Function-preserving CD8⁺ T Cell Immunogenicity minimization through protein design

Rapid advances in protein design enable new approaches in adoptive cell therapy, but foreign proteins can elicit cytotoxic T cell responses, and hence there is considerable need for approaches which reduce immunogenicity without compromising protein function. Here, we develop a computational framework integrating structure-guided sequence design with MHC class I epitope prediction to efficiently tune protein immunogenicity while preserving function. Using a de novo-designed luciferase as a model, we demonstrate epitope elimination while preserving function across 5 common mouse alleles and extend our computational optimization to 25 common human MHC-I alleles. In mice immunized with mRNA-lipid nanoparticles, variants designed to have few MHC-I epitopes elicited little detectable CD8⁺ T cell response, whereas variants designed to include multiple epitopes induced robust responses. Together, these results demonstrate that the CD8⁺ T cell immunogenicity of designed proteins can be tuned while preserving function, opening the door to incorporation of designed proteins in a next generation of adoptive cell therapies.