SF3B1 and EIF1AX mutations occur in primary leptomeningeal melanocytic neoplasms; yet another similarity to uveal melanomas

Abstract

Introduction: Like uveal melanomas, primary leptomeningeal melanocytic neoplasms (LMNs) frequently carry GNAQ and GNA11 mutations. However, it is currently unknown whether these LMNs harbor mutations in BAP1, SF3B1 and/or EIF1AX like uveal melanomas as well. In this study, we used Sanger sequencing for the detection of mutations in SF3B1 (hotspots in exon 14 and 15) and EIF1AX (exon 1 and 2 and flanking intronic regions) in a series of 24 primary LMNs. Additionally, BAP1 immunohistochemistry was used as a surrogate marker for the detection of inactivating mutations in the BAP1 gene.

Results: Mutations in either SF3B1 or EIF1AX were identified in 8 out of 24 primary LMNs (33 %). The presence of these mutations was mutually exclusive and occurred in primary LMNs of different malignancy grades (melanocytomas, intermediate-grade melanocytic tumors, melanomas). Complete absence of nuclear BAP1 staining as is typically seen in BAP1-mutated tumors was not observed.

Conclusions: Our finding that an SF3B1 or EIF1AX mutation is present in a substantial subset of primary LMNs underscores that these tumors genetically resemble uveal melanoma and are different from cutaneous melanoma at the genetic level. This information may not only aid in the differential diagnosis of primary versus metastatic melanocytic tumor in/around the central nervous system, but also in the identification of more promising therapeutic approaches targeting the molecular pathways involved in the oncogenesis of LMNs. As none of the primary LMNs in our series showed complete loss of nuclear BAP1 protein, it is unlikely that BAP1 mutations are frequent in these tumors but the role of this gene warrants further investigation.

Fig. 1

Examples of SF3B1 mutation in a primary leptomeningeal melanocytoma and intermediate-grade melanocytic tumor. a. Hematoxylin-and-Eosin (H&E) staining of the melanocytoma of patient #4 showing round to oval, slightly pleomorphic, vesicular nuclei, often with a prominent nucleolus, and with dispersed melanin pigment in the cytoplasm of the tumor cells. b. BAP1 immunostaining of this melanocytoma revealed heterogeneous staining of the tumor cell nuclei, the majority of these nuclei being positive. The arrows indicate nuclear staining in endothelial cells. Note that the tumor cells also show variable cytoplasmic staining. c. H&E staining of the intermediate-grade melanocytic tumor of patient #18 showing a proliferation of spindle cells with invasion in glial tissue (at the right). d. BAP1 immunostaining of the tumor depicted in (c) reveals positive nuclei in more than 90 % of tumor cells. The arrows indicate nuclear staining in endothelial cells. e. Forward sequence tracing surrounding codon 634 of SF3B1 showing the c.1900G > A (p.(Val634Ile)) mutation detected in the tumor depicted in (a) and (b). f. Forward sequence tracing surrounding codon 625 of SF3B1 showing the c.1873C > T (p.(Arg625Cys)) mutation present in the tumor depicted in (c) and (d)

Fig. 2

SF3B1 mutation in primary leptomeningeal melanoma in a patient with neurocutaneous melanocytosis. a. H&E staining of the primary LMN diagnosed as melanoma; the arrows indicate mitotic figures (patient #21). b. H&E staining of the congenital melanocytic nevus of the buttocks; in the right lower corner higher magnification of the superficial part of the nevus with a proliferation of bland nevoid cells. c. BAP1 immunostaining of the melanoma depicted in (a) with nuclear staining in more than 90 % of tumor cells. d. Sequence tracing surrounding codon 61 of NRAS showing a c.182A > G (p.(Gln61Arg)) mutation present in both the CNS melanoma as well as in the congenital melanocytic nevus (reverse sequence/antisense strand). e. Forward sequence tracing surrounding codon 625 of SF3B1 showing a c.1874G > A (p.(Arg625His)) mutation in the CNS melanoma. f. The SF3B1 mutation depicted in (e) is absent in the congenital melanocytic nevus of this patient

Fig. 3

Examples of EIF1AX mutation in a primary leptomeningeal melanocytoma and intermediate-grade melanocytic tumor. a. H&E staining of the melanocytoma of patient #2, consisting of epithelioid cells with moderate to strong melanin pigmentation. b. BAP1 immunostaining of the melanocytoma depicted in A revealing positive staining of nuclei in more than 90 % of tumor cells. The arrows indicate nuclear staining in endothelial cells. Note that cytoplasmic staining is also present. c. H&E staining of the intermediate-grade melanocytic tumor of patient #19 showing a nested proliferation of epithelioid cells; the arrow indicates a mitotic figure. d. BAP1 immunostaining of the intermediate-grade melanocytic tumor depicted in C revealing positive staining of nuclei in more than 90 % of tumor cells. e. Forward sequence tracing surrounding codon 3 of EIF1AX showing a c.9G > C (p.(Lys3Asn)) mutation in the melanocytoma depicted in (a) and (b). f. Forward sequence tracing surrounding codon 10 of EIF1AX showing a c.28A > G (p.(Lys10Glu)) mutation in the intermediate-grade melanocytic tumor depicted in (c) and (d)