Whole genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition
Menée par une technique de séquençage du génome entier sur 5 échantillons de métastases prélevés chez un patient atteint d'un mélanome, cette étude identifie la présence de mutations associées à la résistance à un inhibiteur de BRAF
Background. BRAF is mutated in ∼42% of human melanomas [1] and pharmacological BRAF inhibitors such as vemurafenib and dabrafenib achieve dramatic responses in patients whose tumours harbour BRAFV600 mutations [2-5]. Objective responses occur in ∼50% of patients and disease stabilisation in a further ∼30%, but ∼20% of patients present primary or innate resistance and do not respond. Here we investigated the underlying cause of treatment failure in a patient with BRAF mutant melanoma who presented primary resistance. Methods. We performed whole genome sequencing and SNP array analysis of five metastatic tumours from the patient. We validated mechanisms of resistance in a cell line derived from the patient's tumour. Results. We observed that the majority of the single nucleotide variants (SNVs) identified were shared across all tumour sites, but also saw site-specific copy number alterations in discrete cell populations at different sites. We found that two ubiquitous mutations mediated resistance to BRAF inhibition in these tumours. A mutation in GNAQ sustained MAPK signalling, whereas a mutation in PTEN activated the PI3K/AKT pathway. Inhibition of both pathways synergised to block the growth of the cells. Conclusions. Our analyses show that the five metastases arose from a common progenitor and acquired additional alterations after disease dissemination. We demonstrate that a distinct combination of mutations mediated primary resistance to BRAF inhibition in this patient. These mutations were present in all five tumours and in a tumour sample taken before BRAF inhibitor treatment was administered. Inhibition of both pathways was required block tumour cell growth, suggesting that combined targeting of these pathways could have been a valid therapeutic approach for this patient.