model, eGFP–IL-4 reporter mice were aspergillus allergen–challenged (ASP-challenged) intranasally with and without C4 (1 mg coadministration). IL-4–eGFP expression in CD4+ cells was analyzed by FACS. (F and G) Lung tissue CD4+ lymphocytes were assayed for Th1 and Th2 cytokine production by FACS. (H) The bronchoalveolar fluid (BALF) cells were quantified for major leukocyte populations. EOS, eosinophils; PMN, polymorphonuclear neutrophils; LYM, lymphocytes; MΦ, macrophages. All scatter plots are presented as mean ± SEM, and all experiments were repeated at least 3 times (*P < 0.05, **P < 0.01, ***P < 0.001; 2-tailed t test).