Jumping Genes Put a Target on Cancerous Cells

T cells mark cancers for destruction by homing in on unique proteins that tumor cells display on their surfaces called tumor-specific antigens, in a process that leaves healthy cells untouched. This can lead to the regression and sometimes disappearance of tumors, but so far, scientists have yet to discern the sequences of the vast majority of tumor-specific antigens or how they arise.

Two new studies in mice and human tumors—both published on February 3 in Science—bring researchers a step closer to finding the origin of tumor-specific antigens. In both, scientists showed that some tumor-specific antigens might be the result of transposable elements, also called “jumping genes,” sneaking into an mRNA molecule by tacking themselves onto exons. Some of the resulting peptides are exclusively found on tumor cells and were shown to trigger an immune response. The finding could help researchers design more effective cancer therapies that can be better directed to tumors.

“These papers are very, very interesting,” says Claude Perreault, an immunogeneticist at the University of Montreal, who was not involved with the studies. “They address a fundamental question: What is the nature of the antigens that can mediate tumor recognition and rejection in patients with cancer?”

When a gene is first copied from DNA, it contains introns: short DNA sequences that don’t code for parts of the protein and are summarily cut out. The remaining pieces, called exons, are glued together into an mRNA molecule that is ready for protein synthesis. This whole process is known as splicing. Introns can come in the form of transposable elements (TEs), also called “jumping genes,” which are DNA sequences that can move to other segments of the genome.

See “Adapting with a Little Help from Jumping Genes

Eight years ago, study coauthor of both papers Sebastian Amigorena, a cancer immunologist at the Institut Curie, was working in epigenetic regulation, not transposons. His interest in transposons was piqued after finding that, like regular genes, transposons are also under epigenetic control. But at the same time, he encountered a different, fascinating puzzle. Next-generation sequencing, a technique that sequences mRNA molecules in cells, flags intact sequences of transposons next to exons. “These were dismissed as artifacts by many people,” says Amigorena. But these events weren’t rare. Amigorena became curious about whether these strange splicing events might have a link to an aberrant biological function, like cancer.

“It was a wild idea,” says Amigorena. “But it ended up working out.”

The first step in testing this wild idea, Amigorena says, was to show that the peptides formed from transposon-exon junctions, which he named JETs, activated the immune system. So, in the first paper, in a mouse model of non–small-cell lung cancer, the researchers used RNA sequencing to map JETs in three tumor cell lines and in normal cells. While they found a large number of JETs in both healthy cells and tumor cells, about one percent of these odd splicing events occurred only in tumors. Now, Amigorena says, they had sequence information on potential proteins embedded in tumor cells. That allowed them to do mass spectrometry on all of the tumor cell membrane proteins and confirm that the proteins normally sit on the surface of the cell.

From there, the researchers asked whether these peptides could mobilize anti-tumor T cells and protect the mice against tumors. They injected mice with a cocktail of cancerous cells, and at the same time, treated some with an injection of synthetic JET-derived peptides. Mice slowly developed tumors, but those that received the treatment ended up with smaller tumors than those that didn’t, indicating that the JETs triggered a tumor-specific immune response.

“When we found that JETs were immunogenic in mice, that was a big, big step,” says Amigoreta.

In the other paper, the researchers followed a similar procedure in human cells, garnering similar results. Using a database of RNAseq data from tumors of non–small-cell lung cancer patients, they searched for unique transposon-exon splicing sequences. And at first, “it was really bizarre. It was a big mess,” Amigorena says. They found thousands of these unique splicing events in the cells of different patients. But eventually, Amigorena began seeing the same splicing events across patients. “That was a big step,” he says.

Focusing only on these sequences, the team discovered that some of these JETs were unique to the patients’ tumors, suggesting that they might be tumor-specific antigens. When the group used mass spectrometry to compare all of the tumor cell membrane proteins to these putative tumor-specific antigens, they again found matches.

In addition, the researchers analyzed tumor biopsies from five cancer patients, finding anti-JET T cells inside their tumors.

JETs also sparked an immune response in human cells. In vitro the researchers created cancer-fighting T cells using these JET-derived antigens, finding that the engineered T cells successfully targeted and killed cancer cells.

Amigorena says that he hopes that his findings will have clinical impacts. He plans to test whether JETs can be used as potential markers or targets for cancer therapies. “Now we can devise tools like [T cell receptors] or antibodies that can recognize noncanonical splicing events in tumor cells,” he says.

Perreault says that he agrees that the findings have translational potential but adds that most JETs are not tumor-specific, which may be a barrier to implementation. “Those that are tumor-specific are sometimes shared, but not most of the time,” he explains. This might make it difficult to create treatments like cancer vaccines, which may need thousands of antigens to be successful.

Still, “they had a very original hypothesis,” says Perreault. “I think it’s a very important piece of work.”

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