Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

Nat Commun. 2020 Apr 14;11(1):1801. doi: 10.1038/s41467-020-15543-y.

Abstract

Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, bulk RNA-seq, and single-cell RNA-seq of over 40,000 human naïve and memory CD4+ T cells to show that responses to cytokines differ substantially between these cell types. Memory T cells are unable to differentiate into the Th2 phenotype, and acquire a Th17-like phenotype in response to iTreg polarization. Single-cell analyses show that T cells constitute a transcriptional continuum that progresses from naïve to central and effector memory T cells, forming an effectorness gradient accompanied by an increase in the expression of chemokines and cytokines. Finally, we show that T cell activation and cytokine responses are influenced by the effectorness gradient. Our results illustrate the heterogeneity of T cell responses, furthering our understanding of inflammation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CD28 Antigens / metabolism
  • CD4-Positive T-Lymphocytes / drug effects
  • CD4-Positive T-Lymphocytes / immunology*
  • Cell Polarity / drug effects
  • Cytokines / pharmacology*
  • Gene Expression Regulation / drug effects
  • Humans
  • Lymphocyte Activation / drug effects
  • Lymphocyte Activation / immunology
  • Male
  • Middle Aged
  • Principal Component Analysis
  • Proteome / metabolism
  • Receptors, Antigen, T-Cell / metabolism
  • Single-Cell Analysis*
  • Transcriptome / drug effects
  • Transcriptome / genetics*

Substances

  • CD28 Antigens
  • Cytokines
  • Proteome
  • Receptors, Antigen, T-Cell