Integrating Next-Generation Sequencing with Morphology Improves Prognostic and Biologic Classification of Spitz Neoplasms

Abstract

The newest World Health Organization classification of skin tumors suggests the elimination of cases with BRAF and NRAS mutations from the categories of Spitz tumors (ST) and Spitz melanoma (SM). The objective of this study is to better characterize the genomics of Spitz neoplasms and assess whether the integration of genomic data with morphologic diagnosis improves classification and prognostication. We performed DNA and RNA sequencing on 80 STs, 26 SMs, and 22 melanomas with Spitzoid features (MSF). Next-generation sequencing data were used to reclassify tumors by moving BRAF and/or NRAS mutated cases to MSF. In total, 81% of STs harbored kinase fusions and/or truncations. Of SMs, 77% had fusions and/or truncations with eight involving MAP3K8. Previously unreported fusions identified were MYO5A-FGFR1, MYO5A-ERBB4, and PRKDC-CTNNB1. The majority of MSFs (84%) had BRAF, NRAS, or NF1 mutations, and 62% had TERT promoter mutations. Only after reclassification, the following was observed: (i) mRNA expression showed distinct clustering of MSF, (ii) six of seven cases with recurrence and all distant metastases were of MSFs, (iii) recurrencefree survival was worse in MSF than in the ST and SM groups (P ¼ 0.0073); and (iv) classification incorporating genomic data was highly predictive of recurrence (OR 13.20, P ¼ 0.0197). The majority of STs and SMs have kinase fusions as primary initiating genomic events. The elimination of BRAF and/or NRAS mutated neoplasms from these categories results in the improved classification and prognostication of melanocytic neoplasms with Spitzoid cytomorphology.

BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases

“…In Wiesner et al's original study describing the presence of fusions in Spitz tumors, they identified BRAF fusions in 7 of 140 (5%) cases 1 . Similarly, Quan et al recently reported BRAF fusions in 6 of 106 (5.7%) of Spitz neoplasms 2 . BRAF fusions tend to be part of the more atypical spectrum of fusions in Spitz tumors and hence in cohorts of more difficult consult cases, their frequency may be overestimated.…”

“…This includes Spitz neoplasms, cutaneous non‐spitzoid melanomas, desmoplastic melanoma, acral melanoma, mucosal melanoma, and melanoma arising in a congenital nevus. Two independent studies performing next generation sequencing (NGS) on larger cohorts of Spitz neoplasms suggests that BRAF fusions can be found in 5% to 6% of Spitz neoplasms 1,2 . However, the number of reports providing detailed descriptions of the clinical, genomic, and morphological findings in BRAF fusion Spitz tumors is still limited 3‐11 …”

“…neoplasms 2. BRAF fusions tend to be part of the more atypical spectrum of fusions in Spitz tumors and hence in cohorts of more difficult consult cases, their frequency may be overestimated.…”

microRNAs Biogenesis, Functions and Role in Tumor Angiogenesis

“…However, these experimental approaches to define the role of small non-coding RNAs in the biological and pathological processes are not enough. The morphology-based approach, such as dual in situ Dual ISH-IHC Technology, should walk together with the most modern computational and molecular technologies for a more precise characterization of the biological events in a more realistic molecular context (296)(297)(298).…”

Allosteric and ATP-Competitive MEK-Inhibition in a Novel Spitzoid Melanoma Model with a RAF- and Phosphorylation-Independent Mutation

“…Another study found MAPK pathway effecting mutations [4] in 66% of 27 spitzoid melanoma samples. Furthermore, RNA and DNA sequencing of 80 Spitz tumors (ST), 26 Spitz melanomas (SM) and 22 melanomas with spitzoid features (MFS) showed that in STs and SMs, kinase fusions were prevalent, while in MSFs, mostly BRAF, NRAS and NF1 mutations were present [5]. These results indicate that spitzoid melanomas are a genetically diverse group despite their histological similarity.…”