In a stunning leap forward for immunotherapy, researchers from the Arc Institute, Gladstone Institutes, and the University of California, San Francisco have unveiled a groundbreaking epigenetic editing platform that redefines the genetic programming of human T cells. Published in the prestigious journal Nature Biotechnology on October 21, 2025, this innovative approach combines cutting-edge CRISPR technologies—dubbed CRISPRoff and CRISPRon—to modify multiple genes in primary human T cells, offering a safer and more scalable pathway toward next-generation cell therapies.
The promise of T cell–based therapies, particularly those involving chimeric antigen receptor (CAR) T cells, has revolutionized treatment modalities for blood cancers. However, their application against solid tumors remains fraught with challenges. Solid tumors establish a hostile microenvironment that leads to T cell overstimulation and subsequent exhaustion, limiting therapeutic efficacy. Traditional methods that utilize CRISPR to engineer complex “armored” T cells by editing multiple genes simultaneously have met a recurring obstacle: the toxicity resulting from double-stranded DNA breaks. Such damage frequently triggers cell death or impairs cell function, severely hampering the development of effective therapies for solid tumors.
The newly developed epigenetic editing platform circumvents these problems by harnessing the power of epigenetic modifications rather than direct genomic cuts. CRISPRoff, a novel reagent, selectively deposits methylation marks on gene promoters, thereby silencing genes without altering the underlying DNA sequence. Conversely, CRISPRon removes these methylation marks to reactivate gene expression. This programmable and reversible gene regulation charts a paradigm shift by enabling multiplexed gene modifications—up to five genes simultaneously—without compromising T cell viability. The result is the generation of T cells that “remember” desired gene expression patterns long term, even through numerous cell divisions and immune triggers.
Luke Gilbert, a core investigator at the Arc Institute and Associate Professor at UCSF, articulated the significance: “The T cells essentially memorize our programming instructions. We deliver the epigenetic editors transiently for just a few days, yet the epigenetic modifications persist robustly, enabling stable gene silencing across prolonged cellular expansion.” This stability makes it possible to enhance T cells sustainably without the collateral damage inherent in traditional gene-editing techniques.
To validate this platform’s therapeutic potential, the research team engineered CAR-T cells combining two genetic approaches. First, a cancer-specific receptor was introduced via targeted DNA insertion, ensuring precise antigen recognition. Concurrently, CRISPRoff was deployed to epigenetically silence RASA2, a gene known to act as an inhibitory molecular brake on T cell activation. This elegant dual programming created an enhanced CAR-T cell subtype with superior functionality. In sequential laboratory assays, these dual-engineered T cells sustained their tumor-killing capacity long after control CAR-T cells had succumbed to exhaustion.
In vivo experiments corroborated these findings: in murine models of leukemia, the epigenetically enhanced CAR-T cells demonstrated significantly improved tumor clearance and survival benefits compared to conventional CAR-T cells. This result heralds a potential breakthrough in overcoming intrinsic resistance mechanisms that undermine CAR-T efficacy, particularly in solid tumors where immunosuppression is rampant.
Co-senior author Alex Marson, director of the Gladstone-UCSF Institute of Genomic Immunology, emphasized the transformative nature of integrating genetic and epigenetic engineering modalities. “Our strategy empowers T cells not only to identify and target cancer cells but to modulate the intensity of their anti-cancer activity with precision,” he explained. “This dual-layered programming framework elevates the sophistication of T cell therapies, promising more customizable and effective interventions.”
First author Laine Goudy, a doctoral candidate working in collaboration with Gilbert and Marson, underscored the translational potential: “Our data strongly support advancing this approach into clinical trials. By enabling scalable, multiplexed gene programming without DNA damage, CRISPRoff technology addresses a critical bottleneck in manufacturing complex cellular therapies.”
Beyond oncology, this epigenetic editing platform opens avenues for treating autoimmune diseases, improving transplant compatibility, and managing chronic infections by reprogramming T cells to execute finely tuned immunoregulatory functions. Importantly, the protocol is compatible with established CAR-T cell manufacturing workflows, requiring only adaptation to clinical-grade reagents. The research consortium is actively exploring translational steps to evaluate safety and efficacy in human trials.
Reflecting on the arduous development path, Gilbert noted, “We encountered substantial challenges early on, particularly in adapting epigenetic editing to T cells, which are notoriously sensitive. Years of optimization refined the method into a robust, reliable tool that holds transformative potential.” The success marks a pivotal advance that could overcome longstanding limitations in immunotherapy, especially against the formidable obstacle of solid tumors.
The collaborative effort featured additional co-senior authors Brian Shy, Associate Professor at UCSF and director of the Investigational Cell Therapy Program; Justin Eyquem, Associate Professor in UCSF’s Department of Microbiology and Immunology; and Alex Marson himself, who is also a senior investigator at Gladstone. Together, they represent an interdisciplinary convergence of expertise in immunology, genomic engineering, and translational medicine.
This pioneering research was supported by a constellation of prominent funding sources, including the National Institutes of Health, Parker Institute for Cancer Immunotherapy, Cancer Research Institute, Simons Foundation, and various dedicated CRISPR and cancer initiatives. The authors have also filed patent applications related to CRISPRoff technology, underscoring its commercial and therapeutic potential.
As the landscape of cellular immunotherapy evolves at an unprecedented pace, the integration of epigenetic and genetic programming heralds an era of precision engineering that could overcome prior barriers to treating solid tumors and beyond. This dual approach marries the targeting specificity of genetic modification with the subtlety and safety of epigenetic regulation, promising to unlock new dimensions of efficacy and durability in T cell therapies.
Efforts are underway to translate this technology from the laboratory bench to the clinic, where it may offer patients with previously intractable cancers and immune disorders new hope. The Arc Institute and its partners stand at the forefront of this revolution, exemplifying how interdisciplinary collaboration and innovative thinking can accelerate the next generation of life-saving medical interventions.
Subject of Research: Animals
Article Title: Integrated Epigenetic and Genetic Programming of Primary Human T Cell
News Publication Date: 21-Oct-2025
Web References: Not provided
References: Goudy, L. E., Ha, A., Borah, A. A., et al. (2025). Integrated Epigenetic and Genetic Programming of Primary Human T Cells. Nature Biotechnology. DOI: 10.1038/s41587-025-02856-w
Image Credits: Chiara Ricci-Tam
Keywords: Cancer, Gene editing, Biotechnology
