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Genome-wide high-resolution SNP-array analysis of childhood melanocytic tumor with ambiguous histopathological features

ABSTRACT: In our clinical practice, we perform genome-wide high-resolution SNP-array analysis as an adjunct to the histopathologic diagnosis for diagnostically challenging melanocytic tumors. The concept of using array-based DNA copy number analysis to screen for gene fusions associated with unbalanced genomic aberrations flanking the fusion points was applied in the diagnostic setting, and intragenic copy number changes involving common receptor kinase genes are typically further analyzed and, if necessary, studied by alternative methods. Here we present the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms based on genome-wide high-resolution SNP-array analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE90644 | GEO | 2017/02/01

SECONDARY ACCESSION(S): PRJNA355275

REPOSITORIES: GEO

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Project description:Spitzoid neoplasms are a challenging group of cutaneous melanocytic proliferations that occur in children or adolescents but can also arise in the elderly. They are characterized by epithelioid and/ or spindle-shaped melanocytes with a stromal background of variable amounts of lymphocytes, blood vessels and sclerosis. According to the WHO 2018 classification, Spitzoid melanocytic lesions are classified as benign Spitz nevi (SN), atypical Spitz tumors (AST) or malignant Spitz tumors (MST). The intermediate AST category represents a diagnostically challenging group since on purely histopathological grounds, their benign or malignant character remains unpredictable. This results in uncertainties in patient management and prognosis. The molecular properties of Spitzoid lesions, especially their transcriptomic landscape, remain poorly understood and genomic alterations in melanoma-associated oncogenes are typically absent. The aim of this study was to characterize the transcriptome of Spitzoid melanocytic neoplasms with digital mRNA expression profiling. Formalin-fixed-paraffin-embedded samples (including 27 SN, 10 AST and 14 MST) were analyzed using the RNA NanoString nCounter PanCancer Pathways Gene Expression panel. The number of significantly differentially expressed genes in SN vs. MST, SN vs. AST and AST vs. MST was 68, 167 and 18, respectively. Gene set enrichment analysis revealed an upregulation of pathways related to epithelial mesenchymal transition, immunomodulatory-, angiogenesis- as well as myogenesis associated processes in AST and MST. In addition, a specific gene expression signature of SN vs. MST was discovered based on the top-ranked six most informative gene expression markers: NRAS, NF1, BMP2, EIF2B4, IFNA17 and FZD9. The AST samples showed intermediate levels of the identified signature. This implies that the identified gene expression signature can potentially be used to distinguish high-grade from low-grade AST. This combined histopathological and transcriptomic methodology is promising for diagnostics of Spitzoid neoplasms and patient management in dermatological oncology in the future.

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Genome-wide high-resolution SNP-array analysis of childhood melanocytic tumor with ambiguous histopathological features

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