Systemic profiling of immune responses in healthy adults vaccinated with an RBD-targeting COVID-19 mRNA vaccine

Coronavirus disease 2019 (COVID-19) messenger RNA (mRNA) vaccines have succeeded unprecedentedly due to high protection efficacy and robust immune response. The most widely vaccinated mRNA vaccines are severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein targeting with modified mRNAs. Immune response to other types of mRNA vaccines remains less investigated. Here, we comprehensively profiled human immune responses elicited by ARCoV, a non-modified mRNA vaccine encoding the receptor-binding domain (RBD) of the S protein, using multifaceted approaches. ARCoV vaccination induced potent neutralizing antibodies, RBD-specific polyfunctional T cell responses, and elevated cytokines including C-X-C motif chemokine ligand 10 (CXCL10), interferon-gamma (IFN-γ), extracellular newly identified receptor for advanced glycation end-products binding protein (EN-RAGE), and interleukin-18 (IL-18). Single-cell sequencing revealed that ARCoV immunization induced an increased relative abundance of interferon-activated T cells, proliferative T cells and naïve T cells. Monocytes and dendritic cells exhibited innate immune activation, downregulated hypoxia and glycolysis pathways, and transiently decreased proportions. Integrative single-cell RNA and T cell receptor (TCR) sequencing identified clonal expansion of effector T cells and killer cell immunoglobulin-like receptor (KIR)-expressing natural killer (NK)-like cells after the second dose. These insights advance our understanding of COVID-19 mRNA vaccine immunology and inform next-generation vaccine design.