It’s
been a burning question in melanoma research: Tumor cells are full of
ultraviolet (UV)-induced genetic damage caused by sunlight exposure, but
which mutations drive this cancer?
None
have been conclusively tied to melanoma. The sheer abundance of these
passenger mutations has obscured the search for genetic driver mutations
that actually matter in melanoma development and progression.
By
creating a method to spot the drivers in a sea of passengers,
scientists at the Broad Institute of MIT and Harvard, the Dana-Farber
Cancer Institute and The University of Texas MD Anderson Cancer Center
have identified six genes with driving mutations in melanoma, three of
which have recurrent ‘hotspot’ mutations as a result of damage inflicted
by UV light. Their findings are reported in the July 20 issue of the
journal Cell.
“Those
three mutations are the first ‘smoking gun’ genomic evidence directly
linking damage from UV light to melanoma,” said co-senior author Lynda
Chin, M.D., Professor and Chair of MD Anderson’s Department of Genomic
Medicine. “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,” said
Chin, who also is scientific director of MD Anderson’s Institute for
Applied Cancer Science.
The
six new melanoma genes identified by the team are all significantly
mutated and provide potential targets for new treatments.
Puzzle has thousands of potential pieces, but only requires a few dozen
A
number of important mutations had previously been identified as
melanoma drivers. These include BRAF (V600) mutations, present in half
of all melanomas, and NRAS (Q61) mutations. However, the vast majority
of these mutations do not appear to be caused by direct damage from UV
light exposure.
Those
known mutations are important, but don’t tell the whole story.
Melanoma, the authors note, has higher genetic mutation rates than most
other types of solid tumors. The majority are attributable to passenger
mutations caused by UV light damage resulting in a DNA alteration called
a cytidine (C) to thymidine (T) transition.
Chin
together 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, sequenced the exons—active
portions of DNA involved in protein synthesis—in 121 melanoma samples
paired with normal DNA and found 86,813 coding mutations. The resulting
mutation rate was higher than that ever reported in any other tumor
type.
Among
the most frequently mutated genes, 85% of the active coding mutations
resulted from C to T transitions caused by UV light exposure.
Statistical
approaches to identify driver mutations have often assumed that the
baseline mutation rate is uniform across the genome. The abundance of
UV-induced passenger mutations that vary in frequency confounds this
assumption in melanoma, the researchers report.
“When
a gene is found to be repeatedly mutated, we naturally assume that it
must be important to the cancer,” said Garraway, who is co-senior author
with Chin on the study. “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.”
To
counter this effect, the researchers turned to parts of the genome that
don’t code for proteins, called introns, and other inactive DNA
segments that flank exons. By comparing the frequency of mutations in
the inactive segments to the frequency of mutations in the exons, the
researchers built a framework for assessing the statistical significance
of functional mutations.
Approach identifies six known cancer genes, six new ones
The analysis identified functional mutations in the well-known cancer genes BRAF, NRAS, PTEN, TP53, CDKN2A and MAP2K1.
It
also uncovered five new genes, RAC1, PPP6C, STK19, SNX31, and TACC1.
Most are associated with molecular pathways involved in cancer but had
not been previously recognized as significantly mutated in melanoma.
Their presence in the tumor samples ranged from 3% to 9%.
The
sixth new gene tied to melanoma was ARID2, an apparent tumor-suppressor
gene possessing a significant number of loss-of-function mutations
found in 7% of patient samples.
“Six
new melanoma genes have been picked out from thousands of mutated
genes,” said Eran Hodis, co-lead author who is a computational biologist
in the Garraway lab at the Broad Institute and an M.D.-Ph.D. student at
Harvard and MIT. “The same approach may bring clarity to genome
sequencing studies of other cancers plagued by high passenger mutation
rates, for example lung cancer.”
UV damage causes 46% of driver mutations
The
team then cross-referenced their findings with a database of recurrent
mutations called COSMIC and gained new insights in the frequency and
characteristics of driver mutations, old and newly discovered, in 21
genes.
Out
of 262 driver mutations in the 21 genes, 46% were caused by UV-induced
damage. The well-known tumor-suppressing gene TP53 had the greatest
number of UV-caused mutations. Other tumor-suppressors also had
loss-of-function mutations and all of the newly identified genes had a
high percentage of mutations caused by UV damage.
Most
exciting, three of the discovered genes possessed ‘hotspot’ mutations
found in the exact same position in multiple patients providing another
line of evidence indicating these mutations contribute to melanoma.
“We
have now discovered the third 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.
New insights provide opportunity to better understand, treat melanoma
Much
work remains following the most comprehensive analysis of the genetics
of melanoma, the authors noted. If diagnosed early, melanoma is highly
curable, but in its metastatic stage is lethal. Determining the role
these mutated genes play in biological processes important for melanoma
progression and metastasis provides a new avenue of investigation into
the molecular basis of this disease.
With
the advent of the BRAF inhibitor vemurafenib, melanoma has emerged as
the latest success story for genomics-guided targeted therapy in
treatment of patients with metastatic disease. However, melanoma
eventually resists this therapy and effective treatment options for
patients that do not possess a BRAF (V600) mutation are limited.
Determining
whether these newly discovered genes are amenable to targeted therapy,
or whether their mutations predict sensitivity to currently available
drugs, Chin said, will be an important next step in translating these
findings into the clinic.
