GAB2 amplifications refine molecular classification of melanoma

Abstract

Purpose: Gain-of-function mutations in BRAF, NRAS, or KIT are associated with distinct melanoma subtypes with KIT mutations and/or copy number changes frequently observed among melanomas arising from sun-protected sites, such as acral skin (palms, soles, and nail bed) and mucous membranes. GAB2 has recently been implicated in melanoma pathogenesis, and increased copy numbers are found in a subset of melanomas. We sought to determine the association of increased copy numbers of GAB2 among melanoma subtypes in the context of genetic alterations in BRAF, NRAS, and KIT.

Experimental design: A total of 85 melanomas arising from sun-protected (n = 23) and sun-exposed sites (n = 62) were analyzed for copy number changes using array-based comparative genomic hybridization and for gain-of-function mutations in BRAF, NRAS, and KIT.

Results: GAB2 amplifications were found in 9% of the cases and were associated with melanomas arising from acral and mucosal sites (P = 0.005). Increased copy numbers of the KIT locus were observed in 6% of the cases. The overall mutation frequencies for BRAF and NRAS were 43.5% and 14%, respectively, and were mutually exclusive. Among the acral and mucosal melanomas studied, the genetic alteration frequency was 26% for GAB2, 13% for KIT, 30% for BRAF, and 4% for NRAS. Importantly, the majority of GAB2 amplifications occurred independent from genetic events in BRAF, NRAS, and KIT.

Conclusions: GAB2 amplification is critical for melanomas arising from sun-protected sites. Genetic alterations in GAB2 will help refine the molecular classification of melanomas.

Fig.1

GAB2 amplifications in melanoma by array-based comparative genomic hybridization. Supervised hierarchical clustering of copy number data shows clustering among melanomas arising from sun-protected sites (acral and mucosal melanoma subtypes).

Fig.2

Representative examples of cases with GAB2 amplifications that are wild-type for BRAF, NRAS, and KIT. These cases show high levels of GAB2 protein expression by immunohistochemistry. Note the absence of staining of the overlying epidermis as a negative control (top).

Fig.3

Frequency distributionof genetic alterations in GAB2,KIT, BRAF, and NRAS among two groups of melanoma. Sun-protected sitesinclude cases occurring onacral sites (palms and soles) and mucous membranes. Sun-exposed sites include melanomas arising from the head, neck, trunk, and extremities. BRAF and NRAS mutations were mutually exclusive. Two cases, one occurring on a sun-protected site and the other on a sun-exposed site, showed increased copy numbers in both GAB2 and KIT. **, P = 0.005, statistically significant association of GAB2 amplification with melanomas arising from sun-protected sites (acral and mucosal melanomas).