Detection of mutations in SF3B1, EIF1AX and GNAQ in primary orbital melanoma by candidate gene analysis

Abstract

BackgroundOcular melanoma is a rare but often deadly malignancy that arises in the uvea (commonest primary site), conjunctiva or the orbit. Primary orbital melanoma (POM) is exceedingly rare, with approximately 60 cases reported to date. Despite recent advances in our understanding of the genetics of primary uveal and conjunctival melanomas, this information is lacking for POM.MethodsDNA was extracted from 12 POM tissues, with matched germline DNA (where available). MLPA was conducted to detect chromosomal alterations and Sanger sequencing used to identify point mutations in candidate melanoma driver genes (BRAF, NRAS, KRAS, GNA11, GNAQ), and other genes implicated in melanoma prognosis (EIF1AX, SF3B1). Immunohistochemistry was performed to analyse BAP1 nuclear expression.ResultsMLPA detected copy number alterations in chromosomes 1p, 3, 6 and 8. Sequencing of melanoma driver genes revealed GNAQ (p.Q209L) mutations in two samples; although it is possible that these samples represent extraocular spread of an occult uveal melanoma. A recurrent mutation in SF3B1 (p.R625H) was observed in indolent, but not aggressive, tumours; a mutation in EIF1AX (p.N4S) was detected in one patient with non-aggressive disease.ConclusionsEIF1AX and SF3B1 mutations appear have a role in determining the clinical course of POM and detection of these changes could have clinical significance. Further in depth analysis of this rare group using differing ‘omic technologies will provide novel insights into tumour pathogenesis.

Primary orbital melanoma

“…3,4 The clinicopathological features of primary orbital melanoma are very similar to those of uveal melanoma. The findings of GNAQ, SF3B1, EIF1AX mutations 5 and GNA11 mutation in this case provide further evidence that primary orbital melanoma has a close pathogenic relationship with uveal melanoma.…”

Design and Testing of a Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA

“…Both DDX3X and EIF1AX mutations account for 10% of melanomas and they generally co-occur with NRAS mutations [27,28]. Although their removal from the panel should have no significant impact on the overall detection rate of mutations in ctDNA, these mutations may have prognostic value [31][32][33] and improving amplicon design will be explored. Another option to improve the detection rate of our panel would be to increase the mutation analysis coverage of NF1.…”

The biological function and clinical significance of SF3B1 mutations in cancer

“…These mutations are also present in 20% of patients with myelodysplastic/myeloproliferative neoplasm (MDS/MPN) [ 41 ] and in 15% of patients with chronic myeloid leukemia (CLL) [ 58 – 60 ] . More recently, SF3B1 mutations have been identified at relatively high frequency in some solid tumors, such as various pigmented tumors, including uveal melanoma (UM) [ 61 , 62 ], mucosal melanoma [ 63 ], leptomeningeal melanoma [ 64 ] and blue nevus-like cutaneous melanoma [ 65 ], and neuroblastomas that arise following chromothripsis [ 66 ], estrogen receptor-positive breast cancers (BC) [ 67 ], pancreatic ductal adenocarcinoma [ 68 ], prostate cancer [ 69 ], prolactinomas [ 70 ], acute myeloid leukemia [ 71 , 72 ], and many others [ 73 – 75 ].…”