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bioRxiv · 10.1101/2025.10.12.681819

Geometric Tuning of Cytokine Receptor Association Modulates Synthetic Agonist Signaling

Exposit, M.·Abedi, M.·Krishnakumar, A.·Jain, S.·Yu, T.-Y.·Hercus, T. R.·Mathew, D.·Gray-Gaillard, S.·Chen, Z.·Grubbe, W. S.·Favor, A.·Kan, W. L.·Schlichthaerle, T.·Chen, W.·Parker, M. W.·Mendoza, J. L.·Lopez, A. F.·Wherry, E. J.·Baker, D.
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Abstract

Cytokines signal by bringing receptor subunits together, but the role of receptor geometry in shaping signaling remains unclear because natural ligands enforce fixed assemblies. Here, we present a de novo protein design platform that rigidly scaffolds receptor-binding domains into defined spatial arrangements. Applying this across IL-7, type I and III interferons, IL-10, gp130, {beta} common, and synthetic receptor pairs, we show that by varying geometry, we can bias pSTAT pathway usage and tune functional outcomes. Geometric control allowed us to decouple pSTAT1 from pSTAT5 in IL-7, separate antigen presentation (MHC-I) from checkpoint induction (PD-L1) in type I interferons, and suppress pro-inflammatory IFN{gamma} secretion while retaining anti-inflammatory activity in IL-10. We further created minimal IL-6 and IL-3 agonists and strengthened synthetic receptor pairings inaccessible with present cytokines. These results establish receptor geometry as a central determinant of cytokine activity and provide a platform for programmable immune modulation.

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Exposit, M., Abedi, M., Krishnakumar, A., Jain, S., Yu, T.-Y., Hercus, T. R., Mathew, D., Gray-Gaillard, S., Chen, Z., Grubbe, W. S., Favor, A., Kan, W. L., Schlichthaerle, T., Chen, W., Parker, M. W., Mendoza, J. L., Lopez, A. F., Wherry, E. J., Baker, D.. 2025-10-13. Geometric Tuning of Cytokine Receptor Association Modulates Synthetic Agonist Signaling. https://doi.org/10.1101/2025.10.12.681819

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