Fig. 6: VARS translation targets in the resistant melanoma phenotype.
From: Valine aminoacyl-tRNA synthetase promotes therapy resistance in melanoma
a, A heat map representing amino acid enrichment analysis of proteins (proteomics) downregulated in M395 RES depleted of VARS (chi-squared test). b, A graph representing genes commonly detected by RNA sequencing (y axis) and proteomics (x axis) of M395 RES VARS-depleted cells (shVARS-1) compared with control cells (shCTRL). Four groups were assigned depending on their log2 FC. ‘Translation down’ and ‘translation up’ groups were appointed with: −1 < log2 FC (y axis) < 1 and log2 FC (x axis) < −0.32 or 1 < log2 FC (x axis) < 1 and log2 FC (x axis) > 0.32, respectively. c,d, The VARS signature was superposed with genes presenting differential RPFs (c) or polysomal fractions (d) of control (shCTRL) or VARS-depleted cells (shVARS) (chi-squared test). e, A bubble plot of the top five enriched terms (using Gene Ontology (GO) Hallmark) for VARS signature (n = 84). The size of the bubble represents the −log10 (FDR q value). f, A Venn diagram highlighting 22 proteins commonly overlapping in proteins that are upregulated during RES (n = 706) and in VARS signature (n = 84). g, A bubble plot of the top five enriched (using GO Hallmark) for the 22 valine-enriched candidates. The size of the bubble represents the log10 (FDR q value). h, Cell death measurement of MM029 resistant to trametinib/dabrafenib by fluorescence staining with PI by FACS after the depletion of the indicated candidate using specific esiRNA and after treatment or not with the indicated drug combination. The red arrows depict the top five candidates (showing highest percentage of nuclear fragmentation upon treatment with no or little nuclear fragmentation in untreated condition) (n = 1). i,j, Heat maps highlighting the log2 (FC shVARS/shCTRL) of the top five candidates (HADH, KIF13B, SLC7A5, QDPR and GOLT1B) in ribosome footprints (i) and polysomal fractions (j). The red squares represent significant values. k, Western blot analysis of VARS and the indicated proteins expression in control (shCTRL) and VARS (shVARS)-depleted M395 RES cultures (n = 1).
