Analysis uncovers thousands of potential cancer markers

A newly published analysis “opens a huge opportunity for the discovery of new biomarkers” for multiple cancers, including aggressive prostate cancer, a leading urologic cancer expert says.

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For the study, which was published online in Nature Genetics (Jan. 19, 2015), researchers at the University of Michigan Comprehensive Cancer Center, Ann Arbor analyzed the global landscape of long non-coding RNAs (lncRNAs). They pulled together 25 independent datasets totaling 7,256 RNA sequencing samples. The data came from public sources such as The Cancer Genome Atlas project, as well as from the Michigan Center for Translational Pathology’s archives.

Researchers led by senior author Arul M. Chinnaiyan, MD, PhD, applied high-throughput RNA sequencing technology to identify more than 58,000 lncRNA genes across normal tissue and a range of common cancer types.

“We used all of this data to decipher what the genomic landscape looks like in different tissues as well as in cancer. This opens up a Pandora’s box of all kinds of lncRNAs to investigate for biomarker potential,” Dr. Chinnaiyan said in a press release from the University of Michigan.

The authors also identified one lncRNA, SChLAP1, as a potential biomarker for aggressive prostate cancer. SChLAP1 was more highly expressed in metastatic prostate cancer than in early-stage disease. In addition, it was found primarily in prostate cancer cells, not in other cancers or normal cells, which gives researchers hope that a noninvasive test could be developed to detect SChLAP1. Such a test could be used to help patients and their physicians make treatment decisions for early-stage prostate cancer, study authors say.

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“Some long non-coding RNAs tend to be exquisitely specific for cancer, while protein-coding genes are often not. That’s what makes lncRNAs a very promising target for developing biomarkers,” Dr. Chinnaiyan said.

“We hope that researchers will investigate the MiTransciptome compendium and begin to nominate lncRNAs for further study and development. It’s likely that only a subset of these have true function but as a previously untapped area, it holds great promise.”

The complete dataset, named the MiTranscriptome compendium, has been made available on a public website, www.mitranscriptome.org, for the scientific community to explore.

Urology Times Editorial Consultant J. Brantley Thrasher, MD, of the University of Kansas, Kansas City, praised the authors’ efforts.

“These authors are finding thousands of RNAs that have not been well researched in areas of the genome where the RNA does not code for proteins. However, they are finding that many of these segments may actually be very important regulators of normal and abnormal tissue physiology,” said Dr. Thrasher, who not involved with the study.

“This opens a huge opportunity for the discovery of new biomarkers for a variety of tumors. It appears from the report that this is just the tip of the iceberg, and there is likely going to be a significant amount of research in this area following this report.”

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