PNAS: Researchers develop new technologies for cancer gene expression analysis

Researchers at the University of Michigan Comprehensive Cancer Center have developed a new technology that can better understand the possible differences in RNA between cancer cells and normal cells, and will promote a deeper understanding of tumor genome sequencing testing. The researchers published this result in the journal Proceedings of the National Academy of Sciences (PNAS).

When researchers sequence RNA from cancer cells, they can compare it with normal cells to see where more RNA is present. This helps them find genes and proteins that may cause cancer.

But besides identifying some known inducing factors, what is the point of it? Is there more RNA because it is synthesized too fast or because it degrades too slowly? Which part of the biological balance has diverged?

After more than ten years of research work, researchers at the University of Michigan Comprehensive Cancer Center have developed a new technology to help answer these questions.

This technique involves a compound called bromouridine, which can be used to label nascent RNA. After 30 minutes of labeling with bronouridine, the researchers isolated the RNA and then observed the site of nascent RNA production. They called this process Bru-Seq.

On the other hand, researchers can use a cleaning agent with a chemical uridine to track the bromouridine label at different times. They called it BruChase-Seq because uridine can remove new RNA. In this way, they can observe the aging of RNA in the following 1 hour, 2 hours or 6 hours. In other words, is it to see if RNA is degraded as expected?

"We can see all synthetic RNA, and the overall pattern of stable RNA versus degraded RNA. We can classify it according to synthesis and stability to see if there are more stable cells in cancer cells than normal cells, or in cancer. Special RNA that degrades longer in cells, "said study author Dr. Mats Ljungman, associate professor of radiation oncology at the University of Michigan School of Medicine.

"Using our technology, we have increased the depth of gene expression images by more than 10 times," he added.

Ljungman is a member of the Cancer Center's new translational oncology project. This project brings together cancer researchers from the University of Michigan to accelerate the transformation of basic science into clinical trials and provide patients with new treatment opportunities.

The cancer center is currently using gene sequencing technology, based on the tumor composition of advanced cancer patients, to help provide them with potential clinical trial opportunities.

In addition to helping cancer sequencing, Ljungman also sees the potential of this new technology to help identify diseases such as diabetes and inflammation. In the new paper, the researchers also described how they used this technique to understand an inflammatory response in cells. The researchers also used this technique to test blood samples.

As more research unfolds, Ljungman envisions that one day it may be possible to provide this test to patients, making it a way to detect changes in RNA.

"If there is a significant change between one test and another test, it may be an early warning sign of the disease. This technology will have the most widespread application," Ljungman said.

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