BAP1 mutations in uveal melanoma

Abstract

Purpose: Uveal melanoma (UM) is the most common primary intra-ocular malignancy in adults. It has a strong tendency to metastasize to the liver. Monosomy of chromosome 3 is the most frequent found chromosomal aberration in UM and predominantly found in metastasizing tumours. Inactivating somatic mutations have been described in the BRCA-associated protein 1 (BAP1) gene, located on chromosome 3q21.1, in class II UMs (Harbour et al, 2010). In this study we determine the prevalence of BAP1 mutations in specific subgroups of UM patients and examine BAP1 expression in UM tissue.

Methods: Ciliary body and choroidal melanomas were subjected to BAP1 mutation analysis using several techniques such as targeted Next Generation Sequencing, deep sequencing with a custom designed HaloPlex Target Enrichment kit, and exome sequencing. Variations were validated by Sanger sequencing. Protein expression of BAP1 in UM samples was analyzed by immunohistochemical staining in which expression in the RPE functioned as our internal positive control. BAP1 mutation status was correlated with disease-free survival, clinical and histopathological factors and copy number variations detected by fluorescence in situ hybridization (FISH) and SNP-array analysis.

Results: Mutations in BAP1 have hitherto been identified in 31.4% (16/51) of the tumors. More specific, the analyzed set of UM samples contained 3 missense mutations, 2 nonsense mutations, 5 frameshift deletions, 2 non-frameshift deletions, and 4 splice site mutations. Positive BAP1 immunohistochemical staining was observed in 52.9% (27/45) of UMs and no expression was seen in 35.3% (18/45) of the cases. Two out of the 15 tumors with BAP1 mutations and 5 out of 30 wild type BAP1 tumors showed no staining. Correlations were found between BAP1 mutation status and BAP1 expression at tissue level, and also between BAP1 mutations and monosomy 3 (P=0.000 and P=0.000, respectively). Univariate analyses of BAP1 mutated cases compared to wild type showed a significantly decrease in disease-free survival (43.2 versus 94.0 months, respectively, P=0.002).

Conclusions: Deep sequencing revealed somatic mutations in the BAP1 gene in nearly a third of the UMs. BAP1 mutations and gene expression seems to play a role in the UM pathogenesis towards metastatic disease.

Keywords: 589 melanoma • 745 uvea • 604 mutations