Mapping the dynamic RNA binding proteome in human effector T 1 cells identifies differentiation and cytotoxicity regulators

Lattanzio, M. V. M.; Rooijers, K.; Bresser, K.; Bradaric, A.; Kanagasabesan, N.; Sostaric, N.; Nestor Martin, M.; Servaas, N. H.; Van Alphen, F. P. J.; Hoogendijk, A. J.; Wolkers, M. C.

doi:10.64898/2025.12.05.692493

bioRxiv · 10.64898/2025.12.05.692493

Mapping the dynamic RNA binding proteome in human effector T 1 cells identifies differentiation and cytotoxicity regulators

Lattanzio, M. V. M.·Rooijers, K.·Bresser, K.·Bradaric, A.·Kanagasabesan, N.·Sostaric, N.·Nestor Martin, M.·Servaas, N. H.·Van Alphen, F. P. J.·Hoogendijk, A. J.·Wolkers, M. C.

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Abstract

RNA-binding proteins (RBPs) are key regulators of T cell function by controlling (m)RNA fate and fine-tuning protein expression dynamics. Dysregulated RBPs can drive immune diseases and malignancies, highlighting their potential as therapeutic targets. To achieve this, a systematic analysis of the dynamic RBP-RNA interactions is required. Here, we mapped the RNA-binding proteome in human T cells and measured its alterations upon T cell activation using orthogonal organic phase separation (OOPS), analysed with PROMOGEB, a Bayesian linear regression model. This approach uncovered the intricate RNA-binding dynamics of the RBProteome. Gene-editing of such dynamic RNA binders revealed that TUT1 (Star-PAP) maintains the integrity of the T cell differentiation program, and that mutating SF3A1 enhanced the cytotoxic molecule expression and thus target cell killing. Our work provides the most comprehensive analysis of the effector T cell RBProteome to date and shows the potential of identifying RBPs and their binding dynamics as therapeutic agents. TeaserOOPS analysed with PROMOGEB maps RBP dynamics in human Teff cells, identifying TUT1 and SF3A1 as regulators of T cell fidelity.

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Lattanzio, M. V. M., Rooijers, K., Bresser, K., Bradaric, A., Kanagasabesan, N., Sostaric, N., Nestor Martin, M., Servaas, N. H., Van Alphen, F. P. J., Hoogendijk, A. J., Wolkers, M. C.. 2025-12-09. Mapping the dynamic RNA binding proteome in human effector T 1 cells identifies differentiation and cytotoxicity regulators. https://doi.org/10.64898/2025.12.05.692493

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