Integrated epigenetic and genetic programming of primary human T cells [RNA-seq]

Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable, and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations, and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Finally, we successfully combined genetic and epigenetic-engineering using orthogonal CRISPR Cas12a/dCas9 systems for targeted CAR knockin and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR T cell-mediated in vivo tumor control and survival. RNA-sequencing of human primary T cells that have been treated with CRISPRoff mRNA and sgRNAs targeting genes of interest or a NTC. Samples also include primary human T cells that have been treated with nuclease active Cas9 mRNA and sgRNAs targeting genes of interest or a NTC.