Oliver Takacsi-Nagy, Sivakanthan Kasinathan, Austin Hartman, Yajie Yin, Lujing Wu, Andy Y Chen, Laura M Moser, Audre P May, Gabriella C Reeder, Emily Celallos Fuentes, Courtney Kernick, Johnathan Lu, Alison K McClellan, Colin J Raposo, Brendan Terrall, Nicole E Theberath, Patrick K Yan, Peng Xu, Elena Sotillo, Justin Eyquem, Crystal L Mackall, Theodore L Roth, Ansuman T Satpathy
Human protein-coding genes evolved via rearrangement of domains from ancestral genes. We develop a scalable, evolutionarily guided method to assemble novel genes from constituent domains within a protein family, termed DESynR (domain engineered via synthesis and recombination) genes. In primary human T cells, DESynR activator protein-1 (AP-1) transcription factors (TFs) significantly outperform natural AP-1 TFs across in vitro and in vivo antitumor assays. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming and establish non-natural T cell states that optimize features of exhaustion, effector and cytotoxic function, and persistence-sometimes co-opting gene modules from disparate cell types. Reprogramming is primarily driven by differential regulation of established AP-1-bound regulatory elements rather than unique binding. Finally, we screen DESynR erythroblast transformation-specific (ETS) and forkhead box (FOX) TFs to support generalizability across protein families. Overall, we demonstrate that reconfiguring existing protein domains may uncover non-evolved genes that program therapeutically relevant cell states.