UC Merced researchers map melanoma drivers in new study

New research at UC Merced is taking a closer look at melanoma and its genetic makeup in hopes of improving diagnosis and treatment.

The study, led by Fabian V. Filipp, an assistant professor of systems biology at UC Merced, set out to find the genomic factors that give rise to cancer. By comparing the genetic material of more than 300 melanoma patients, the research group confirmed the top genetic drivers of the disease and identified new melanoma genes.

According to Filipp, this is the largest study of melanoma genes ever conducted.

Melanoma, known as the most dangerous form of skin cancer, is caused by exposure to ultraviolet light. Skin cancer can be particularly difficult to analyze, researchers said, as UV radiation tends to cause DNA damage.

In the course of two years, researchers went over billions of DNA base pairs, which resulted in a map showing a solid network of mutational hotspots – or areas where a series of genetic mutations occur.

“This is very much different from other studies we have conducted because we comprehensively looked at the entire genome instead of isolated genes,” Filipp said. “Ten years ago nobody was doing work like this, but in the future this will be the standard.”

He explained that by finding the factors that drive the disease, scientists can have a better understanding of the cancer and help develop tools to treat it.

For example, the study showed that in melanoma patients, “proto-oncogene BRAF,” a gene that if mutated causes cancer, is hyperactive, causing uncontrolled cell division. Researchers determined that these BRAF mutations are one of the top drivers of melanoma.

They also found that the same mutation is also prominent in thyroid cancer. The similarity was unexpected, Filipp said, but the new information could be beneficial to developing therapeutic and diagnostic tools for different types of cancer.

“We can transfer everything we’ve learned from one cancer type to another,” he said.

Now that researchers have a comprehensive map of the genetic makeup of melanoma, Filipp said their next goal is to collaborate with local hospitals, collect data and move forward in the development of medicines.

For this research, Filipp worked alongside Dr. Jian Guan, a medical doctor from Heidelberg University in Germany, and UC Merced Ph.D. student Rohit Gupta.

The study, “Cancer systems biology of TCGA SKCM: Efficient detection of genomic drivers in melanoma,” was published Tuesday in “Scientific Reports,” a research publication from the publishers of “Nature.”

Filipp, whose work focuses on melanoma and cancer metabolism, was recently honored with the Thomas B. Fitzpatrick Medal, an award presented only once every three years to researchers worldwide who have contributed to the study of melanoma and pigment cells.

The study was made possible with data from The Cancer Genome Atlas and with an $800,000 grant from the National Cancer Institute at the National Institutes of Health.

This story was originally published January 20, 2015 at 8:43 PM with the headline "UC Merced researchers map melanoma drivers in new study."