NEJM Study: Mutations ID'd That Lead to Melanoma

Janis C. Kelly

November 11, 2015

A sequence of gene changes associated with melanoma progression has been identified and might lead to tools to help clinicians identify the subgroup of intermediate lesions likely to progress to invasive disease, according to new research.

The findings, which were published online today in the New England Journal of Medicine,are from a proof-of-concept study, said senior author Boris C. Bastian, MD, of the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.

"Future studies should clarify the genetic criteria to stratify low- and high-risk lesions," he told Medscape Medical News.

The team now has a framework that can be used to validate genetic markers that provide diagnostic and/or prognostic value using relevant clinical endpoints, said Dr Bastian.

The goal is to genetically characterize suspicious lesions. "Ideally, this approach would be cost effective and scalable, and a chip-based or a sequencing-based assay could certainly fulfil these criteria," Dr Bastian said.

Melanomas are not a singular entity and will need a protean assay, he suggested. "We anticipate that premalignant lesions are heterogeneous, harboring different propensities to progress towards malignancy," he explained.

In the new study, the team sequenced 293 cancer-relevant genes in 150 areas of 37 primary melanomas and their adjacent precursor lesions. The histopathologic spectrum of these areas included benign lesions, intermediate lesions, and intraepidermal or invasive melanomas.

"The researchers clearly identified DNA changes (mutations) that occur in a stepwise fashion from benign nevi to melanoma," said Anthony J. Olszanski, RPh, MD, a melanoma expert at the Fox Chase Cancer Center, Philadelphia, Pennsylvania, who was not involved in the study.

The team also tied those changes to the age of the individuals whose tissue samples were used and to their related sun exposure.

"Dr Bastian and colleagues provide some of the most compelling scientific evidence to date that UV radiation exposure is a major risk factor for the development of melanoma," Dr Olszanski told Medscape Medical News.

Strong Evidence of the Toxicity of UV Light

The 37 formalin-fixed, paraffin-embedded melanocytic neoplasms were from the archives at the University of California, San Francisco; St. John’s Hospital, London; and University Hospital, Zurich.

Samples were analyzed using targeted sequencing of prespecified cancer genes. The authors write, "We obtained an average sequencing coverage of 281x for the 150 samples, which enabled us to identify somatic mutations even in the presence of a high level of stromal-cell contamination."

The researchers next plotted the mutant allele frequencies of all somatic mutations for the precursor and descendant neoplasms for each case. They write, "In every case, a mutation known to activate the mitogen-activated protein kinase (MAPK) signalling pathway, usually in BRAF or NRAS, could be nominated as the putative initiating oncogene."

There were usually additional mutations in the descendant neoplasms not found in their precursors. These included mutations that contributed to progression, such as disabling frame-shift mutations in the tumor suppressor gene ARIDIA, progression mutations in the TERT promoter, CDKN2A, and genes encoding SWI/SNF subunits.

The researchers found that copy-number alterations were infrequent in benign precursors but were common in descendent neoplasms.

Those associated with progression included deletions of CDKN2A, deletions of PTEN, gains in chromosome 7q that increased the dosage of mutant BRAF, and focused amplifications of MDM2, TERT, and YAP1. Most intermediate areas had multiple pathogenic mutations and a higher mutational burden than benign lesions, and most lesions classified as intermediate on morphologic grounds also had genetic profiles that fell between those for benign lesions and those for malignant neoplasms.

Lesions with BRAF V600E mutations were more common in younger patients with intermittently sun-damage skin, whereas NRAS and BRAF V600K or K601E mutations occurred mainly in older patients with chronically sun-damaged skin. Point mutations accumulated with each histologic stage and in the melanoma areas correlated with cumulative sun exposure.

The authors write, "In aggregate, these results suggest that ultraviolet radiation is a dominant mutagen in the pathogenesis of sun-exposed melanomas that acts throughout all stages of progression, starting with the initiation of precursor lesions, whereas chromosomal instability arises as an additional factor at the transition to the invasive stage."

The Paths to Melanoma

Progression followed two paths. Melanomas arising from benign nevi had BRAF V600E mutations. Melanomas arising from intermediate lesions or melanomas in situ had NRAS mutations or BRAF V600K or K601E mutations.

Only invasive melanomas had loss of both CDKN2A copies, and mutations in SI/SNF chromatin remodeling genes were predominantly found in melanomas. PTEN and TP53 losses were seen only in thicker, invasive melanomas.

The researchers suggest that taken together, the pattern of genetic changes suggested that mutations known to activate the MAPK pathway triggered the progression cascade, followed by activation of telomerase and disruption of the G1-S checkpoint, with TERT promoter mutations as the earliest secondary alterations. They propose that this pattern could help improve melanoma diagnosis.

Dr Olszanski noted that the distinction between an "innocent" mole and melanoma can be difficult for a pathologist to make on the basis of microscopy, and the DNA mutation signatures identified in this study might lead to more aggressive treatment or closer dermatologic follow-up.

Sequencing panels of common cancer genes overlapping with the key mutations identified in this study is currently done primarily to identify "actionable" mutations that might influence treatment. Dr Bastian said that his group does envision clinicians sequencing earlier-stage melanomas with the intention of staging or to determine prognostic information.

A Shift in Understanding Melanoma

This in-depth analysis changed previous assumptions about melanoma biology, sometimes in surprising ways.

Dr Bastian said, "We found that TERT promoter mutations occur early during melanoma progression, a finding that surprised us. TERT encodes the enzymatic subunit of the telomerase complex. Every time a cell divides, the ends of its chromosomes, called telomeres, become shorter until they become exhausted, and the cell will then die.... Upregulation of TERT, through promoter mutations, prevents telomere exhaustion, allowing cells to immortalize, a requirement for cancer cells. We anticipated that TERT mutations would eventually occur, but we expected them to occur significantly later, at a point when the tumors had grown larger, reflecting a higher number of cell divisions."

This contradicts the current dogma that benign lesions are senescent. Dr Boris Bastian

Dr Bastian said that the fact that this occurred so early highlighted a mismatch between the number of cells in the lesion and the number of divisions that had occurred when the lesion was removed. "A significant number of cells must have gotten lost during the evolution of the lesions. Cells making up these lesions must have been proliferating, with the increase in cell number offset by attritional factors. This contradicts the current dogma that benign lesions are senescent," he said.

The fact that the analysis showed that melanomas evolve through distinct progression trajectories linked to specific precursor lesions, not according to the common assumption that a melanocyte becomes a nevus, then transforms into a dysplastic nevus, then to melanoma in situ, and finally to invasive melanoma.

Dr Olszanski advised that while melanoma science moves forward, people should heed known sun damage prevention measures.

"Further studies such as the present one, on a larger sample size, may be able to define patients with the highest probability to develop melanomas, based the mutations found in their lesions. One thing is perfectly clear ― limiting UV radiation exposure through the use of clothing, sunscreen, avoidance of tanning beds, and avoidance of sun exposure, especially at peak times, is sound advice for any person age 0 to 100+," he commented.

One study author has financial relationships with multiple pharmaceutical companies, which are listed in the original article. Dr Bastian and Dr Olszanski report no relevant financial relationships.

N Engl J Med. 2015;373:1926-36. Published online November 11, 2015.


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