Adaptive translational reprogramming of metabolism limits the response to targeted therapy in BRAFV600 melanoma

Lorey Smith ,Teresa Ward,David Goode,Aparna D Rao,Vihandha O Wickramasinghe,Emily J Lelliott,Richard B Pearson,Rodney J Hicks,David Papadopoli,Ola Larsson,Carleen Cullinane,Julie Lorent,Anna S Trigos ,Margarete Kleinschmidt,Peter K H Lau ,Claire Martin ,Jian Kang,Kaylene J Simpson,Karen E Sheppard,Tony Tiganis,Tiffany J Parmenter ,Benjamin J Blyth ,Riyaben P Patel ,Eric Kusnadi ,Grant A Mcarthur

doi:10.1038/s41467-022-28705-x

Abstract

Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that ultimately results in relapse. This residual disease is often characterized by non-genetic adaptive resistance, that in melanoma is characterised by altered metabolism. Here, we examine how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNA interference (RNAi) screen and global gene expression profiling. Using this systematic approach we demonstrate post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA processing kinase U2AF homology motif kinase 1 (UHMK1) associates with mRNAs encoding metabolism proteins and selectively controls their transport and translation during adaptation to BRAF-targeted therapy. UHMK1 inactivation induces cell death by disrupting therapy induced metabolic reprogramming, and importantly, delays resistance to BRAF and MEK combination therapy in multiple in vivo models. We propose selective mRNA processing and translation by UHMK1 constitutes a mechanism of non-genetic resistance to targeted therapy in melanoma by controlling metabolic plasticity induced by therapy.

Highlights

Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that results in relapse
These data suggest that maximal suppression of glycolysis and concurrent inhibition of adaptive mitochondrial metabolism may lead to improved outcomes to MAPK pathway targeted therapy by interfering with metabolic reprogramming underpinning drug-induced cellular adaptation
To identify regulators of metabolic response following treatment with oncogene targeted therapy, we performed a genome-wide RNA interference (RNAi) screen using BRAFV600 melanoma cells treated with the BRAF inhibitor (BRAFi) vemurafenib (Vem) as a paradigm (Fig. 1a)[17]

Summary

Results

RNA binding, transport and translation pathways regulate metabolic response to inhibition of oncogenic BRAF signalling. To identify regulators of metabolic response following treatment with oncogene targeted therapy, we performed a genome-wide RNAi screen using BRAFV600 melanoma cells treated with the BRAF inhibitor (BRAFi) vemurafenib (Vem) as a paradigm (Fig. 1a)[17]. To identify genes that regulate viability and glycolytic response to BRAFi, genes were grouped based on fold change data for each parameter in DMSO versus Vem treatment conditions (see supplementary information). This analysis identified 717 genes (Supplementary Data 3) that were enriched for MAPK and GPCR signalling, and histone methylation, consistent with previous studies investigating BRAFi resistance (Fig. 1c and Supplementary Fig. 2D)[22]. The identification of RNA binding and transport genes in our screen was a Genome-wide siRNA Functional Screen Transfection with Dharmacon Human siGENOME SMARTPool Library (18,120 siRNA SMARTPools)

MAP kinase kinase activity

30 Sub Polysome 20

H K NP1 UH K NP1

Methods