Didier Auboeuf

Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease the intracellular concentration of aspartate and glutamate in melanoma cells. This coincides with the accumulation of ribosomes on codons corresponding to these amino acids and triggers the translation-dependent degradation of mRNAs encoding aspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNA replication and repair. Consequently, cells that survive MAPKi degrade aspartate and glutamate likely to generate energy, which simultaneously decreases their requirement for amino acids due to the downregulation of aspartate- and glutamate-rich proteins involved in cell proliferation. Concomitantly, the downregulation of aspartate- and glutamate-rich proteins involved in DNA repair increases DNA damage loads. Thus, DNA repair defects, and therefore mutations, are at least in part a secondary effect of the metabolic adaptation of cells exposed to MAPKi.

Despite the initial efficacy of using tyrosine kinase inhibitors of epidermal growth factor receptors (EGFR‐TKIs) for treating patients with non‐small cell lung cancer (NSCLC), resistance inevitably develops. Recent studies highlight a link between alternative splicing and cancer drug response. Therefore, we aimed to identify deregulated splicing events that play a role in resistance to EGFR‐TKI. By using RNA sequencing, reverse‐transcription PCR (RT‐PCR), and RNA interference, we showed that overexpression of a splice variant of the autophagic gene ATG16‐L1 that retains exon 8 and encodes the β‐isoform of autophagy‐related protein 16‐1 (ATG16‐L1 β) concurs acquired resistance to EGFR‐TKI in NSCLC cells. Using matched biopsies, we found increased levels of ATG16‐L1 β at the time of progression in 3 of 11 NSCLC patients treated with EGFR‐TKI. Mechanistically, gefitinib‐induced autophagy was impaired in resistant cells that accumulated ATG16‐L1 β. Neutralization of ATG16‐L1 β restored autophagy in response to gefitinib, induced apoptosis, and inhibited the growth of in ovo tumor xenografts. Conversely, overexpression of ATG16‐L1 β in parental sensitive cells prevented gefitinib‐induced autophagy and increased cell survival. These results support a role of defective autophagy in acquired resistance to EGFR‐TKIs and identify splicing regulation of ATG16‐L1 as a therapeutic vulnerability that could be explored for improving EGFR‐targeted cancer therapy.