Codon-specific translation reprogramming promotes resistance to targeted therapy

Abstract

Reprogramming of mRNA translation has a key role in cancer development and drug resistance . However, the molecular mechanisms that are involved in this process remain poorly understood. Wobble tRNA modifications are required for specific codon decoding during translation. Here we show, in humans, that the enzymes that catalyse modifications of wobble uridine 34 (U) tRNA (U enzymes) are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF oncogene and by resistance to targeted therapy in melanoma. We show that BRAF -expressing melanoma cells are dependent on U enzymes for survival, and that concurrent inhibition of MAPK signalling and ELP3 or CTU1 and/or CTU2 synergizes to kill melanoma cells. Activation of the PI3K signalling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U enzymes. Mechanistically, U enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A mRNA and the maintenance of high levels of HIF1α protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U enzymes and HIF1α. Together, these results demonstrate that U enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation.

Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression

“…Thus far, our data point out that regulation of mcm 5 s 2 ‐U34 tRNA‐modifying enzymes plays a major role in translational offsetting as a function of alterations in ERα signaling. Intriguingly however, ERα‐dependent suppression or decrease in the expression of U34‐modifying enzymes did not correlate with global changes in mcm 5 s 2 ‐U‐modified tRNAs as quantified by the [(N‐acryloylamino)phenyl]mercuric chloride (APM) method [Igloi, ; as reported in a recent study (Rapino et al , )] or mass spectrometry (Appendix Fig S6A and B). We reasoned that this may be a consequence of accumulation of modified tRNAs during chronic ERα depletion (e.g., due to reduction in global protein synthesis).…”

A wobbly road to drug resistance in melanoma: tRNA ‐modifying enzymes in translation reprogramming

“…The mechanisms that control this metabolic reprogramming by immediate changes in specific gene expression programs remain less clear. Now, an exciting new study by Rapino et al () provides evidence for an unexpected role of enzymes that modify transfer RNA (tRNA) in this process. Specifically, they show that enzymes modifying uridine 34 (U 34 ) of tRNA are important for the maintenance and therapeutic resistance of an aggressive skin cancer known as melanoma.…”

“…While U 34 tRNA‐modifying enzymes have been implicated in metabolism, DNA damage response, and exocytosis (Esberg et al , ; Begley et al , ; Laxman et al , ), their role in cancer has not been extensively studied until now. By employing a combination of approaches and patient samples, Rapino et al () demonstrate that key enzymes required for U 34 tRNA modifications are increased in melanomas exhibiting highly glycolytic phenotypes that are often associated with mutations in BRAF (one of the most commonly mutated genes in melanoma patients). Rapino and colleagues provide compelling evidence that BRAF V600E melanomas are “addicted” to high levels of U 34 tRNA‐modifying enzymes.…”

“…An exciting question arises as to why a reduction in U 34 tRNA‐modifying enzymes elucidates such a profound growth inhibition phenotype in highly metabolic melanomas. Rapino et al () employ an elegant combination of proteomics and ribosome profiling experiments to identify a role for specific codons in rewiring translation mediated by U 34 tRNA‐modifying enzymes in skin cancer cells. The authors show that the abundance of proteins enriched in codons, known to require thiolated tRNAs for decoding, such as Gln, Glu, and Lys codons, are significantly increased in BRAF V600E ‐driven melanoma.…”

Queuing up the ribosome: nutrition and the microbiome control protein synthesis

“…Lastly, recent studies demonstrated that tRNA‐modifying enzymes can be implicated in disease. For example, a recent study provided evidence that certain wobble‐modifying enzymes are involved in resistance to cancer targeted therapy (Rapino et al , ). Since queuine is obtained from the diet, it will be interesting to determine whether Q deficiency or excess can result in disease.…”