A Clinicopathological Study of 29 Spitzoid Melanocytic Lesions With ALK Fusions, Including Novel Fusion Variants, Accompanied by Fluorescence In Situ Hybridization Analysis for Chromosomal Copy Number Changes, and Both TERT Promoter and Next-Generation Sequencing Mutation Analysis

Abstract

ALK-fused spitzoid neoplasms represent a distinctive group of melanocytic lesions. To date, few studies addressed genetic and chromosomal alterations in these lesions beyond the ALK rearrangements. Our objective was to study genetic alterations, including ALK gene fusions, telomerase reverse transcriptase promoter (TERT-p) mutations, chromosomal copy number changes, and mutations in other genes. We investigated 29 cases of Spitz lesions (11 Spitz nevi and 18 atypical Spitz tumors), all of which were ALK immunopositive. There were 16 female and 13 male patients, with age ranging from 1 to 43 years (mean, 18.4 years). The most common location was the lower extremity. Microscopically, all neoplasms were polypoid or dome shaped with a plexiform, predominantly dermally located proliferation of fusiform to spindled melanocytes with mild to moderate pleomorphism. The break-apart test for ALK was positive in 17 of 19 studied cases. ALK fusions were detected in 23 of 26 analyzable cases by Archer FusionPlex Solid Tumor Kit. In addition to the previously described rearrangements, 3 novel fusions, namely, KANK1-ALK, MYO5A-ALK, and EEF2-ALK, were found. Fluorescence in situ hybridization for copy number changes yielded one case with the loss of RREB1 among 21 studied cases. TERT-p hotspot mutation was found in 1 of 23 lesions. The mutation analysis of 271 cancer-related genes using Human Comprehensive Cancer Panel was performed in 4 cases and identified in each case mutations in several genes with unknown significance, except for a pathogenic variant in the BLM gene. Our study confirms that most ALK fusion spitzoid neoplasms can be classified as atypical Spitz tumors, which occurs in young patients with acral predilection and extends the spectrum of ALK fusions in spitzoid lesions, including 3 hitherto unreported fusions. TERT-p mutations and chromosomal copy number changes involving 6p25 (RRB1), 11q13 (CCND1), 6p23 (MYB), 9p21 (CDKN2A), and 8q24 (MYC) are rare in these lesions. The significance of mutation in other genes remains unknown.

An Update on Molecular Genetic Aberrations in Spitz Melanocytic Proliferations: Correlation with Morphological Features and Biological Behavior

“…Genetic alterations of the ALK gene include point mutations, gene fusions, ALK locus amplification, alternative transcription, and small deletions (35) and influence cell proliferation and survival via constitutive activation of the RAS-ERK, JAK3-STAT3, and PI3K-AKT-mTOR pathways (36)(37)(38). Fusions involving the ALK gene have been discovered in diverse cutaneous neoplasms, including primary cutaneous anaplastic large cell lymphoma (39), epithelioid fibrous histiocytoma (40), acral melanomas (41,42), and Spitz melanocytic proliferations (2,(43)(44)(45)(46)(47)(48)(49)(50).…”

“…In Spitz melanocytic proliferations, various different fusion partners have been identified, including TPM3 (2,11,45,(51)(52)(53)(54), DCTN1 (2,23,45,50,54), MLPH (9,44,45,55), KANK1 (9, 45), CLIP1 (50), DDX3Y (9), EEF2 (45), GTF3C2 (50), MYO5A (45), NPM1 (47), PPFIBP1 (9), SPTAN1 (9) and TPR (50), in descending order of frequency. Lesions from the whole biological spectrum ranging from Spitz nevi, atypical Spitz tumors to Spitz melanomas have been distributed fairly equally among different fusion partners (2,9,11,23,44,45,47,(50)(51)(52)(54)(55)(56). Although different fusions in Spitz melanocytic proliferations are generally believed to be mutually exclusive with BRAF mutations, a few examples (two Spitz melanomas, one atypical Spitz tumor, and an acral melanoma) with concurrent ALK fusion and a BRAF mutation have been reported in the literature (41,54,57).…”

“…Melanocytes may appear discohesive with clefts or small vesicle-like spaces in between (23,50,55,59). Ulceration may be present, as may be dermal (even deep) mitoses and perineural invasion, but Kamino bodies are rare (23,43,45,47,50,58). Melanin pigment is typically lacking or presents in limited amounts in the cytoplasm of melanocytes.…”

“…Melanin pigment is typically lacking or presents in limited amounts in the cytoplasm of melanocytes. Focal mucin deposits have been described (45). Proliferations with abundant myxoid areas with ALK+/SOX10+/ MelanA-spindle cells underneath the superficial nevoid or Spitzoid component have been termed melanocytic myxoid spindle cell tumors with ALK rearrangement (MMySTAR) (56).…”

“…ALK immunohistochemistry is a reliable surrogate marker for molecular genetic techniques in cases with diffuse and strong immunopositivity in most melanocytes (Figure 2c) (2,(43)(44)(45)(46)50). In contrast, weak and focal or heterogeneous ALK staining has been demonstrated in non-Spitz melanocytic proliferations with ALK overexpression due to other molecular mechanisms (e.g., alternative transcription initiation that leads to the expression of a novel ALK isoform ALK ATI (60,61) or in cases with chromosome 2p23 gain (62)), in rare cases of cellular blue nevi and in a single case of deep penetrating nevus (63).…”