Cancer research often focuses on gene mutations in the parts of the human genome that produce cellular machinery called proteins. But the rest of the genome — sometimes called the “dark genome” — can also play a role.
Dana-Farber researcher William Freed-Pastor, MD, PhD, a physician-scientist in the Dana-Farber Center for Gastrointestinal Oncology and Hale Family Center for Pancreatic Cancer Research at Dana-Farber, has found that pancreatic cancer cells read the dark genome in a way that deviates from the norm. This results in the creation of small protein building-blocks, called peptides, from DNA sequences there.
These peptides, called “cryptic peptides,” end up presented on the surface of cancer cells and can act as flags that alert the immune system, the study showed. Cryptic peptides have been observed in other cancers, including melanoma and colon cancer, but this is the first time they have been observed in pancreatic cancer.
The research also showed that some of these cryptic peptides are unique to cancer and that immune cells can be trained to recognize them. The work, which was jointly led by Freed-Pastor and Tyler Jacks, PhD, the David H. Koch Professor of Biology at MIT, was published in Science.
“Many of these cryptic peptides were found only in pancreatic cancer cells and also were common across many different patient samples,” says Freed-Pastor. “This opens the possibility that we could develop novel therapies for pancreatic cancer that target these peptides.”
Dana-Farber researcher William Freed-Pastor, MD, PhD, a physician-scientist in the Dana-Farber Center for Gastrointestinal Oncology and Hale Family Center for Pancreatic Cancer Research at Dana-Farber, has found that pancreatic cancer cells read the dark genome in a way that deviates from the norm.
Discovering novel therapeutic targets
Pancreatic cancer is the third leading cause of cancer-related death in the United States. There is a dire need for research that drives therapeutic innovation, as patients diagnosed with the disease have a five-year survival rate of about 10 percent.
To find leads on new ways to treat pancreatic cancer, Freed-Pastor partnered with Jennifer Abelin, PhD, and Steven Carr, PhD, at the Broad Institute, to perform immunopeptidomics, a method that creates an inventory of the flags, called antigens, presented on the surface of a cell. The process involves extracting peptide antigens and then using mass spectrometry to identify them.
“This approach lets us identify the antigens that are actually present on the tumor cells and that could potentially make good targets for T cells,” says Freed-Pastor.
The team, which also included first authors Zackery A. Ely, PhD and Zachary J. Kulstad, used immunopeptidomics to analyze three-dimensional replicas of pancreatic cancer, called organoids, that were created using tumor samples from about a dozen patients.
They found approximately 1,700 unique cryptic peptides. Of these, about 30 percent were observed only on tumor cells and not on healthy cells.
“Those are the ones that we think could be very good targets for future immunotherapies,” Freed-Pastor says.
Toward new immune-based therapies
To determine if immunotherapies targeting cryptic peptides were possible, the team needed to determine if any of the cancer-specific cryptic peptides could generate an immune response. An immune response occurs when the immune system recognizes a foreign antigen that might indicate disease, like an infection or cancer, and creates T cells to search for and destroy cells that present it.
They found that 12 of the cancer-specific cryptic peptides generated large numbers of T cells that targeted them. The team then developed cellular therapies targeting these cryptic antigens, called T-cell receptor engineered T (TCR-T) cell therapy, which involves modifying a patient’s T cells in the lab so they can recognize specific tumor antigens.
The engineered T cells recognized pancreatic cancer cells and slowed cancer growth in both organoid and animal models of pancreatic cancer. This is the first use of T cells targeting cryptic peptides to kill pancreatic cancer cells. The tumors were not eradicated by the approach, but the results are promising and could be improved with further research.
Freed-Pastor’s lab is building on this work, particularly focused on clinical translation of these discoveries. Early efforts are underway to explore the possibility of developing novel therapeutics, designed to target the cryptic peptides discovered in this study that were specific to cancer and seen across multiple patient samples. Possibilities include cancer vaccines, TCR-T cell therapy, or T-cell engagers, which are antibodies designed to activate the anti-tumor activities of T cells.
The research was funded in part by the Hale Family Center for Pancreatic Cancer Research, the Lustgarten Foundation, Stand Up To Cancer, the Pancreatic Cancer Action Network, the Burroughs Wellcome Fund, a Conquer Cancer Young Investigator Award, the National Institutes of Health, and the National Cancer Institute.