The Genetic Evolution of Melanoma from Precursor Lesions

New England Business Journal

Dr. Shain and others from the University of California, San Francisco, Cleveland Clinic, Orlando Health, University Hospital of Zurich, Dorset County Hospital and St. John’s Institute of Dermatology recently published research entitled The Genetic Evolution of Melanoma from Precursor Lesions in The New England Journal of Medicine (Shain, 2015).

These researchers used the NEXTflex™ Rapid DNA-Seq Kit and NEXTflex™ DNA Barcodes to prepare libraries for Illumina sequencing from 25 to 250 ng of DNA isolated from 37 FFPE samples of primary melanomas and their adjacent precursor lesions to determine the order of the occurrence of pathogenic mutations in melanoma. Using targeted sequencing, 293 cancer-relevant genes in 150 areas were sequenced from each melanoma and lesion. The histopathological spectrum of the melanomas and their adjacent lesions included unequivocally benign lesions, intermediate lesions, and intraepidermal or invasive melanomas.

This sequencing revealed that precursor lesions were initiated by mutations of genes that are known to activate the mitogen-activated protein kinase pathway. Unequivocally benign lesions harbored BRAF V600E mutations exclusively, whereas those categorized as intermediate were enriched for NRAS mutations and additional driver mutations. A total of 77% of areas of intermediate lesions and melanomas in situ harbored TERT promoter mutations, a finding that indicates that these mutations are selected at an unexpectedly early stage of the neoplastic progression. Biallelic inactivation of CDKN2A emerged exclusively in invasive melanomas. PTEN and TP53 mutations were found only in advanced primary melanomas. The point-mutation burden increased from benign through intermediate lesions to melanoma, with a strong signature of the effects of ultraviolet radiation detectable at all evolutionary stages. Copy-number alterations became prevalent only in invasive melanomas. Tumor heterogeneity became apparent in the form of genetically distinct subpopulations as melanomas progressed.

This study defined the succession of genetic alterations during melanoma progression, showing distinct evolutionary trajectories for different melanoma subtypes. It identified an intermediate category of melanocytic neoplasia, characterized by the presence of more than one pathogenic genetic alteration and distinctive histopathological features. The study also implicated ultraviolet radiation as a major factor in both the initiation and progression of melanoma.

Shain, A. H., et al. (2015) The Genetic Evolution of Melanoma from Precursor Lesions. The New England Journal of Medicine. 373:1926-1936. doi: 10.1056/NEJMoa1502583.

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