Systems biological assessment of T cell responses to vaccination

ABSTRACT - Project 2 The goal of Project 2 is to assess T cell responses in the context of proposed studies of: (i) COVID-19 vaccines that utilize novel platforms (mRNA) or adjuvants (Matrix M used in the Novavax vaccine) and (ii) Humans given broad spectrum antibiotics that disrupt their microbiome, prior to and during rabies vaccination. This goal is highly synergistic with those of Projects 1 and 3, which will evaluate innate and B cell responses respectively, in the context of the same clinical trials. We will use new developed state-of-the-art techniques that will allow us to probe the vaccine responses here with an unprecedented scale and depth. The three methods are: (1) spheromer probes for specific T cells, (2) GLIPH (for Grouping of Lymphocyte Interactions by Paratope Hotspots) analysis of TCR specificity groups, and (3) immune organoids. We will apply these tools in the following aims: Aim 1: Assessment of T cell responses to vaccination against COVID-19. Sub-aim 1a. Analyze T cell responses induced by the BNT162b2 mRNA vaccine in healthy versus atopic individuals. We will use the spheromer technology mentioned above, to create and use a panel of pMHC Spheromers SARS-CoV-2 spike epitopes covering the major class I and II HLA alleles, to analyze the T cell response, in healthy versus atopic subjects. In addition, we will perform TCR repertoire analysis using GLIPH2 to analyze both bulk and single cell TCR sequences in order to define the frequency, phenotype, function and TCR diversity of antigen specific T cell responses to primary and secondary vaccination in blood and the draining lymph nodes of both healthy adults and allergy prone subjects. Sub-aim 1b: Assessment of T cell responses induced by the Novavax Matrix-M adjuvanted subunit vaccine. We will also analyze samples collected from a Novavax sponsored trial done at the University of Witwatersrand with spheromers and TCR sequence analysis and determine how the response to an adjuvanted subunit vaccine differs from that induced by mRNA vaccination Aim 2: Assessment of the impact of the microbiota on the antigen-specific T cell response to vaccination. We will assess the impact of broad-spectrum antibiotics on the primary T cell response to rabies vaccination. In particular, we will analyze the TCR repertoire and phenotype of T cells responding to this vaccine, since there are clear indications that the microbiome can influence T cell phenotype, and we hypothesize that there might be an influence on the repertoire as well.