BCG vaccination at birth shapes the TCR usage and functional gene expression profile of MR1T cells at 9 weeks of age

Tuberculosis (TB) is the leading infectious disease killer worldwide and children suffer disproportionately. The ongoing burden of disease, despite widespread vaccination with BCG, highlights the need for novel vaccines. MR1-restricted T (MR1T) cells recognize small molecules, including microbial-derived molecules, presented by the monomorphic MHC class 1-related molecule (MR1). They have both “innate” effector capacity, allowing them to quickly respond to pathogens including Mycobacterium tuberculosis (Mtb), while also having adaptive features (effector memory cell surface phenotype and selective TCR usage). Feasibility of an MR1T cell-based vaccination remains underexplored and critical to this is whether or not MR1T cells possess the capacity for immunological memory. To begin to address this question, peripheral blood mononuclear cells (PBMC) were collected at 9-weeks of age from healthy term-infants in South Africa, who had either received BCG vaccination at birth (n = 10) or who had BCG vaccination delayed (n = 10). MR1/5-OP-RU tetramer positive cells were sorted using flow cytometry and single-cell RNA and TCR-seq was performed. Ex-vivo MR1T cells from vaccinated infants demonstrated increased expression of type I interferon response genes consistent with a cytokine mediated response to BCG vaccination. Using the TCR clustering algorithm TCRdist3, TCRs predicted to recognize similar antigens were grouped together, revealing a cluster significantly enriched in BCG-vaccinated infants. This cluster exhibited elevated expression of pro-inflammatory and cytotoxic genes, consistent with gene expression patterns driven by a TCR-mediated antigen-selective response to BCG. This work provides the first step in addressing if MR1T cells demonstrate immunological memory, however, further work is needed to understand if these clonal expansions persist and possess the capacity for antigenic recall.