Fig. 1: RNA binding, transport and translation pathways regulate metabolic response to BRAF inhibition.

a Schematic summarizing screen workflow (see methods). b WM266.4 cells were transfected with the indicated siRNA and treated with DMSO or 300 nM Vem for 48 h. Cell number was calculated using high content image analysis of DAPI stained cells (top panel) and growth media was collected for determination of lactate levels. Lactate absorbance values were normalized to cell number to determine lactate production per cell (bottom panel). Data are presented as mean fold change relative to DMSO siOTP control, ±StDev; Data points are individual replicate wells from two technical replicate screening plates. c Functional annotation enrichment analysis was performed on 717 genes that enhanced the effects of Vem on lactate production (DMSO lactate per cell ratio <0.5-fold change and Vem lactate per cell ratio >0.5-fold change; see Supplementary Data 1) using DAVID. Data is displayed as Log2 fold change versus −Log10 p-value. Annotations previously linked with BRAFi response and/or resistance are shown in blue, and the top 4 annotations linked with RNA binding and transport are shown in red. d Network analysis was performed on 622 viability screen hits and 717 hits that enhanced the effects of Vem on lactate production using String (see Supplementary Fig. 1). Comparative network analysis was performed using Cytoscape, and hubs connecting the two networks are highlighted. e Heat map displaying viability and lactate screening data for the indicated genes. f Heatmap displaying percentage of melanoma patients with upregulation of the indicated mRNA transport and translation genes on progression following treatment with MAPK pathway inhibitors (data sourced from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65186²⁴; see Supplementary Data 4). See also Supplementary Figs. 1–2. Source data for b–f are provided as a Source Data file.