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Evolutionarily guided transcription factor design programs novel T cell states [bulkRNA-seq]

ABSTRACT: Evolutionarily guided transcription factor design programs novel T cell states [bulkRNA-seq]

PROVIDER: PRJNA1178726 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31143100_1.fastq.gz	Fastqsanger.gz
	SRR31143100_2.fastq.gz	Fastqsanger.gz
	SRR31143101_1.fastq.gz	Fastqsanger.gz
	SRR31143101_2.fastq.gz	Fastqsanger.gz
	SRR31143102_1.fastq.gz	Fastqsanger.gz

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Evolutionarily guided transcription factor design programs novel T cell states [scRNA-seq, MULTI-seq]

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Evolutionarily guided transcription factor design programs novel T cell states [bulkRNA-seq]

Project description: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.

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Project description:Human protein-coding genes 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) genes. Using primary human chimeric antigen receptor T cells as a model, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the overexpression of natural AP-1 TFs in multiple functional assays in vitro and in vivo. Top DESynR AP-1 TFs exhibit non-intuitive domain architectures, including from TFs not canonically expressed in T cells. 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— in some cases co-opting gene expression modules from disparate cell types. We show that this reprogramming is primarily driven by differential regulation of established AP-1-bound regulatory elements, rather than unique binding. Finally, we extend the DESynR methodology to Erythroblast Transformation Specific (ETS) and Forkhead box (FOX) TFs to support the generalizability across protein families. Overall, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutic relevance.

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