Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine

Abstract

RNA-based vaccines against SARS-CoV-2 are critical to limiting COVID-19 severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. We used single-cell technologies to identify and characterized antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 in a longitudinal cohort of healthy donors. Mass cytometry and machine learning pinpointed a novel expanding, population of antigen-specific non-canonical memory CD4+ and CD8+ T cells. B cell sequencing suggested progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlated with eventual SARS-CoV-2 IgG and a donor lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms reveal an antigen-specific cellular basis of RNA vaccine-based immunity.

Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine

“…The discovery of similarities in clonal antigen-specific antibody sequences between our two subjects and with those of published SARS-CoV-2 antibodies from CoV-AbDab suggests that vaccination induces the development of antibody clonotypes with antigen specificity and variable region sequences that are similar to those found during natural infection. Moreover, it supports the case for convergent antibody maturation that has also been observed in uninfected mRNA vaccinees [ 21 , 22 , 32 ].

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“…Vaccination of healthy (no prior COVID-19 history) individuals has been shown to induce the production of antibodies that undergo clonal expansion and that are homologous to known SARS-CoV-2 targeting antibodies elicited during natural viral infection [ 21 , 32 ]. To determine whether these phenomena would similarly be observed in convalescent COVID-19 subjects, we compared the clonal structure of BCR repertoires of SARS-CoV-2 Spike-specific B cells in both individuals before and after vaccination.…”

“…Matching B cell heavy chain V and J genes and assessing sequence similarity in the heavy chain CDR3 (CDRH3) region are criteria typically used to identify similar B cell clonotypes in different subject cohorts [ 19 , 21 , 22 , 32 , [34] , [35] , [36] , [37] , [38] ]. Clonotypes from both naïve BNT162b2 vaccinees [ 21 , 22 , 32 ] and convalescent unvaccinated individuals [ 19 , [34] , [35] , [36] , [37] , [38] ] have been found to be homologous with published antibodies and/or amongst different individuals based on the above criteria, showing convergent development of conserved variable region genes and sequences that work to target SARS-CoV-2. Many of these clonotypes have been identified to specifically target RBD, with subsets of these antibody clones shown to be neutralizing [ 32 , 34 , 36 ].…”

“…Many studies have separately assessed the effects of both natural SARS-CoV-2 infection [ [17] , [18] , [19] , [20] ] and prophylactic mRNA vaccination [ 17 , [20] , [21] , [22] , [23] ] on B cell populations by single-cell RNA sequencing. These next-generation sequencing technologies have facilitated the elucidation of clonality amongst specific B cell subsets [ 17 , 20 ], as well as the detection of sequence homologies amongst published SARS-CoV-2 clonotypes [ 21 ] within and between subject cohorts. However, there has been limited research thus far utilizing these techniques to analyze B cell responses in convalescent COVID-19 vaccinees.…”

What Happens to the Immune System after Vaccination or Recovery from COVID-19?

“…Exploring this technology, Kramer and colleagues analyzed the single-cell profiling of the mRNA-based vaccine BNT162b2 (Pfizer-BioNTech) antigenic response. Data revealed a novel expanding population of non-canonical memory CD4 and CD8 T-cells following vaccination [80]. In addition, Cao and colleagues also explored this technique and described the immune dynamics during immunization with the viral vector based-vaccine Ad5-nCoV that revealed enhanced cellular immunity and boosted SARS-CoV-2 specific antibodies [81].…”