Evolutionarily guided transcription factor design programs novel T cell states [scRNA-seq, MULTI-seq]
Protein-coding genes in the human genome evolved via modular rearrangement of domains from ancestral genes. Here, we develop a scalable, evolutionarily guided method to assemble novel protein-coding genes from constituent domains within a protein family, termed DESynR (Domain Engineered via Synthesis and Recombination) factors. Using primary human chimeric antigen receptor-T cells as a model system, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the expression of natural AP-1 TFs in multiple functional assays in vitro and in vivo. Top DESynR AP-1 TFs exhibit non-intuitive architectures of constituent domains, including from TFs that are not canonically expressed in T cells. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming of T cells and in some cases, lead to the development of non-natural T cell states, engaging gene modules from disparate human cell types. Taken together, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutically-relevant functions. Overall design: Live-sorted and MULTI-seq-barcoded human CD19-28z CAR T cells overexpressing various natural and engineered AP-1 transcription factors were analyzed using 5' scRNA-seq (10x Genomics) following repetitive stimulation with Nalm6 targets in vitro.