Rewriting Cellular Instructions to Make Better Tumor-Fighting Immunotherapies

A growing number of cancer treatments known as CAR-T cell therapies genetically modify a patient’s own immune cells to target and destroy cancer throughout their body.

These therapies have shown great success against certain blood cancers such as leukemias and lymphomas, but tend to fail when applied to solid tumors that comprise the vast majority of cancer cases.

That’s because T cells—the immune cells at the core of CAR-T therapies—can become suppressed or exhausted when faced with solid tumors. Over the years, scientists have attempted to give those cells stronger cancer-fighting power by altering many of their genes, but doing so has potential to damage the cells’ DNA or even destroy the cells.

Now, a breakthrough from researchers at Arc Institute, Gladstone Institutes, and UC San Francisco (UCSF) may overcome these and other limitations of today’s CAR-T cell therapies.

Rather than adding more genetic modifications to the therapeutic T cells, the scientists found a way to make "epigenetic" changes, which modify the cells’ behavior without altering their underlying DNA sequence. Detailed in Nature Biotechnology, the epigenetic editing method created enhanced CAR-T therapies, while also overcoming key manufacturing and scalability issues.

Marson and his collaborators developed a new platform to reprogram CAR-T cells so they can better destroy cancer cells.

“Our new platform offers broad hopes for developing distinct programs to treat not only cancer, but a wide range of different diseases,” says Alex Marson, MD, PhD, director of the Gladstone-UCSF Institute of Genomic Immunology and co-senior author of the study.

On and Off Switches

While genetic changes permanently alter the DNA code, epigenetic changes leave those sequences intact; what’s changed are instructions about which parts of the code are active or inactive. As part of the new platform, the team used technologies called “CRISPRoff” and “CRISPRon” to instruct cells to turn off certain genes or re-activate genes that would otherwise be silenced. And unlike traditional CRISPR approaches that require cutting the DNA helix, which can harm or kill T cells, these epigenetic editors can modify up to five genes simultaneously while maintaining high cell survival rates.

Scientists used genetic engineering to program T cells to search for cancer cells, then combined it with so-called “epigenetic engineering” to program the strength of their anti-cancer functions.

“The T cells essentially memorize our programming instructions,” says co-senior author Luke Gilbert, PhD, an Arc Institute core investigator and an associate professor at UC San Francisco (UCSF). “We deliver the epigenetic editors for just a couple of days, but the gene silencing effects remain stable through dozens of cell divisions and multiple rounds of immune activation.”

Innovation in Action

To demonstrate the platform’s potential, the researchers created enhanced CAR-T cells by first inserting cancer-targeting receptors, and then simultaneously using CRISPRoff to silence the gene RASA2, which normally acts as a brake on T cells’ ability to destroy cancer cells.

The dual-engineered cells maintained their cancer-killing ability through repeated challenges in laboratory tests, while CAR-T cells where RASA2 was not silenced became exhausted. In mouse models of leukemia, the enhanced CAR-T cells provided significantly better tumor control and improved survival compared to standard CAR-T approaches.

“Instead of just adding targeting capabilities, we can systematically reprogram how these cells function in a scalable manner to create more effective therapeutic products,” says first author Laine Goudy, a PhD student in the Marson and Gilbert labs. “The data in this paper could support moving directly into clinical trials for certain applications.”

“Our new platform offers broad hopes for developing distinct programs to treat not only cancer, but a wide range of different diseases.”

Alex Marson, MD, PhD

Notably, CRISPRoff works with cell manufacturing protocols already used to produce FDA-approved CAR-T treatments, requiring only the conversion of research-grade reagents to clinical-grade versions. The research team is considering next steps for testing the technology in humans.

Beyond cancer, the approach opens new possibilities for treating autoimmune diseases, creating new transplant medicines, and addressing other areas of medicine in which reprogrammed T cells could provide benefit to patients.

“When we started, we weren’t sure this would be successful in T cells, and it took years of methodical optimization to overcome some fundamental challenges, but it’s been so gratifying to see that the core technology is extremely robust,” Gilbert says. “CAR-T therapies are an incredible success story, but in the context of solid tumors we believe our approach could boost the next generation of CAR-T approaches to benefit patients.”

In addition to Marson and Gilbert, co-senior authors of the paper are Brian Shy, MD, PhD, assistant professor in the UCSF Department of Laboratory Medicine and director of the UCSF Investigational Cell Therapy Program, and Justin Eyquem, PhD, an affiliate of the Gladstone-UCSF Institute for Genomic Immunology and associate professor in the UCSF Department of Microbiology and Immunology.