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
the RAS family of GTPases, Macrophage Scavenger Receptor 1 (MSR1), Collagen Type XI Alpha 2
Chain (COLL11A2), and LY6/PLAUR Domain Containing 1 (LYPD1). The Gene Ontology terms of
differentially expressed splice variants showed no enrichment for functional gene sets of melanoma
vs. nevus lesions, but between type 1 (pigmentation type) and type 2 (immune response type)
melanocytic lesions. A number of genes such as Checkpoint Kinase 1 (CHEK1) showed an association
of mutational patterns and occurrence of splice variants in melanoma. Moreover, mutations in
genes of the splicing machinery were common in both benign nevi and melanomas, suggesting a
common mechanism starting early in melanoma development. Mutations in some of these genes of
the splicing machinery, such as Serine and Arginine Rich Splicing Factor A3 and B3 (SF3A3, SF3B3),
were significantly enriched in melanomas as compared to benign nevi. Taken together, a map of
splice variants in melanoma is presented that shows a multitude of differentially expressed splice
genes between benign nevi and primary melanomas. The underlying mechanisms may involve
mutations in genes of the splicing machinery.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:88786 |
| Date | 29 December 2023 |
| Creators | Hakobyan, Siras, Loeffler-Wirth, Henry, Arakelyan, Arsen, Binder, Hans, Kunz, Manfred |
| Publisher | MDPI |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:article, info:eu-repo/semantics/article, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | 7165, 10.3390/ijms22137165 |
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