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 3

Bulk CD3+ RNA-seq analysis of tissue lymphocytes.

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Bulk CD3+ RNA-seq analysis of tissue lymphocytes. (A) CD3+ T cells were ...
(A) CD3+ T cells were sorted from autologous blood and tissue from control (normal [N], n = 3) individuals and patients with EoE with active (active [A], n = 4) or inactive (complete remission [R], n = 4) EoE for bulk RNA-seq analysis. The bidirectional expression profile difference between blood and tissue T cells are displayed in the heat diagram, with each column representing a patient sample. A set of 331 genes reflected tissue-specific functions (paired moderated t test; FDR-adjusted P < 0.05, fold change >10). (B) Gene expression (150 genes) tracking with disease activity, 147 of which were significantly upregulated and 3 of which were downregulated in active EoE tissue lymphocytes compared with healthy controls (moderated t test, FDR-adjusted P < 0.05, fold change >10). (C) Among the 147 genes in B, the expression trends of 6 Th2-related genes across tissue and disease states are shown (blue: autologous blood CD3+; red: tissue CD3+). (D) The top 10 genes (fold change [FC] = 323–1449, NL tissue CD3+ vs. EoE tissue CD3+) from the volcano plot are displayed in a heat diagram. The expression pattern among the 6-comparison group is summarized in the adjacent dot plots showing 3 distinct trends labelled by roman numerals I–III. The fold change (FC, blue) and the FDR-adjusted P value (FDR-P, orange) were exhibited in a radar map in the context of the 10 top genes.