A new tool that can map transcriptional regulatory programs has been developed. Chromatin run-on and sequencing (ChRO-seq), created by researchers at the Baker Institute for Animal Health at Cornell University, was designed to map the location of RNA polymerases for almost any input sample. A paper published today in Nature Genetics, details the use of ChRO-seq to study genetic "switches" active in glioblastoma tumors that drive growth of the cancer.
Using ChRO-seq data, the team was able to classify the glioblastomas into subtypes, based on which particular switches were active in the different tumors compared to healthy brain tissues. They also identified three switches that will be tested in larger studies to determine their ability to predict which patients will survive longer with the disease, including two switches whose connections were previously unknown.
Co-author Hojoong Kwak, Cornell assistant professor of molecular biology and genetics, initially invented ChRO-Seq as a graduate student at Cornell University, and collaborated with Charles Danko's lab to develop the new application.
Tinyi Chu, lead author and a graduate fellow in Danko's lab, is now analyzing an even larger group of glioblastomas to link patient survival and treatment outcomes with the active switches in each tumor. He hopes the results could inform personalized treatment plans for patients or help to develop new therapies in the future.
The new technique studies not only cancer, but many other diseases caused by malfunctions in gene regulation, such as certain types of heart or autoimmune diseases. "ChRO-seq gives you a lot of information about what switch is turning on a tumor or a diseased cell," said Danko. "It gives you a starting point to think about how you can shut that switch off."