Cell-by-cell deciphering of T cells in allergic inflammation

Abstract

Technical advances in single-cell RNA sequencing (scRNA-seq) render it possible to examine the transcriptomes of single cells in patients with allergic inflammation with high resolution in the context of their specific microenvironment, treatment, and disease status. Using a recently published scRNA-seq study of tissue T cells as an example, we introduce the major pipeline steps, illustrate the options of scRNA-seq platforms, summarize new knowledge gained from this study, and provide directions for future research. The presented scRNA-seq study elucidated the T-cell heterogeneity present in an allergic inflammatory tissue focused on eosinophilic esophagitis, a prototypic, chronic, allergic disease, which provided a unique opportunity to probe the pathogenesis of allergic inflammation at the tissue level through readily available endoscopically procured biopsy specimens. scRNA-seq analysis identified 8 populations of CD3+ T cells and defined 2 disease-specific populations of CD3+CD4+ T cells, including a markedly activated type 2 cytokine-producing pathogenic cell population distinguished by expression of the short-chain fatty acid receptor free fatty acid receptor 3 and a population of regulatory T cells. In addition to presenting and interpreting new findings within the prior literature, we postulate about future single-cell next-generation sequencing platforms in this burgeoning field.

Keywords: T(H)2 cells; T(H)2 cytokine; eosinophilic esophagitis; food allergy; scRNA-seq.

Conflict of interest statement

Conflicts of interest statement. MER is a consultant for Pulm One, Spoon Guru, ClostrBio, Celgene, and Astra Zeneca and has an equity interest in the first three listed and royalties from reslizumab (Teva Pharmaceuticals) and UpToDate. MER and TW are inventors of patents, owned by Cincinnati Children’s Hospital Medical Center and unrelated to the study described herein. None of the other authors declare any conflicting financial interests related to the content of the study.

Copyright © 2019 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Figures

Figure 1.. Schematic work flow of single-cell RNA sequencing with tissue cells from biopsy tissue

A visual summary of the major steps involved in the single-cell RNA sequencing platform that was applied to studying tissue cells isolated from biopsies is shown. The major steps are listed sequentially, consisting of 4 indispensable modules: single-cell acquisition, single-cell barcoding (to ensure each single cell is specifically represented by a unique molecular DNA sequence), cDNA library generation, and next-generation sequencing (NGS).

Figure 2.. The proposed short-chain fatty acid (butyrate)-mediated interactome of microbiota, EoE diet, and effector Th2 cells

The FFAR3–short-chain fatty acid (SCFA) axis represents a novel and EoE-specific pathway identified by single-cell RNA sequencing (scRNA Seq) on tissue T cells. This finding could have significant impact on upper gastrointestinal Th2 mechanisms in EoE, as the mucosal immunocyte-luminal content interactome has been little known. The gastrointestinal luminal microbiota provides the source of butyrate as a major metabolite of the butyrate-capable flora. To a certain degree, the diet of a person with eosinophilic esophagitis (EoE) would also contribute to variations in SCFA concentration due to dietary fiber differences. These two factors would also interact with the commensal flora dysbiosis observed in EoE and collectively contribute to the Th2 pathogenesis centered on tissue effector Th2 cells. DC, dendritic cells; peTh2, pathogenic effector Th2.