Intra‐ and inter‐tumor heterogeneity in a vemurafenib‐resistant melanoma patient and derived xenografts

Kristel Kemper,Fleur Weeber,Lodewyk F Wessels,Christian U Blank,John B Haanen,David J Adams,Ji‐Ying Song,Aida Shahrabi,Emile E Voest,Daniel S Peeper,Daniel J Vis,Oscar Krijgsman,Ton Nm Schumacher,Paulien Cornelissen‐Steijger,Thomas Kuilman

doi:10.15252/emmm.201404914

Abstract

The development of targeted inhibitors, like vemurafenib, has greatly improved the clinical outcome of BRAFV600E metastatic melanoma. However, resistance to such compounds represents a formidable problem. Using whole-exome sequencing and functional analyses, we have investigated the nature and pleiotropy of vemurafenib resistance in a melanoma patient carrying multiple drug-resistant metastases. Resistance was caused by a plethora of mechanisms, all of which reactivated the MAPK pathway. In addition to three independent amplifications and an aberrant form of BRAFV600E, we identified a new activating insertion in MEK1. This MEK1T55delinsRT mutation could be traced back to a fraction of the pre-treatment lesion and not only provided protection against vemurafenib but also promoted local invasion of transplanted melanomas. Analysis of patient-derived xenografts (PDX) from therapy-refractory metastases revealed that multiple resistance mechanisms were present within one metastasis. This heterogeneity, both inter- and intra-tumorally, caused an incomplete capture in the PDX of the resistance mechanisms observed in the patient. In conclusion, vemurafenib resistance in a single patient can be established through distinct events, which may be preexisting. Furthermore, our results indicate that PDX may not harbor the full genetic heterogeneity seen in the patient’s melanoma.

Highlights

Until recently, for BRAFV600E metastatic melanoma, few if any treatments have been available, because it poorly responds to chemotherapy
To increase our understanding of its mechanistic basis, and to explore to what extent the heterogeneity of drug resistance can be captured in patient-derived xenografts (PDX), we have studied the variation and extent of vemurafenib resistance mechanisms present in a melanoma patient and xenografts derived thereof (Fig 8)
We have sequenced five resistant metastases and a pre-treatment sample derived from the same BRAFV600E melanoma patient

Summary

Introduction

For BRAFV600E metastatic melanoma, few if any treatments have been available, because it poorly responds to chemotherapy. The development of inhibitors targeting the mutant BRAFV600E protein, such as vemurafenib and dabrafenib, has changed the clinical outcome for patients with this type of tumor. In a randomized phase III clinical trial (BRIM 3), vemurafenib was compared to dacarbazine, the former standard of care. Vemurafenib showed an impressive response rate of 48% compared to 5%, with an increased progression-free survival (5.3 months vs 1.6 months) (Chapman et al, 2011). The initial success of the treatment was soon overshadowed by the discovery that almost all patients developed therapy resistance after a period of approximately 6 months (Trunzer et al, 2013). The cause of resistance has since been elaborately studied by many research groups

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Conclusion