Fatal melanoma with a novel MYO5A-BRAF fusion and small associated conventional nevus: A case report and review of literature

Melanoma With RNF11::BRAF Fusion: A Novel Fusion Previously Undescribed in Melanoma

ABSTRACT

B-Raf Proto-Oncogene ( BRAF ) fusions are rare in melanomas. We present a case of cutaneous melanoma with a Ring Finger Protein 11 ( RNF11 ) ::BRAF fusion in a 63-year-old man with a history of stage IB melanoma on the right upper back (pT2apN0cM0; nonulcerated with a Breslow thickness of 1.2 mm). Despite initial treatment, the melanoma progressed to multiple metastases. Histopathologically, the tumor cells exhibited epithelioid and rhabdoid morphologies, with occasional giant pleomorphic cells and multinucleation, and were positive for antimelanocytic cocktail (HMB45, Melan-A, tyrosinase) and S100. Next-generation sequencing of a metastatic specimen identified an RNF11::BRAF fusion and TERT promoter mutation, but no other somatic mutations (eg, BRAF , NRAS , KIT ) or copy number variations were detected. The patient died to melanoma approximately 58 months after initial diagnosis, despite several lines of systemic therapy, including immunotherapies and a mitogen-activated protein kinases 1 and 2 inhibitor. RNF11::BRAF fusions are known oncogenic drivers in histiocytic disorders such as Erdheim-Chester disease and non-Langerhans cell histiocytosis. Although BRAF fusions are commonly observed in Spitz melanocytic neoplasms, the discovery of the RNF11::BRAF fusion in melanomas is unprecedented. Our case represents a triple wild-type, clinically aggressive melanoma of possibly non-Spitz lineage with an ultraviolet signature and a rare BRAF fusion, contributing to the expanding body of literature on BRAF -fused melanomas.

Spitz melanoma

It has long been recognized that the histopathologic differential diagnosis between Spitz nevus and melanoma is sometimes extraordinarily difficult. Both can be composed of large oval to spindled melanocytes with abundant cytoplasm and large nuclei. Genomic studies over the last decade have clarified that Spitz tumors have diverse genetic initiating events, and that for each of these, there are benign, intermediate grade, and malignant lesions. Another discovery is that some melanomas can resemble Spitz tumors morphologically but have conventional initiating mutations (eg, BRAF and NRAS). The current World Health Organization definition of Spitz tumors restricts the spectrum to neoplasms with an activating mutation affecting the MAP kinase pathway, mostly fusions involving kinase genes. Whether splitting off Spitz tumors from other neoplasms that are only morphologically spitzoid will stand the test of time is uncertain, but for now, it does bring order to what has been a complex area. The recognition of Spitz melanoma will enable classification, follow-up, and the delineation of rational treatment guidelines for this important group of tumors, most of which are in young people. The author reviewed the logic of the World Health Organization definition of Spitz tumors, the spectrum of tumors produced by initiating mutations, and problems with the definition of Spitz melanoma and provides an example of this rare entity in the context of related tumors.

Fatal Spitz Melanoma With MAD1L1::BRAF Fusion: A Case Report and Literature Review

Spitz melanoma is extremely rare, and only a few cases of distant metastases have been reported. Herein, we describe a case of Spitz melanoma with multiple distant metastases. A 37-year-old woman presented with a 5.5-mm-diameter nodule on the right lower leg. She experienced multiple distant metastases, involving the lungs, liver, thyroid, stomach, ovary, bones, and skin, along with multiple lymph node metastases within 1 year. The patient succumbed to the disease 1 year and 6 months following the first excision. Histopathological examination revealed a dense distribution of large solid nests comprising large, atypical epithelioid melanocytes with abundant eosinophilic cytoplasm in the upper dermis. Diffuse PRAME and loss of p16 immunoexpression profiles were observed. Targeted DNA and Sanger sequencing revealed an in-frame MAD1L1(e16)::BRAF(e9) fusion in both primary tumor and metastatic subcutaneous lesion. A review of previously reported cases confirmed as Spitz melanoma with distant metastases (n = 7) revealed a broad age range (11-71 years, median 46 years), high mortality (5/7), frequent BRAF fusions (6/7), and recurrent TERT promotor mutations and CDKN2A/B deletions. This report adds valuable insights into our understanding of the clinical and genetic characteristics of Spitz melanoma with distant metastases.

[Clinical, histological and genetic correlations in melanocytic tumours with chromosomal rearrangements]

In some tumoral subtypes chromosomal translocations lead to an oncogenic chimeric protein acting as a tumorigenesis driver event. The main fusion model combines the promoter swapping of an inactivated tumor suppressor gene and a functional kinase that evades its regulatory system. The range of described fusions keeps growing in the 2023 WHO classification of melanocytic tumours. It is not limited to the group of Spitz tumours as previously but now extends to blue tumours and dermal tumours with a melanocytic phenotype. Molecular pathology helps detect these anomalies using clinical and morphological features. This analysis is essential as this strongly conditions the adapted local treatment of such tumours who are often overtreated.

Histopathologic, genomic, transcriptomic, and functional characteristics of eight melanocytic tumors with BRAF fusions showing stronger MAPK pathway activation compared to BRAF V600E tumors

BACKGROUND

Activating BRAF gene alterations are central to melanocytic tumor pathogenesis. A small, emerging subset of melanocytic tumors driven by BRAF fusions has distinct therapeutic implications and has been described to have Spitzoid morphology patterns. However, such morphological patterns do not encompass all cases, and little is known about the functional molecular events.

MATERIALS AND METHODS

We conducted a retrospective search through our molecular archives to identify melanocytic tumors with BRAF fusions. We reviewed clinical, histopathological, and genomic features. We further explored transcriptomic and protein-level findings.

RESULTS

Histopathologic patterns varied, with many cases without a distinctive pattern. We identified novel and diverse BRAF gene fusion partners. Differential transcriptomic analysis between low-risk BRAF fusion tumors and reference BRAF V600E tumors showed no differentially expressed genes. However, quantitatively stronger MAPK pathway activation of BRAF fusion tumors over BRAF V600E tumors was demonstrated by statistically significant stronger staining of p-ERK immunohistochemistry. Gene-specific RNA analysis shows comparable BRAF transcript levels between the two groups.

DISCUSSION AND CONCLUSION

The quantitatively stronger activation of the MAPK pathway of BRAF fusion tumors, instead of qualitatively different transcriptomes, may account for the morphology difference from conventional BRAF V600E tumors. BRAF fusions likely act through dysregulated protein function rather than RNA upregulation related to the characteristics of the fusion partners.

Novel gene fusion discovery in Spitz tumours and its relevance in diagnostics

In addition to morphologic analysis, molecular diagnostic work up of Spitz tumours is often of great value for their accurate diagnosis/classification. Nowadays, next-generation sequencing (NGS) is the predominant screening method in molecular diagnostics. Up to 80% of these melanocytic neoplasms comprise gene fusions as genetic anomalies for which the driver codes for a protein harbouring a kinase domain. However, because of the variety of fusion partners the use of PCR-based targeted enrichment NGS methods is not recommended. We describe a series of four Spitz tumour samples in which distinct gene fusions were detected by hybridisation-based capture NGS (TPM3::ALK, LIMA1::ROS1, LRRFIP2::ROS1 and MYO5A::RET). Two of these fusions are not previously described. All 4 fusions were confirmed by reverse transcription-PCR. These findings demonstrate the need for molecular analysis that can detect unknown fusions in Spitz neoplasms for optimal diagnosis.