MI2025 – Dongyun Lu

Title:
Single-Cell RNA Sequencing Reveals High-Avidity Antigen-Specific CD4⁺ T Cells

Abstract:
CD4⁺ T cells are central orchestrators of immune responses in the context of infection and vaccinations, yet the molecular determinants of potent CD4⁺ T-cell responses remain largely unclear. We have established an assay to assess the TCR avidity of antigen-specific CD4+ and CD8+ T cells by analyzing the expression of the transcription factor IRF4, induced by SARS-CoV-2 infection and mRNA vaccinations. In this study, we aimed to define their transcriptional and T-cell receptor (TCR) features at single-cell resolution. To this end, we analyzed spike protein-specific CD4⁺ T cells in subjects at post-2nd dose of the BNT162b2 mRNA vaccine. PBMCs were cultured with SARS-CoV-2 spike protein for 24 hours, and specific CD4+ T cells were sorted as cells expressing activation-induced markers (AIM), followed by analysis with single-cell RNA and paired TCR sequencing. We found that high-avidity CD4⁺ T cells were clearly separated on the gene expression (GEX) UMAP space. High-avidity CD4⁺ T cells are exhibited stronger expression of TCR signaling and proliferation-related genes, with greater clonal expansion. The TCR repertoire analysis revealed minimal overlaps with low-avidity T cells, indicating that high-avidity T cells do not merely represent a highly activated status. Moreover, high-avidity CD4⁺ T cells were enriched with public clonotypes that exist in more than 2 individuals. Collectively, these findings highlight the unique biological features of high-avidity CD4⁺ T cells, and thus provide important insights into the conceptual framework for the generation of T cell–targeted vaccines.

Biography:
I graduated from Shanghai Jiao Tong University in 2022, majoring in Biotechnology. With a great interest in infectious diseases, especially COVID-19. I have been enrolled as a master student in Kyoto University since 2024.