Skip to main content
Premium Trial:

Request an Annual Quote

Examining Genetic Mutations in Melanoma, Researchers Find 'Intermediate Type' of Lesion

NEW YORK (GenomeWeb) – By examining the order in which genetic mutations crop up in melanoma, a University of California, San Francisco-led team of researchers uncovered genetic evidence for an intermediate type of lesion that falls between benign lesions and unequivocal melanoma.

The team sequenced nearly 300 cancer-linked genes in 150 samples that included both primary melanomas and their adjacent precursor lesions. As they reported yesterday in the New England Journal of Medicine, the researchers found that benign lesions harbored BRAF V600E mutations, while intermediary ones were enriched for NRAS and other driver mutations. Advanced melanomas were the only lesions with PTEN and TP53 mutations.

At all stages, the researchers noted mutational signatures that are associated with ultraviolet radiation, suggesting sun exposure is a key element in melanoma development and progression.

"[O]ur study defined the succession of genetic alterations during melanoma progression and can serve as the foundation for formulation of refined criteria for diagnosis and prognostication," UCSF's Boris Bastian and his colleagues wrote in their paper. "It revealed an intermediate category of melanocytic neoplasia, characterized by the presence of more than one pathogenic genetic alteration."

Bastian and his colleagues gathered 37 FFPE melanocytic neoplasms and microdissected 150 regions, which included melanomas and their nearby precursor regions, for sequencing. They then performed targeted sequencing on these samples, focusing on 293 cancer genes. Overall, the researchers obtained an average sequencing coverage of 281X for these samples.

This level of coverage, they said, enabled them to identify somatic mutations and compare mutations and copy number changes among the samples.

The researchers plotted the somatic mutations for each precursor and descendant neoplasm. Clonal mutations seen in both early and later lesions — such as BRAF V600E — likely occurred early on in melanoma development. This, they added, indicates that MAPK pathway-activating mutations touch off melanoma progression.

Descendant neoplasms, they noted, then accumulated additional mutations not present in the precursors, such as ARID1A, TERT, CDKN2A, and SWI/SNF gene mutations. That is, they noted, initiating events were followed by mutations that activated telomerase and disrupted the G1-S cell cycle checkpoint.

They further examined differences in copy number through uncovering deviations in read depth as compared to a reference pool of normal tissues. CNVs, the researchers noted, were more common in latter-stage lesions, and changes linked to progression included CDKN2A and PTEN deletions as well as chromosome 7q gains and MDM2, TERT, and YAP1 amplifications.

Using all this, the researchers developed a phylogenetic tree for each case.

While most melanocytic neoplasms can be easily classified into benign or malignant categories with high inter-observer agreement, a number of neoplasms fall into a grey area that's less easily classifiable.

Thirteen samples unanimously considered to be benign had only BRAF V600E mutations, while 19 out of the 21 intermediate samples had multiple pathogenic mutations. This, they noted, indicates that most intermediate lesions classified morphologically also had genetic characteristics that aren't quite benign and not quite malignant neoplasms.

This, Bastian and his colleagues, could help resolve a decades-long controversy about dysplastic nevi, enlarged acquired nevi that have a propensity to evolve into melanoma.

The researchers also noted two modes of progression: melanomas with BRAF V600E mutations arose from benign nevi, while melanomas with NRAS mutations, BRAF V600K, or BRAF K601E mutations were associated with intermediate lesions of melanomas in situ that had already accumulated other mutations.

Despite differences in the initiating oncogenes, the researchers found strong similarities in mutations that were later accumulated. For instance, TERT promoter mutations were found in early intermediate lesions and melanomas in situ, while loss of CDKN2A was only observed in invasive melanomas and mutations in the SWI/SNF chromatin remodeling genes were mostly found in invasive melanomas.

That is, melanocytic neoplasms evolved linearly initially, then as they progressed, they switched to branch evolution, leading to tumor heterogeneity.

Bastian and his colleagues also noted that the number of point mutations increased with each histological stage and exhibited a signature reflecting the effect of ultraviolet radiation. This increase in mutational burden, they added, correlated with cumulative sun exposure.