Expansion of memory Vδ2 T cells following repeated BNT162b2 mRNA-based vaccine revealed by temporal single-cell transcriptomics

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a novel Coronavirus, whose infection causes Coronavirus Disease-2019 (COVID-19). SARS-CoV-2 mRNA-based vaccines have been shown to have high clinical efficacy, providing robust protection against the onset of the severe form of the COVID-19 disease and limiting the virus's spread. Although the humoral and adaptive immune responses following BNT162b2 vaccination have been investigated in depth, the involvement of innate immunity, with a focus on gamma delta (γδ) T cells and their mRNA-based vaccines’ transcriptional changes following immunization remain poorly understood. Herein, by using high-throughput technologies and unsupervised learning algorithms combining single-cell RNA sequencing (scRNA-seq) with single-cell γδ TCR-sequencing (γδ scTCR-seq), we longitudinally depicted the transcriptional changes of γδ T cells in the peripheral blood of a cohort of six healthy subjects naïve for the SARS-CoV-2 infection, investigating the temporal and subject heterogeneous composition of γδ TCR repertoire, before and after the administration of two doses of BNT162b2 vaccine. At single-cell resolution, different Vδ2 T cell populations show multiple grades of responsiveness to the SARS-CoV-2 vaccine: while the first dose of mRNA SARS-CoV-2 vaccine induces the priming of Vδ2 T cells, the second administration significantly boosts their immune response, with a rapid adaptation of activating profiles defined by immune modulation, proliferation, and cytotoxicity. Specifically, the double vaccination uncovers memory features of Vδ2 T cells shaped by the pronounced induction of AP-1 family transcription factors and characterized by a convergent central memory signature, clonal expansion, and enhanced effector potential. This temporally distinct effector response of Vδ2 T cells was also confirmed in vitro upon stimulation with SARS-CoV-2 spike-peptides. Indeed, the second challenge triggers a significantly higher production of IFNγ by Vδ2 T cells. Taken together, our findings indicate that repeated vaccination might benefit from the establishment of long-lasting central memory Vδ2 T cells to possibly confer protection against SARS-CoV-2 infection.