The expansion of adaptive-like NK cells following BNT162b2 vaccination contributes to the vaccine-induced protection against SARS-CoV-2 infection

SARS-CoV-2 mRNA vaccines are revolutionizing the field of vaccinology thank to their safety, efficacy, rapid development and low-cost manufacture. Specifically, formulations such as the Pfizer-BioNTech mRNA vaccine BNT162b2 (Comirnaty) can stimulate a robust antibody response to the SARS-CoV-2 Spike protein and can confer great protection against the natural infection. However, despite its high immunogenicity, the memory responses and the antibody-mediated protection induced upon this mRNA vaccine administration wan already 6 months after the second dose administration. Still, vaccinated subjects have a reduced infection risk and a lower probability to develop severe COVID-19 disease, probably due to other protective immune mechanisms. Among immune cells, Natural Killer (NK) cells are a group of cytotoxic lymphocytes which are pivotal in controlling viral infections thanks to their ability to target infected cells. Despite they have always been considered innate lymphocytes, NK cells stimulation can induce their maturation toward adaptive or ”memory-like” subsets endowed with greater functional abilities against a second challenge. Therefore, they can play an important role in the vaccine-induced protection against viral infections. To investigate the impact of the Pfizer-BioNTech mRNA vaccine BNT162b2 administration on the NK cell compartment, we employed a longitudinal computational profiling by single-cell RNA sequencing analysis of six SARS-CoV2-naïve individuals. We identified six phenotypically distinct NK cell clusters which all harbor an activated profile following the vaccine infusion. However, despite being stimulated soon after the first dose infusion, these cells respond better following a second vaccine injection, as this additional administration induces greater differential gene expression compared to the first one. Interestingly, pseudotime analysis showed how a second vaccine challenge induces a potent NK cell maturation toward a more adaptive phenotype. Accordingly, we performed a pathway enrichment assay to better understand the contribution of the differentially expressed genes (DEGs) to the observed NK cell activation and maturation processes. In line with previous findings on SARS-CoV-2-infected subjects, type I and II IFNs, Toll-like receptors cascade and pro-inflammatory cytokine pathways are engaged upon these cells’ recognition of the mRNA-vaccine and, thus, they contribute to the protective anti-viral response mounted by these innate immune cells. Collectively, our data highlights the importance of a second dose administration of the BNT162b2 (Comirnaty) vaccine to stimulate a stronger immune response against the SARS-CoV2 infection and highlights a central role of the non-conventional NK cell “memory” for the vaccine-induced protection against the virus. Further investigation is warranted to disclose the real involvement of these adaptive NK cells in controlling SARS-CoV-2 infection.