️ 26: Reannotation in Focus — Uncovering Functional Non-Coding Mutations in Melanoma

️ Episode 26: Reannotation in Focus — Uncovering Functional Non-Coding Mutations in Melanoma In this episode of Base por Base, we delve into a breakthrough study by Pepe et al. (2025) in The American Journal of Human Genetics that challenges conventional cancer mutation annotation. The authors present an automated pipeline combining RNA-seq–based transcript quantification and Ensembl VEP reannotation to map somatic variants to the transcripts actually expressed in melanoma tumors. By integrating TCGA and COSMIC datasets, deep-learning predictions, and functional assays, this framework exposes a hidden layer of non-coding promoter mutations driving melanoma pathogenesis. Study Highlights:The reannotation approach revealed that many mutation clusters previously labeled as synonymous or missense events in cancer databases instead reside in promoter regions of expressed genes and adjacent loci, with 22% of 52 hotspots in melanoma belonging to this non-coding category. Functional validation using CRISPR-Cas9–edited melanocyte models and luciferase reporter assays demonstrated that IRF3/BCL2L12 promoter variants downregulate IRF3, BCL2L12, and downstream TP53 signaling, and disrupt ETS and SP/E2F transcription factor binding motifs as predicted by the DeepMEL2 model and PhysBinder/FABIAN-variant analyses. Systematic reannotation of KNSTRN and SLC27A5 clusters further confirmed non-coding promoter activity alterations, underscoring the prevalence and significance of regulatory mutations overlooked by reference-transcript annotation. Conclusion:By anchoring mutation annotation to expressed transcripts, the BayesMRnet reannotation pipeline (Salmon + VEP) ushers in a more precise era of cancer genomics, uncovering functional non-coding drivers in melanoma and offering a scalable tool to refine driver mutation discovery and guide future therapeutic strategies. Reference:Pepe, D., Janssens, X., Timcheva, K., Marrón-Liñares, G. M., Verbelen, B., Konstantakos, V., … De Keersmaecker, K. (2025). Reannotation of cancer mutations based on expressed RNA transcripts reveals functional non-coding mutations in melanoma. The American Journal of Human Genetics, 112, 1–21. https://doi.org/10.1016/j.ajhg.2025.04.005 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – http://creativecommons.org/licenses/by/4.0/

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