Jumbled proteins paint a bold target on the backs of brain tumors

Now, researchers at UC San Francisco have found that some cancers, like deadly brain cancer (glioma), make unique, jumbled proteins that make them stand out. These newly recognized cancer-specific proteins, or antigens, could speed the development of potent immunotherapies that recognize and attack hard-to-treat tumors.

The study, which was supported through grants from the National Institutes of Health, appears in Nature on Feb. 19.

The newly discovered antigens were the product of mistakes in RNA splicing, which controls how RNA molecules -- the blueprints for proteins -- are pieced together from smaller parts. The study found that in cancers of the brain, prostate, liver and colon, among others, the tumors spliced together bits of RNA to create new forms that had never been seen before, and which were absent in healthy tissues.

Some of these new RNAs produced antigens that attached to the surface of tumor cells, creating an entry for immune therapy. The researchers then engineered immune T-cells to recognize these antigens and were able to destroy glioma in the lab.

Such antigens from alternative RNA splicing could vastly expand the number of targets available for immunotherapy -- and the options available to patients in need of a cure.

"We think these first antigens could be actionable in the near future, leading to new therapies for glioma patients," said Hideho Okada, MD, PhD, professor of neurosurgery at UCSF and co-corresponding author of the paper. "But they are the tip of the iceberg and we're excited to look into many more from the data we generated."

Fishing antigens from a sea of RNA

Precision medicine today relies on either drugs that disable the mutant proteins that cause cancer or on the immune cells that track down cancer-related antigens. But many tumors don't have such mutant proteins or antigens. Even if they do, those targets might not cover all of a tumor.

"One of the reasons we think a lot of glioma therapies fail is that they only target one part of the tumor. The rest of the tumor escapes unscathed," said Joe Costello, PhD, professor of neurosurgery at UCSF and co-corresponding author of the paper. "These new antigens lift us over that major hurdle of brain tumor heterogeneity."

To hunt for new targets for cancer therapies, Darwin Kwok, PhD, focused on RNA splicing, which sometimes produces several versions of a protein based on a single gene.

"Many cancer therapies today are based on unique DNA mutations found in tumors, but we suspected that tumors might also have altered RNA splicing leading to new cancer-specific antigens," said Kwok, who is a PhD graduate from the Okada and Costello labs, current UCSF medical student, and first author of the paper.

Kwok pored through RNA sequencing data from thousands of tumors held by The Cancer Genome Atlas, a program at the National Cancer Institute. He homed in on uniquely-spliced RNA messages (mRNAs) that were consistently found in multiple biopsies per tumor and in multiple patients. The tumors came from prostate, liver, colon, stomach, kidney, and lung cancers.

He also teamed up with the UCSF Brain Tumor Center to look for these mRNAs in glioma samples donated by 51 UCSF patients. The researchers obtained up to ten biopsies per tumor, kept track of where in each tumor each biopsy had come from, and again looked for unusual mRNAs.

From this broad analysis, the team found nearly 1,000 cancer-specific mRNAs, common across tumors, cancer types, and patients, that had never been documented. None were ever found in healthy tissue.

Predicting the best targets for new therapies

Not every mRNA becomes a protein. Not every protein is attached to the cell surface as an antigen. And not every antigen can be recognized by the immune system. So, the researchers modeled what might happen to each of these mRNAs on the hopeful path to becoming a viable target for immunotherapy.

They ended up with 32 antigen candidates, all borne of cancer's alternative RNA splicing, that showed promise as an immunotherapy target, and chose the top four for more rigorous testing. These four antigens had similar shapes to other antigens known to provoke an immune attack.

The researchers first programmed cells to display the four antigens. Then they challenged immune cells obtained from healthy donor blood to react to the antigens. The experiment revealed receptors on these natural immune cells that reliably detected the cancerous antigens -- a crucial step toward engineering them into a potential therapy.

The chances of finding these immune receptors in donated blood were remote -- "like one in five or 10 million," according to Okada. But the team struck gold. For two of the top four antigens, the experiment unearthed complementary immune receptors in two different donors.

Making a new immunotherapy from scratch

Laboratory T-cells were programmed to make these immune receptors and unleashed on glioma cells in petri dishes. The cancer cells were no match for these specially-trained immune cells and were quickly eliminated.

The scientists are now testing this approach in animal models of cancer and hope to bring them quickly to patients if successful. There are many more antigens worthy of follow-up, including the 28 antigens that didn't make the final cut in this study, and countless others.

The team can only speculate why so many cancers make the same handful of jumbled proteins. It could be a mere artifact of cancer biology. In the meantime, a new front has been opened in treating cancer.

"This advance for cancer patients is the epitome of collaboration at UCSF, from computational modeling to laboratory validation and new techniques in brain surgery," Okada said. "It's exactly what the field needs to overcome the most stubborn cancer cases and bring relief to our patients."