Single-cell RNA sequencing identifies distinct transcriptomic signatures between PMA/ionomycin-and αCD3/ αCD28-activated primary human T cells

Jung Ho Lee, Brian H. Lee, Soyoung Jeong, Christine Suh Yun Joh, Hyo Jeong Nam, Hyun Seung Choi, Henry Sserwadda, Ji Won Oh, Chung Gyu Park, Seon Pil Jin, Hyun Je Kim

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell–derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55+) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.

Original languageEnglish
Article numbere18
JournalGenomics and Informatics
Volume21
Issue number2
DOIs
StatePublished - Jun 2023
Externally publishedYes

Keywords

  • scRNA-seq
  • T cell
  • T cell activation
  • transcriptome

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