Comprehensive evaluation of mutation spectra detected in primary cutaneous melanomas including the identification of novel loss-of-function mutants


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Nikola Hájková1
1Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague

Abstract

Background

Melanoma is a malignant tumor with an increasing incidence worldwide. Although the spectrum and frequency of mutations in melanoma have (for the most part) already been catalogued, the search for new therapeutic targets continues. We performed an NGS analysis of selected genes and an extensive biostatistical evaluation of the detected variants in a cohort of 114 primary cutaneous melanomas collected from Czech patients.

Method

Genomic DNA from 114 formaline-fixed paraffine embedded primary cutaneous melanomas, including 46 nodular (NMs) and 68 superficial spreading melanomas (SSMs), underwent targeted NGS analysis (Illumina) using a custom designed panel (219 kbp; Roche NimbleGen SeqCap EZprotocol). The data was processed by NextGENe (Softgenetics). The detected non-synonymous variants with a minimal average coverage >100x and a frequency ≥10% were comprehensively evaluated by the in-house biostatistical pipeline. The impact of the TP53 mutations on cellular functions was studied by functional assays.

Results

A total of 43 out of the 54 evaluated genes carried class 4/5 mutations. The mutated genes were most frequently involved in the MAPK pathway, chromatin remodeling, DNA repair, and regulation of cellular tight junctions. Several novel class 4/5 mutations were identified by our biostatistical pipeline and further analysis of the selected cases found the mutations to be correlated with immunohistochemical and/or functional assays. Relatively frequent mutations were described in KDR and MET, which represent potential clinically important targets.

Conclusion

We described the spectrum and prevalence of exclusively class 4/5 mutations in primary NMs and SSMs. Novel loss-of-function mutations of TP53 were identified by functional analysis. Our findings suggested new clinically interesting targets.

This work was supported by Ministry of Health, Czech Republic (Conceptual development of research organization 64165, General University Hospital in Prague, and by project AZV 16-30954A, AZV 17-28404A).