Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome

Beusch, C. M.; Dawood, A. S.; Ozdilek, A.; Welbourn, S. L.; Flegle, A.; Malik, S.; Niavi, C.; Akhtar, A.; Roman, C.; Gavora, A. A.; Gordon, D. E.; Abdel-Hakeem, M. S.

doi:10.1101/2024.05.14.593504

bioRxiv · 10.1101/2024.05.14.593504

Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome

Beusch, C. M.·Dawood, A. S.·Ozdilek, A.·Welbourn, S. L.·Flegle, A.·Malik, S.·Niavi, C.·Akhtar, A.·Roman, C.·Gavora, A. A.·Gordon, D. E.·Abdel-Hakeem, M. S.

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Abstract

CD8 T cell exhaustion impedes immune responses to cancer and chronic infections, and a biochemical understanding of exhaustion is essential to improving immunotherapy. Here, we present the first longitudinal protein abundance and phosphoproteomic analysis of antigen-specific CD8 T cells undergoing differentiation in vivo during acute (LCMV-Armstrong) and chronic (LCMV-Clone 13) infection. Comparing protein abundance across the two infection conditions identified over 180 known and novel exhaustion-associated proteins, including proteins missed by transcriptional analyses. Phosphoproteomic analysis identified >900 differentially regulated phosphosites on >400 proteins, including known inhibitory phosphosites on PD1, PAG1, SHP-1/PTPN6, SLAMF1/CD150. We also calculated phosphosite conservation across mammals, to direct follow-up studies towards sites with likely essential function. Lastly, our analysis uncovers exhaustion-associated kinases with clinical-stage inhibitors, underscoring the translational utility of our dataset to guide immunotherapy development. Together, our datasets define a biochemical atlas of T cell exhaustion in vivo, shedding light on the molecular mechanisms of T cell dysfunction.

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Beusch, C. M., Dawood, A. S., Ozdilek, A., Welbourn, S. L., Flegle, A., Malik, S., Niavi, C., Akhtar, A., Roman, C., Gavora, A. A., Gordon, D. E., Abdel-Hakeem, M. S.. 2024-05-15. Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome. https://doi.org/10.1101/2024.05.14.593504

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