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

Immunity. 2019 Jul 16;51(1):169-184.e5. doi: 10.1016/j.immuni.2019.05.014. Epub 2019 Jun 20.


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.

Keywords: ATAC-seq; T helper; Th2; asthma; house dust mite; interleukin; metabolism; single-cell RNA Sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Dermatophagoides / immunology
  • Asthma / immunology*
  • Disease Models, Animal
  • Humans
  • Lipid Metabolism / genetics
  • Mice
  • Mice, Inbred C57BL
  • Mice, Knockout
  • Orexin Receptors / genetics
  • Pyroglyphidae / immunology
  • Respiratory Hypersensitivity / immunology*
  • Respiratory System / immunology*
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • T-Lymphocyte Subsets / immunology*
  • Th2 Cells / immunology*
  • Transcriptome


  • Antigens, Dermatophagoides
  • Cd200r1 protein, mouse
  • Orexin Receptors