Probing the Melanoma Genome Reveals New Targets and Challenges

Jane de Lartigue, PhD
Published: Friday, Jun 17, 2016
The past 5 years have witnessed a dizzying pace of progress for the treatment of melanoma, with nearly a dozen new molecularly targeted and immune-based therapies transforming the disease from an aggressively lethal malignancy into one that is readily treatable.

Next-generation sequencing technology is providing greater insight and has uncovered new and unexpected players in melanoma. It has also revealed one of the highest rates of somatic mutations among all types of cancer, presenting a significant challenge to pick out the true drivers of this disease. Tackling this challenge will likely have important implications for prognosis and therapy in the future.

Expanding Treatment Options

Melanoma is a malignant tumor of the skin pigment–producing melanocytes. As researchers have begun to characterize melanoma at the molecular level, it has become clear that the mitogen- activated protein kinase (MAPK) pathway is a key mediator of growth and proliferation.

Meanwhile, attempts to target other components of the MAPK pathway led to approval of inhibitors of the kinase immediately downstream of BRAF, mitogen-activated protein kinase kinase (MEK). Melanoma also has been the poster child for immunotherapies that boost the antitumor immune response, particularly immune checkpoint inhibitors. The cytotoxic T-lymphocyte antigen 4 (CTLA-4) inhibitor ipilimumab (Yervoy) launched the field and was followed by drugs targeting programmed cell death-1 (PD-1) receptor and its ligands PD-L1 and PD-L2. Pembrolizumab (Keytruda) and nivolumab (Opdivo) both received regulatory approval in 2014, and were joined by the first immune combination therapy of ipilimumab plus nivolumab in 2015.

UV Damage Leaves Characteristic Marks

For the most part, comprehensive genome-wide studies have focused on the most common and aggressive form of melanoma, cutaneous melanoma. Numerous whole-genome and whole-exome studies have been performed, and melanoma was also among the tumor types chosen by The Cancer Genome Atlas (TCGA) as part of its sequencing efforts.


Somatic Mutations in Melanoma

1. Lovly C, Pao W, Sosman J. My Cancer Genome website. Updated January 26, 2016. Accessed June 2, 2016.
2. The Cancer Genome Atlas Network. Cell. 2015;161(7):1681-1696.
3. Harbour JW, Onken MD, Roberson ED, et al. Science. 2010;330(6009):1410-1413.

Ultraviolet radiation (UVR) is the major environmental risk factor for cutaneous melanoma and this has been reflected in the genomic profiles uncovered in sequencing studies. The vast majority of tumors display a genomic signature indicative of damage caused by UVR, dominated by cytosine-to-thymine (C>T) nucleotide substitutions and CC>TT mutations. In the TCGA’s study, 76% of primary and 84% of metastatic tumors displayed a UVR signature of >60% C>T transitions and >5% CC>TT mutations.

Genome sequencing studies also revealed the strikingly high number of somatic mutations in melanoma. According to the TCGA, there were 16.8 mutations/Mb, the highest reported for any cancer evaluated through the program. The high mutational load is thought to result from UV radiation exposure and the high prevalence of C>T substitutions. Furthermore, it’s thought that this is what makes melanomas so immunogenic and thus uniquely susceptible to immunotherapies.

Unveiling Key Players Old and New

Predictably, the standout finding has been the identification of BRAF mutations across all studies, in 50%-60% of cutaneous melanomas. The most common type of BRAF mutation, in up to 90% of cases, results in the substitution of a valine at position 600 to a glutamic acid (V600E).

BRAF mutations are associated with increased sensitivity to BRAF- and MEK-targeted therapies, and determination of BRAF mutation status is a prerequisite for treatment with these drugs. Currently, BRAF and MEK inhibitors are only approved for use in advanced-stage melanomas, but mounting evidence suggests that BRAF mutations can be identified in earlier stages of melanoma.

Numerous other driver genes have now been identified in melanoma, including other components of the MAPK pathway. After BRAF, the most frequently somatically altered gene in melanoma is NRAS, a member of the RAS GTPase family of proteins, which sits upstream of BRAF in the MAPK pathway, recruiting it to the cell membrane to be activated.

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View Conference Coverage
Online CME Activities
TitleExpiration DateCME Credits
Advances in™ Melanoma: Exploring BRAF/MEK in Adjuvant and Neoadjuvant SettingsSep 28, 20191.5
Medical Crossfire®: What Does Data Tell Us About How to Optimize Checkpoint Inhibitor Strategies Across Lines of Care for Patients with Melanoma?Nov 30, 20191.5
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