A pediatric patient at St. Jude came to the clinic with high-grade glioma, a type of brain tumor. St. Jude scientists tried to categorize the tumor to guide treatment. They found contradictory results, leading them to investigate further. They found a novel cause of the cancer.
The researchers found the tumor overexpressed a cancer driver gene called FOXR2. They tried to find out why FOXR2 was activated. The computer algorithms they normally use did not work.
The scientists looked at the data manually. They found a piece of repetitive DNA that looked like a retrotransposon, a piece of DNA that can “jump” to another area in the genome.
Retrotransposons have stretches of DNA called promoters that regulate their mobility. The retrotransposon “jumped” into a new region, bringing its promoter. The promoter drove the expression of FOXR2 and caused the cancer to develop.
“Our study opens the door for people to investigate this mechanism in cancer and other diseases which may involve improving the current computational methods,” said co-corresponding author Jinghui Zhang, PhD, Computational Biology chair.
Retrotransposons are usually considered junk DNA.
“Scientists need to keep their eyes open for all the possibilities,” said co-corresponding author Jason Chiang, MD, PhD, Pathology. “Sometimes the gold is in the garbage.”
The findings appeared in Acta Neuropathologica.