Journal Article

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

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

2015

Overview

The development of targeted inhibitors, like vemurafenib, has greatly improved the clinical outcome of BRAF V600E 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 BRAF V600E , we identified a new activating insertion in MEK1 . This MEK1 T55delins RT 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. Synopsis Vemurafenib resistance in melanoma is caused by different mechanisms occurring independently in each metastasis, some of which exist pre‐treatment. These findings bear several clinical implications in designing treatment strategies. Resistance to targeted therapy is genetically heterogeneous, both within and among metastases. A new 3‐bp insertion in the MEK1 gene (MEK1 T55delinsRT ) confers resistance to vemurafenib. The MEK1 T55delinsRT mutation can be traced back to a fraction of the pre‐treatment tumor. Tumor heterogeneity was only partially recapitulated in corresponding patient‐derived xenografts. Graphical Abstract Vemurafenib resistance in melanoma is caused by different mechanisms occurring independently in each metastasis, some of which exist pre‐treatment. These findings bear several clinical implications in designing treatment strategies.

• Publisher: Nature Publishing Group UK,EMBO Press,John Wiley & Sons, Ltd,Springer Nature
• Subject: Antineoplastic Agents - pharmacology / Antineoplastic Agents - therapeutic use / Drug resistance / Drug Resistance, Neoplasm - genetics / EMBO03 / EMBO38 / Genetic Variation / Heterografts / Humans / Indoles - pharmacology / Indoles - therapeutic use / Insertion / Lymphatic system / MAP kinase / Medical imaging / Melanoma / Melanoma - drug therapy / Metastases / Metastasis / Multidrug resistance / Mutation / Neoplasm Metastasis - drug therapy / Patients / patient‐derived xenografts / Pleiotropy / Proto-Oncogene Proteins B-raf - genetics / Research Article / Sequence Analysis, DNA / Skin Neoplasms - complications / Skin Neoplasms - drug therapy / Sulfonamides - pharmacology / Sulfonamides - therapeutic use / Thorax / tumor heterogeneity / Tumors / Vemurafenib / Xenografts