Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis
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
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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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 4

scRNA-seq identification of 8 lymphocyte subpopulations.

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scRNA-seq identification of 8 lymphocyte subpopulations. (A) Left panel:...
(A) Left panel: with t-SNE dimensionality reduction, the T1–T8 clusters were 2D plotted with each tissue T cell subclass color coded as indicated. Right panel: a 2D plot was color coded in the context of patients with and without EoE (non-EoE group includes NL and EoE remission). (B) With the large rectangle representing all single T cells isolated from NL, EoE remission, and active EoE subjects, the cellularity presence of T1–T8 subclasses was proportionally graphed within the disease status bin that was set to the equal area as 100%. (C) To emphasize the expression profiles of T7 and T8, a heatmap was selectively generated focusing on the T7-specific Treg genes and the T8-specific Th2-functionality genes, as well as those genes common to both clusters. Four patterns were identified on the basis of differential expression. Patterns I, II, III, and IV were enriched with distinct T clusters—I with T7+T8, II with T7 only, III with ubiquitous T clusters but T8 enriched, and IV with T8 only. (D) A volcano plot comparing top differentially expressed genes between T7 and T8, with key significant genes labeled. Colorized entities represent passing the filter of FDR-adjusted P < 0.05 and fold change >16 with red-blue gradient on FDR-adjusted P values. (E) A series of radar plots based on relevant functional gene sets was generated on logarithm scale to depict the expression characteristics of T1–T8 restricted to Th2 cell markers and cytokines, Treg properties, migration molecule expression related to chemotaxis and adhesion, and T cytotoxic cells properties, respectively. T7 (blue line) and T8 (red line) are shown in bold to emphasize the 2 disease-associated clusters.