Atomistic TCR-ligand interactions instruct memory T-cell differentiation

Akitsu, A.; Tan, K.; Mallis, R. J.; Booker, M. A.; Duke-Cohan, J. S.; Brazin, K. N.; Kirkpatrick, E. H.; Parkins, A. N.; Aryal, S.; Cinella, V.; Lee, J. J.; Uberoy, K. I.; Koenig, J. K.; Biddle, M.; Messier, C. M.; Lizotte, P. H.; Tolstorukov, M. Y.; Hwang, W.; Lang, M. J.; Reinherz, E. L.

doi:10.1101/2025.11.05.686789

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bioRxiv · 10.1101/2025.11.05.686789

Atomistic TCR-ligand interactions instruct memory T-cell differentiation

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Abstract

Memory CD8 T cells provide durable protection against recurrent infection and cancer, but how distinct memory fates are specified remains unclear. Here, we define the functional landscape of 242 murine CD8 TCR{beta} clonotypes specific for influenza NP366-374/H-2D ligand (pMHC) by integrating single-cell transcriptomics and TCR sequencing with force-dependent biophysics, structural analysis, and in vivo investigation of memory development. Fate essentially tracks with TCR mechanotransduction: TCM-associated clonotypes preferentially engage pMHC through TCR{beta}, whereas TEM-associated clonotypes preferentially engage through TCR. Clonotypes with balanced, bipolar signaling generate both memory subsets, optimize expansion, and display broad heterosubtypic crossreactivity but with exhaustion susceptibility. In contrast, diverse TCM clonotypes are largely clonal singlets with considerable mutant-epitope recognition in aggregate and stemness preservation, revealing complementary strategies for immunodefense coverage. Atomistically, subtle pMHC contact differences and load transmission through the TCR holoreceptor appear to tune phosphorylation, memory differentiation, and functional durability, features applicable to adoptive T-cell immunotherapies.

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Akitsu, A., Tan, K., Mallis, R. J., Booker, M. A., Duke-Cohan, J. S., Brazin, K. N., Kirkpatrick, E. H., Parkins, A. N., Aryal, S., Cinella, V., Lee, J. J., Uberoy, K. I., Koenig, J. K., Biddle, M., Messier, C. M., Lizotte, P. H., Tolstorukov, M. Y., Hwang, W., Lang, M. J., Reinherz, E. L.. 2025-11-06. Atomistic TCR-ligand interactions instruct memory T-cell differentiation. https://doi.org/10.1101/2025.11.05.686789

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