Fig. 1
A pipeline to identify lncRNAs that are MAPK-pathway associated, expressed in melanoma patient tissue and essential for melanoma cell-survival. (a) A schematic illustration of the pipeline steps. RNASeq data of NRAS-mutant primary human melanocytic cells (PHMQ61), NRAS-mutant melanoma cell lines (D04, MM415), and wild-type primary human melanocytes (PHME, PHM) were compared to identify lncRNAs whose expression is induced through a MAPK-pathway (NRAS) hyperactivating mutation. (b) Venn Diagram showing transcriptome intersections of the three comparisons PHMQ61/PHME, D04/PHM and MM415/PHM. 197 genes were differentially expressed (DE, expression log2-fold change > 1) in all three comparisons. (c) Expression of the 197 DE genes displayed in a heatmap. Genes were classified in the subgroups protein-coding genes, non-coding RNA (ncRNA) and transcripts of unknown coding potential (TUCP). 81 of the 197 DE genes were upregulated lncRNAs (d) 81 upregulated lncRNAs, ranked from lowest, to highest average expression in patient derived NRAS mutant melanoma from The Cancer Genome Atlas (TCGA, n = 86). 24 lncRNAs were expressed in > 90% (gray bar) of patients. The lncRNA AC004540.4 was expressed in > 97% of patients and is highlighted in red (Average FPKM = 11.28). (e) AC004540.4 expression analysis of non-malignant skin biopsies from the GTEx dataset (n = 1305, mean TPM: 0.49), and BRAF- and NRAS-mutated melanoma tissue from the TCGA-SKCM dataset (n = 366, mean TPM: 1.55) shows that AC004540.4 is significantly upregulated (*** = p < 0.001) in MAPK-pathway hyperactivated melanoma. The center line represents median expression, the box represents the lower and upper quartiles, the whiskers extend to the furthest value that is less than 1.5 times the interquartile range from the lower and upper quartiles and the mean expression is marked by an ‘X’