Analysis of 33 tumour types identifies new immunotherapy targets

Jumping genes are short sections of DNA that have been incorporated randomly into the human genome over the long course of evolution. Also called transposable elements, these pieces of DNA have been implicated in the development of cancer. However, new research from Washington University School of Medicine in St. Louis, US, suggests that transposable elements in various cancers potentially may be used to direct novel immunotherapies to tumours that do not usually respond to immune-based treatments. The findings were recently published in Nature Genetics.

Immunotherapy is often most effective in tumours with numerous mutations, such as skin and lung cancers. Mutations in DNA cause cancer cells to produce unusual proteins that distinguish tumour cells from normal cells and serve as targets — called tumour antigens — for immunotherapies, such as antibodies, vaccines and genetically engineered CAR-T cell therapies. But many tumour types do not contain large numbers of mutations and are therefore harder for the immune system to identify as a threat.

“We are excited about this research, because it opens up an entirely new way to identify tumour antigens in types of cancer that have previously been invisible to immunotherapy,” said senior author Dr Ting Wang.

Jumping genes — believed to have possibly originated from viruses — usually are found in parts of the genome that are inactive in adult tissues. But past work by Wang and his colleagues showed that these transposable elements sometimes can function as hidden on switches, forcing a gene to be turned on all the time, even though it should not be. As these stealthy on switches drive cancer growth, they also can churn out unusual pieces of proteins that are unique to the tumour and not present in normal cells.

In an analysis of 33 tumour types from the US National Cancer Institute’s The Cancer Genome Atlas Program, the researchers identified 1,068 transposable element-derived transcripts — or sections of RNA made by the cancer cells — with the potential to produce tumour antigens that could serve as targets for new immunotherapies.

Wang and his colleagues determined that these possible tumour antigens were present on the surfaces of cancer cells, making them ideal for targeting with immunotherapies. Importantly, they found that almost 98 percent of the more than 10,000 tumours analysed had at least one potential antigen target arising from a transposable element. Most tumours had from two to 75 possible antigens.

In another important finding, the researchers showed that many of the candidate proteins that could serve as antigens were present in multiple tumours and, in some cases, across tumour types. Wang and his colleagues speculated that this raises the possibility of a universal antigen-based therapy that could treat multiple tumours with a single cocktail targeting several of the most common tumour antigens that arise from jumping genes. For example, the data suggest that a vaccine with a combination of 20 of the most common protein targets could cover about 75 percent of patients across 27 cancer types.

“With this analysis, we can envision the design of a cancer vaccine that targets the top five or top 10 most common tumour proteins that are caused by transposable elements,” said Wang. “This type of vaccine is still just an idea, but we are excited about the potential, because these common targets could cover a large fraction of tumours. Much more work is necessary, but we are hopeful that this analysis can serve as a starting point for the development of effective immunotherapies across many more cancer types.”