Melanoma researchers have been struggling with this question: Which mutations drive this cancer that lead to ultraviolet (UV)-induced genetic damage in tumor cells caused by sunlight exposure?

There have yet to be any mutations conclusively tied to melanoma. The great quantity of these passenger mutations has pulled away from the search for genetic driver mutations that are most important in melanoma development and progression.

Scientists at the Broad Institute of MIT and Harvard, the Dana-Farber Cancer Institute and The University of Texas MD Anderson Cancer Center created a method to mark the drivers while amongst a great amount of passengers. They then found 6 genes with driving mutations in melanoma, three having damage inflicted by UV light which causes recurrent ‘hotspot’ mutations. The research can be found in the July 20 issue of the journal Cell.

Co-senior author Lynda Chin, M.D., Professor and Chair of MD Anderson’s Department of Genomic Medicine, explained:

“Those three mutations are the first ‘smoking gun’ genomic evidence directly linking damage from UV light to melanoma. Until now, that link has been based on epidemiological evidence and experimental data.”

“This study also is exciting because many of the recent large-scale genomic studies have not discovered new cancer genes with recurrent hot-spot mutations, a pattern strongly indicative of biological importance,” added Chin, who also is scientific director of MD Anderson’s Institute for Applied Cancer Science.

According to the researchers, each of the six new melanoma genes they identified are all significantly mutated and provide possible targets for new treatments.

Thousands of Potential Mutations Recognized, Only Need A Few Dozen Significant Ones

There had previously been a great deal of important mutations recognized as melanoma drivers, but they were falsely identified because the majority of these mutations do not seem to be caused by direct damage from UV light, including:

  • BRAF (V600)- present in half of all melanomas
  • NRAS (Q61)

Although those known mutations are valuable, there is still missing information. Compared with other types of solid tumors, Melanoma has higher genetic mutation rates. Most are attributable to passenger mutations resulting from damage by UV light, resulting in a DNA alteration called a cytidine (C) to thymidine (T) transition.

Chin, along with Levi A. Garraway M.D., Ph.D., associate professor at Dana-Farber Cancer Institute and Harvard Medical School, and senior associate member at the Broad Institute, used 121 melanoma samples paired with normal DNA and sequenced the exons (active portions of DNA that are involved in protein synthesis). The experts found 86,813 coding mutations. The consequential mutation rate was larger than in any other tumor type reported.

85% of the active coding mutations, of the most frequently mutated genes, resulted from C to T transitions caused by exposure to UV light.

In order to recognize driver mutations, statistical approaches in previous research have assumed that the baseline mutation rate is unchanging across the genome. This assumption is proven wrong, according to the researchers, because of the large amounts of UV-induced passenger mutations that differ in frequency.

Garraway, co-author with Chin, said:

“When a gene is found to be repeatedly mutated, we naturally assume that it must be important to the cancer. However, melanoma can fool us- in that cancer, the very high mutation rate means that many genes can be recurrently mutated purely by chance. We needed a solution to this problem.”

The team used introns (parts of the genome that don’t code for proteins) and other inactive DNA segments that flank exons, to change that effect. They built an outline for assessing the statistical importance of functional mutations by comparing the frequency of mutations in the exons to the frequency of mutations in the inactive segments.

6 Known Genes and 6 New Genes Identified

This approach identified six known cancer genes and the analysis identified functional mutations in these well-known genes: BRAF, NRAS, PTEN, TP53, CDKN2A, and MAP2K1.

5 new genes were also identified. Most are involved in cancer because they are associated with molecular pathways; however, had not been recognized before as significantly mutated in melanoma. These genes are RAC1, PPP6C, STK19, SNX31, and TACC1. In the tumor samples, their presence ranged from 3-9%.

ARID2 was the 6th new gene associated with the cancer. This gene is a tumor-suppressor holding a great number of loss-of-function mutations that were found in 7 percent of patient samples.

Eran Hodis, co-lead author, computational biologist in the Garraway lab at the Broad Institute, and M.D.-Ph.D. student at Harvard and MIT, said:

“Six new melanoma genes have been picked out from thousands of mutated genes. The same approach may bring clarity to genome sequencing studies of other cancers plagued by high passenger mutation rates, for example lung cancer.”

46% of Driver Mutations Result from UV Damage

New perceptions about the characteristics and frequency of the 21 genes, both old and newly recognized, came from cross-referencing their discoveries with a database of recurrent mutations called COSMIC.

Results showed:

  • 46% of the 262 driver mutations in the 21 genes were caused by UV damage.
  • TP53, the well-known tumor-suppressor, had the largest number of UV-caused mutations
  • Other tumor-suppressing genes also had loss-of-function mutations
  • Each of the newly discovered genes had a high percentage of mutations resulting from UV damage.
  • 3 of the newly identified genes had ‘hotspot’ mutations found in the exact same position in a great deal of patients, which shows these mutations are linked with melanoma.

“We have now discovered the thirst most common hotspot mutation found in melanoma is present in a gene called RAC1, and unlike BRAF and NRAS mutations, this activating mutation is attributable solely to characteristic damage inflicted by sunlight exposure,” said Ian R. Watson, Ph.D., co-lead author of the study and postdoctoral fellow in the Chin lab at MD Anderson.

This Study Provides an Opportunity To Treat Melanoma Better

The authors concluded by saying that much research still needs to be done following the most comprehensive analysis of the melanoma genetics. Melanoma is highly curable, except in the metastatic stage when it becomes deadly. It is important to determine the role these newly identified mutated genes play in biological processes related to melanoma progression and metastasis.

Melanoma has recently become one of the newest success stories for genomics-guided targeted therapy for patients with metastatic diseases, with the advent of the BRAF inhibitor vemurafenib. Unfortunately, this therapy eventually becomes resisted and melanoma patients who do not possess a BRAF (V600) mutation have a limited set of treatments to choose from.

An important next step is to determine whether these 6 newly identified genes are agreeable to targeted therapy, or if their mutations predict sensitivity to presently available drugs, Chin said.

Written by Sarah Glynn