Reprogramming T Cells Through Epigenetic Editing

A 2025 Nature Biotechnology paper by researchers from the Arc Institute, Gladstone Institutes, and UCSF has introduced a revolutionary way to reprogram human T cells without altering their DNA sequence. The team developed an all-RNA epigenetic editing platform that uses molecular “switches” called CRISPRoff and CRISPRon to silence or activate genes by rewriting their epigenetic code, specifically, DNA methylation marks. Unlike traditional CRISPR, which cuts DNA, this system leaves the genome intact, reducing the risks of unwanted mutations or chromosomal breaks.

In their experiments, the scientists delivered mRNA encoding these editors into primary human T cells using electroporation, a standard clinical method also used in CAR-T therapy manufacturing. The editors act briefly but leave behind lasting epigenetic marks that maintain gene silencing or activation over many cell divisions. For example, the team demonstrated that once a gene was “switched off,” it stayed off even after the T cells multiplied and were transferred into mice. This durability stems from how DNA methylation is copied every time the cell divides, allowing the memory of the change to persist.

To show the clinical potential, they combined this epigenetic control with conventional gene engineering. They inserted a chimeric antigen receptor (CAR) into the T-cell genome and simultaneously used CRISPRoff to silence a regulatory gene called RASA2, which normally limits T-cell activity. The result was a more potent CAR-T cell that maintained tumor-killing ability longer in preclinical mouse models. This multiplex approach allows scientists to tune multiple genes at once; boosting therapeutic effect without the genotoxic risks of cutting DNA in several places.

This discovery is significant because it merges the precision of CRISPR with the safety and reversibility of epigenetics. The method could help create more resilient CAR-T therapies for cancers and autoimmune diseases. Beyond therapy, it offers biologists a new way to study how long-term epigenetic memory works in primary human cells: a long-standing challenge in the field. However, open questions remain: not all genes respond equally to methylation, and scientists still need to map which loci can be stably silenced. Future work will also focus on confirming the safety of epigenetic reprogramming in clinical settings and ensuring that off-target effects are minimal.

In short, this all-RNA epigenetic editing technique represents a paradigm shift, turning CRISPR from a molecular scalpel into a programmable dimmer switch for gene expression. By safely and stably reprogramming immune cells, it could pave the way for the next generation of customizable, precision cell therapies.

References:

1. Goudy, L. et al. “Integrated epigenetic and genetic programming of primary human T cells.” Nature Biotechnology(2025).

2. Nuñez, J. K. et al. “Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.” Cell 184, 2503–2519 (2021).

3. “Safe epigenetic reprogramming enables simultaneous multi-gene editing in T cells.” Bioengineer.org (2025).