Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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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 (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Brian H Lee (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Soyoung Jeong (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Christine Suh-Yun Joh (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Hyo Jeong Nam (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Hyun Seung Choi (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Henry Sserwadda (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Ji Won Oh (Department of Anatomy, Yonsei University College of Medicine) ;
  • Chung-Gyu Park (Department of Biomedical Sciences, Seoul National University Graduate School) ;
  • Seon-Pil Jin (Department of Dermatology, Seoul National University Hospital) ;
  • Hyun Je Kim (Department of Biomedical Sciences, Seoul National University Graduate School)
  • Received : 2023.02.09
  • Accepted : 2023.04.03
  • Published : 2023.06.30
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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.

Keywords

Acknowledgement

This work was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science & ICT (2022M3A9D3016848), and by the Basic Science Research Program through the National Research Foundation (NRF) funded by the Ministry of Education (2020R1F1A1073692 and 2022R1F1A1075235).

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