New RNA-based liquid biopsy detects early colorectal cancer with high accuracy

Liquid biopsies are tests that detect signs of cancer through a simple blood draw. Unlike traditional biopsies, which require removing a piece of tissue, a liquid biopsy typically looks for mutations or modification changes in fragments of DNA from cancer cells circulating in the blood. While liquid biopsies are a promising, non-invasive way to detect and monitor cancer as it progresses, they aren't as sensitive or accurate for the early stages of disease.

Researchers at the University of Chicago have now developed a more sensitive liquid biopsy test that uses RNA instead of DNA for detecting cancer. Using blood samples from patients with colorectal cancer, the test was able to detect the earliest stages of the disease with 95% accuracy, vastly improving on current, commercially available, non-invasive testing methods.

Challenges to early diagnosis

When tumor cells die, they disintegrate and release particles of genetic material into the bloodstream. Standard liquid biopsies rely on this floating DNA, called circulating cell-free DNA (cfDNA) to detect cancer. In the early stages of disease when tumor cells are still growing and thriving, however, there isn't very much cfDNA in the bloodstream.

That has been a major challenge for early diagnosis. You just don't have enough tumor DNA released into the blood. That was a challenge for us and everyone else to do early diagnosis of colon cancer, so we decided to look at RNA instead."

Chuan He, PhD, the John T. Wilson Distinguished Service Professor of Chemistry and Professor of Biochemistry and Molecular Biology at UChicago

Dr. He is the senior author of the new study, published this week in Nature Biotechnology.

RNA is a transitional form of genetic code that copies and carries out instructions from DNA to produce proteins that cells need. Analyzing RNA is a good proxy for genetic activity, because the presence of RNA means that cells are busy doing things and building proteins.

For the new study, graduate student Cheng-Wei Ju and Li-Sheng Zhang, PhD, a former postdoc in Dr. He's lab who is now a faculty member at the Hong Kong University of Science and Technology, began to investigate the possibility of using circulating cell-free RNA (cfRNA), instead of cfDNA, for the diagnosis and detection of cancer.

Measuring the simple abundance of RNA molecules in the blood isn't always reliable, however, because amounts can vary greatly depending on the timing and preparation of samples. Dr. He's lab specializes in studying the biological functions of RNA modifications, chemical changes made to RNA molecules that alter their activity. So, for the new study, the researchers focused on analyzing RNA modification levels in blood samples, which remain relatively stable no matter how much RNA is present. For example, if an RNA transcript is modified by 30%, that percentage remains that the same whether it is measured on 100 or 1,000 copies.

Detecting changes in the microbiome

The team worked with samples from colorectal cancer patients provided by gastroenterologist and longtime collaborator Marc Bissonnette, MD, Associate Professor of Medicine at UChicago. To their surprise, not only were they able to measure modifications on cfRNA from human cells, but they were also able to detect RNA from gut microbes as well. Billions of bacteria coexist with us inside the digestive system, and in the presence of a cancerous tumor, their activity changes too.

Drawing on previous research in plants, Dr. He and his team knew that RNA modification levels reflect an organism's state: the more active the organism, the more modifications are made to certain RNAs to sustain that activity. This same pattern was observed in the colorectal cancer samples as well.

"We found that RNA released from microbes has substantial differences between cancer patients versus healthy individuals," Dr. He said. "In the gut when you have a tumor growing, the nearby microbiome must be reshaped in response to that inflammation. That affects the nearby microbes."

The microbiome population also turns over much more quickly than human cells, with more cells dying more often and releasing RNA fragments into the bloodstream. This means that a test measuring modifications on microbial RNA can detect possible cancerous activity much earlier than tests that rely on DNA released by human tumor cells.

Commercial tests that measure DNA or RNA abundance in the stool are about 90% accurate for later stages of cancer, but their accuracy drops below 50% for early stages. The new RNA modification-based test was almost 95% accurate overall, and also accurate at the earliest stages of cancer.

"This is the first time RNA modifications have been used as a potential biomarker for cancer, and it looks to be much more reliable and sensitive compared to RNA abundance," Dr. He said. "Being able to detect the cancer at those early stages is unprecedented."

The study, "Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples," was supported by the Ludwig Center for Metastasis at the University of Chicago, the Rolfe Foundation, the National Institutes of Health, the Hong Kong Research Grants Council, and the Howard Hughes Medical Institute.

Additional authors include Ruitu Lyu, Han Li, Jiangbo Wei, Urszula Dougherty, Akushika Kwesi, Alexander Luna, Xuanhao Zhu, Xiaolong Cui, Bochen Jiang, Yiyi Ji, Peng Xia, Diana C. West-Szymanski, Chenxi Sun, Yuhao Zhong, Chang Ye, Angelica Moran, Christopher Lehmann, and Eric Pamer from UChicago; Alberto J. Parra Vitela from Advocate Lutheran General Hospital; Shenghai Shen from the Hong Kong University of Science and Technology; Yunzheng Liu from the California Institute of Technology, Liangliang Wang from the Chinese Academy of Sciences; Yuzhi Xu from New York University; and Wei Zhang from Northwestern University.