Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis

Mead, H. L.; Kirschman, J. H.; Harms, C. E.; Kelley, E. J.; Soria-Bustos, J.; Nelson, G. A.; Ogongo, P.; Ouma, G.; Ouma, S. G.; Ernst, J. D.; Altin, J. A.

doi:10.1101/2024.11.05.622086

bioRxiv · 10.1101/2024.11.05.622086

Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis

Mead, H. L.·Kirschman, J. H.·Harms, C. E.·Kelley, E. J.·Soria-Bustos, J.·Nelson, G. A.·Ogongo, P.·Ouma, G.·Ouma, S. G.·Ernst, J. D.·Altin, J. A.

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Abstract

Immunity to Mycobacterium tuberculosis (Mtb), like many pathogens, is encoded jointly by the antigen specificities and functions of responding CD4 T cells. However, these features span a large two-dimensional possibility space - defined on one axis by the Mtb proteome, and on the other by the T cell transcriptome - that exceeds the dimensionality of existing technologies. Here we present an approach ("CRESTA") that combines highly-multiplexed DNA-barcoded epitope probes, single cell sequencing, and clonal analysis of T Cell Receptors (TCRs) to robustly detect rare antigen-specific CD4 T cells across hundreds of epitopes simultaneously and reveal their transcriptome-wide phenotypes. By comprehensively assaying known epitopes in Mtb-infected participants, we reveal polyclonal and multi-epitope responses across a spectrum of differentiation states, uncover previously-unobserved phenotypic diversity within and between epitopes, and increase the total number of known Mtb epitope-mapped TCR:{beta}s by [~]8-fold. We expect CRESTA to enable high-dimensional analyses of CD4 T cell responses in various settings, including infection, cancer, autoimmunity and allergy.

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Mead, H. L., Kirschman, J. H., Harms, C. E., Kelley, E. J., Soria-Bustos, J., Nelson, G. A., Ogongo, P., Ouma, G., Ouma, S. G., Ernst, J. D., Altin, J. A.. 2024-11-08. Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis. https://doi.org/10.1101/2024.11.05.622086

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