ALK mutation dynamics and clonal evolution in a neuroblastoma model exhibiting two ALK mutations
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Simon Durand1,2, Cécile Pierre-Eugène1,2, Olivier Mirabeau1,2, Caroline Louis-Brennetot1,2, Valérie Combaret3, Léo Colmet-Daage2,4, Orphée Blanchard1,2, Angela Bellini2,4, Estelle Daudigeos-Dubus5, Virginie Raynal1,2,6, Gudrun Schleiermacher2,4, Sylvain Baulande6, Olivier Delattre1,2 and Isabelle Janoueix-Lerosey1,2
1 Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris F-75005, France
2 SIREDO: Care, Innovation, and Research for Children, Adolescents, and Young Adults with Cancer, Institut Curie, Paris F-75005, France
3 Centre Léon Bérard, Laboratoire de Recherche Translationnelle, Lyon F-69008, France
4 Equipe SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique), Institut Curie, Paris F-75005, France
5 Gustave Roussy, Vectorology and Anticancer Therapies, UMR 8203, CNRS, University Paris-Sud, Université Paris-Saclay, Villejuif F-94805, France
6 Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris F-75005, France
Keywords: neuroblastoma; ALK mutations; heterogeneity; clonal evolution; ALK inhibitors
Received: March 26, 2019 Accepted: July 17, 2019 Published: August 13, 2019
The ALK gene is a major oncogene of neuroblastoma cases exhibiting ALK activating mutations. Here, we characterized two neuroblastoma cell lines established from a stage 4 patient at diagnosis either from the primary tumor (PT) or from the bone marrow (BM). Both cell lines exhibited similar genomic profiles. All cells in the BM-derived cell line exhibited an ALK F1174L mutation, whereas this mutation was present in only 5% of the cells in the earliest passages of the PT-derived cell line. The BM-derived cell line presented with a higher proliferation rate in vitro and injections in Nude mice resulted in tumor formation only for the BM-derived cell line. Next, we observed that the F1174L mutation frequency in the PT-derived cell line increased with successive passages. Further Whole Exome Sequencing revealed a second ALK mutation, L1196M, in this cell line. Digital droplet PCR documented that the allele fractions of both mutations changed upon passages, and that the F1174L mutation reached 50% in late passages, indicating clonal evolution. In vitro treatment of the PT-derived cell line exhibiting the F1174L and L1196M mutations with the alectinib inhibitor resulted in an enrichment of the L1196M mutation. Using xenografts, we documented a better efficacy of alectinib compared to crizotinib on tumor growth and an enrichment of the L1196M mutation at the end of both treatments. Finally, single-cell RNA-seq analysis was consistent with both mutations resulting in ALK activation. Altogether, this study provides novel insights into ALK mutation dynamics in a neuroblastoma model harbouring two ALK mutations.
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