Many cancer treatments—including chemotherapies and engineered immune cells—can result in side effects. This is in large part because the treatments affect healthy cells in the body as well as targeting tumor cells. Similarly, designing new cancer drugs can be challenging due to the molecular similarities between tumor cells and healthy cells.
University of California San Francisco (UCSF) researchers have now designed highly customizable biological sensors that ensure engineered immune cells are only activated in certain environments—such as the vicinity of a tumor. The team’s developments are centered on a platform of engineered synthetic intramembrane proteolysis receptors (SNIPRs) that can sense molecules in the surrounding environment and, in response, change the expression of genes inside the cells.
In vivo tests in human tumor-bearing mice showed that CAR T-cells modified using the new SNIPR technology specifically targeted and shrank the tumors—with minimal effects on healthy tissue and without the side effects regularly seen with CAR T-cell therapy.
The team says their work could lead to development of cancer therapies that are precisely delivered to tumors, making them more effective, but with fewer side effects than existing treatments. The approach could also lead to new, targeted therapies for other diseases.
“We can now program a cell to localize to a site of disease and then carry out a very specific set of therapeutic tasks,” said Kole Roybal, PhD, an associate professor of microbiology and immunology at UCSF. “This is the culmination of more than a decade of work into the molecular details of these receptors and how they can be modified.”
Roybal is co-senior author of the team’s published paper in Nature, titled “Engineered receptors for soluble cellular communication and disease sensing.” In their paper the team stated, “SNIPRs are an expanding platform for precise control of cells for therapeutic purposes and basic biology applications … SNIPRs possess the unique capability to interact with a range of physiological or synthetic ligands, whether they are tethered or soluble. This versatile feature makes them an asset to the current array of cell-engineering tools, with potential applications in cancer therapy, and engineering development.”
In 2016, Roybal was part of a UCSF team that developed a new class of sensors, known as synNotch receptors, that could be inserted into cells to reprogram their behavior in response to stimuli. Roybal and colleagues created sensors on the surface of immune cells, for example, that recognized tumor cells and activated an immune response. However, the receptors had could only recognize molecules that were on the surface of other cells. The system relied on the tight physical interactions between cells.
Tumor cells often very closely resemble the healthy cells from which they evolved, and the proteins found on their surface are also often found on other cells. “The receptors were limited in scope because they could only be activated by cell surface markers,” explained former UCSF postdoctoral researcher Dan Piraner, PhD, co-first author of the newly published work. “There are many other molecules that tumors produce which might be more useful in identifying the tumor environment.”
Roybal and his colleagues have since been studying how different elements of the synNotch receptors can be altered to fine tune their function. That led them to develop new receptors—synthetic intramembrane proteolysis receptors—which can bind to soluble, or free-floating, molecules in the environment around a cell.
SNIPRs are engineered to detect any soluble molecule of interest, such as an immune signaling molecule. When the molecules bind to corresponding SNIPRs, multiple receptors cluster together and flip to the interior of the cell. There, the receptors directly interact with the DNA inside the cells to alter gene expression. Multiple SNIPRs inserted into one cell could affect different genes—or the same genes in different ways.
“What’s exciting is that we can not only use soluble molecules to flip a genetic switch on, but can customize the SNIPRs so that they turn a genetic program on, turn it off, or dial its activity up and down,” said co-first author María José Durán González, PhD, a former researcher in the Roybal lab and co-first author of the paper.
This could mean coaxing a cell to release a drug, activate an immune response, or send signaling molecules to other cells when it is in a particular environment.
One type of cancer immunotherapy that in recent years has proven incredibly effective against blood cancers is chimeric antigen receptor (CAR) T-cell therapy, in which a patient’s own T cells are re-engineered to recognize and attack their cancer cells. However, CAR T-cell therapy has less successful in solid tumors, in part because of the difficulty of finding molecules that are unique to the cancer cells for the T cells to recognize.
To show the potential utility of SNIPRs, the researchers inserted newly engineered SNIPRs into CAR T-cells. The SNIPRs were designed to respond to two soluble immune molecules, TGF-β and VEGF, which are often found in high levels around tumors. Tests confirmed that only when these molecules were present did the SNIPRs turn on the CAR T-cells’ tumor-fighting activity. In vitro experiments demonstrated that the SNIPR-equipped CAR T-cells were only activated in the presence of TGF-β and VEGF, suggesting that they would not launch an immune response in areas of the body unaffected by cancer.
“This is like two-factor authentication for immunotherapy,” said co-senior author David Baker, PhD, professor of biochemistry at the University of Washington School of Medicine, who won the 2024 Nobel Prize in Chemistry for his work in computational protein design. “The cells have to be in a particular environment to even have the possibility of launching an immune response, which itself requires recognizing cancer cells.”
When tested in mice with human tumors, the engineered cells specifically targeted and attacked the tumors, minimizing damage to healthy tissue. “Here we have shown that T cells engineered with SNIPR technology can effectively react to soluble factors and drive therapeutic payload production in solid tumor animal models,” the team noted. Moreover, the treatment shrank the tumors in mice without causing the side effects. Such as weight loss and organ damage, that may be seen using CAR T-cells. Roybal commented, “This is incredibly exciting for cancer therapies, but it also could be useful in things like autoimmune diseases where we want to regulate immune cells in certain environments.”
The researchers suggest that the SNIPR architecture meets the demands of what they describe as high performance soluble factor sensing. “SNIPRs bearing ligand binding domains targeting cancer-associated factors show robust activation upon titration of recombinant ligands and are capable of driving potent therapeutic responses at the site of disease, mitigating the toxicity potential of cell therapies.”
The group is continuing to work on methods for using the SNIPRs in a variety of cell types, using them to mediate communication between different cell types, and testing them in patients in CAR T-cell clinical trials sponsored by Arsenal Bio, which Roybal co-founded.
“Overall, soluble SNIPRs provide a versatile tool for therapeutic bioengineering and other disciplines in biology,” the team concluded. “The customizability of these receptors could enable them to sense morphogen gradients established by proteins such as NGF and the BMP family during embryonic development, or report on the local immune state in the context of cancer, autoimmunity, and infectious disease.”
