Genomic Profiling of Metastatic Uveal Melanoma Shows Frequent Coexisting BAP1 or SF3B1 and GNAQ/GNA11 Mutations and Correlation With Prognosis

• Published in: American journal of clinical pathology Vol. 158; no. 2; pp. 177 - 186
• Main Authors: Isaacson, Alexandra L, Sompallae, Ramakrishna R, Guseva, Natalya V, Bellizzi, Andrew M, Bossler, Aaron D, Ma, Deqin
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 04-08-2022
• Subjects: Ethylenediaminetetraacetic acid; Genes; Genetic aspects; Health aspects; Immunohistochemistry; Medical prognosis; Melanoma; Metastases; Metastasis; Mutation; Next-generation sequencing; Prognosis; Therapeutic targets; Uveal melanoma; Genomic profiling; SF3B1; BAP1
• ISSN: 0002-9173; 1943-7722
• DOI: 10.1093/ajcp/aqac019

Abstract
Objectives
To identify therapeutic targets and correlate with clinical outcomes from mutation profiling of metastatic uveal melanoma (UM) using next-generation sequencing (NGS).
Methods
Melanoma cases that were tested using DNA-based NGS panels of 25 and/or 214 genes were evaluated retrospectively (263 cases) and identified 27 UM cases. BAP1 expression was examined by immunohistochemistry.
Results
Mutations in GNA11 (14) and GNAQ (12) were found in 96% (n = 27) of cases of UM, and most had coexisting BAP1 (17) or SF3B1 (4) mutations. Coexisting GNAQ/11-SF3B1 mutations correlated with a longer average time to first metastasis compared with GNAQ/11-BAP1 mutations (99.7 vs 38.5 months, P = .047). Three patients with BAP1 mutations received trametinib; two are still alive (15 months; 23 months), and one died (32 months). In non-UMs, only 4.2% (n = 236) had BAP1 and 3.8% had SF3B1 mutations; none had coexisting GNAQ/11 mutations.
Conclusions
Coexisting BAP1/SF3B1 and GNAQ/11 mutations were unique to UM. SF3B1 mutations were reported to be UM-specific in melanoma and associated with rare/no metastasis. The finding of mutated SF3B1 in 14.8% (n = 27) of UMs suggests its role should be further evaluated. The correlation of BAP1/SF3B1 mutation with survival also warrants investigation.