Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells

Abstract

Naive CD4 + T cells differentiate into functionally diverse T helper (Th) cell subsets. Th2 cells play a pathogenic role in asthma, yet a clear picture of their transcriptional profile is lacking. We performed single-cell RNA sequencing (scRNA-seq) of T helper cells from lymph node, lung, and airways in the house dust mite (HDM) model of allergic airway disease. scRNA-seq resolved transcriptional profiles of naive CD4 + T, Th1, Th2, regulatory T (Treg) cells, and a CD4 + T cell population responsive to type I interferons. Th2 cells in the airways were enriched for transcription of many genes, including Cd200r1, Il6, Plac8, and Igfbp7, and their mRNA profile was supported by analysis of chromatin accessibility and flow cytometry. Pathways associated with lipid metabolism were enriched in Th2 cells, and experiments with inhibitors of key metabolic pathways supported roles for glucose and lipid metabolism. These findings provide insight into the differentiation of pathogenic Th2 cells in the context of allergy.

Distinct functions of tissue-resident and circulating memory Th2 cells in allergic airway disease

“…We took this approach to avoid fixation and permeabilization, which is required for intranuclear staining for FoxP3 (to exclude T reg cells) and GATA3 (to identify Th2 cells). Rather, we used YFP fluorescence to exclude T reg cells and the IL-33 receptor ST2 to identify Th2 cells, the latter marker having been shown to be a reliable surface marker for Th2 cells in the murine HDM model (Tibbitt et al, 2019). Along with the above memory Th2 cell populations, we also sorted YFP − ST2 − CD4 + T cells from the lung and YFP − ST2 − CD44 + CD4 + T cells from SLO as control populations of non-Th2 cells.…”

“…A recent study performing single-cell RNA-seq analysis on CD4 + T cells from the primary HDM model demonstrated that effector Th2 cells within the lung are a predominant source of IL-6 and also identified several Th2-specific transcripts, including Pparg, Cd200r1, Igfbp7, and Plac8 (Tibbitt et al, 2019). PPARγ has been shown to be required for effective induction of IL-5 and IL-13 in effector Th2 cells (Angela et al, 2016;Chen et al, 2017;Nobs et al, 2017;Tibbitt et al, 2019). However, whether these Th2 cell-specific genes are expressed in the memory phase and the relative expression within Th2 Trm cells and circulating memory Th2 cells is not known.…”

Single-Cell Analysis of Foot-and-Mouth Disease Virus

“…To date, breakthroughs in single-cell analyses, especially single-cell omics, have been important milestones for some fields, including immunology, cancer, stem cells and virology (Cristinelli and Ciuffi, 2018;Suva and Tirosh, 2019;Tibbitt et al, 2019;Zhou et al, 2019). In the field of virology, singlecell sequencing technologies have allowed the investigation of unresolved issues such as the characterization of gene expression profiles in individual infected versus bystander cells in the mixed bulk population.…”

Single-cell transcriptomics of allo-reactive CD4+ T cells over time reveals divergent fates during gut GVHD

“…ScRNA-seq was previously employed to examine heterogeneity in CD4 + T cells isolated from IL-17a reporter mice undergoing experimental autoimmune encephalomyelitis (EAE) (7). Subsequently, scRNA-seq was used to examine CD4 + T cell differentiation during house dust mite-induced allergy (8), protozoan parasite infection (9), as well as CD8 + T cells in viral infections and cancer (10–12). Many of these studies were cross-sectional, offering insight into heterogeneity amongst clonal TCR transgenic cells at a single timepoint.…”