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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 
 Genomics & Informatics, Vol.21(2) : e18, 2023-06 
Journal Title
Genomics & Informatics
Issue Date
T cell ; T cell activation ; scRNA-seq ; transcriptome
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. © 2023 Korea Genome Organization.
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1. College of Medicine (의과대학) > Dept. of Anatomy (해부학교실) > 1. Journal Papers
Yonsei Authors
Oh, Ji Won(오지원) ORCID logo https://orcid.org/0000-0001-5742-5120
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