International Journal of Molecular Sciences Article A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy Siras Hakobyan 1 , Henry Loeffler-Wirth 2, Arsen Arakelyan 1 , Hans Binder 2,† and Manfred Kunz 3,*,† 1 Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;
[email protected] (S.H.);
[email protected] (A.A.) 2 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany;
[email protected] (H.L.-W.);
[email protected] (H.B.) 3 Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Philipp-Rosenthal-Str. 23, 04103 Leipzig, Germany * Correspondence:
[email protected]; Tel.: +49-341-9718610; Fax: +49-341-9718609 † Shared senior authorship. Abstract: Genetic splice variants have become of central interest in recent years, as they play an important role in different cancers. Little is known about splice variants in melanoma. Here, we analyzed a genome-wide transcriptomic dataset of benign melanocytic nevi and primary melanomas (n = 80) for the expression of specific splice variants. Using kallisto, a map for differentially expressed splice variants in melanoma vs. benign melanocytic nevi was generated. Among the top genes with differentially expressed splice variants were Ras-related in brain 6B (RAB6B), a member of Citation: Hakobyan, S.; the RAS family of GTPases, Macrophage Scavenger Receptor 1 (MSR1), Collagen Type XI Alpha 2 Loeffler-Wirth, H.; Arakelyan, A.; Chain (COLL11A2), and LY6/PLAUR Domain Containing 1 (LYPD1). The Gene Ontology terms of Binder, H.; Kunz, M. A differentially expressed splice variants showed no enrichment for functional gene sets of melanoma Transcriptome-Wide Isoform vs.