Mutations in ALK signaling pathways conferring resistance to ALK inhibitor treatment lead to collateral vulnerabilities in neuroblastoma cells
Creators: name: Berlak, Mareike
name: Tucker, Elizabeth
name: Dorel, Mathurin
name: Winkler, Annika
name: McGearey, Aleixandria
name: Rodriguez-Fos, Elias
name: Costa, Barbara Martins Da
name: Barker, Karen
name: Fyle, Elicia
name: Calton, Elizabeth
name: Eising, Selma
name: Ober, Kim
name: Hughes, Deborah
name: Koutroumanidou, Eleni
name: Carter, Paul
name: Stankunaite, Reda
name: Proszek, Paula
name: Jain, Neha
name: Rosswog, Carolina
name: Dorado-Garcia, Heathcliff
name: Molenaar, Jan Jasper
name: Hubank, Mike
name: Barone, Giuseppe
name: Anderson, John
name: Lang, Peter
name: Deubzer, Hedwig Elisabeth
name: Künkele, Annette
name: Fischer, Matthias
name: Eggert, Angelika
name: Kloft, Charlotte
name: Henssen, Anton George
name: Boettcher, Michael
name: Hertwig, Falk
name: Blüthgen, Nils
name: Chesler, Louis
name: Schulte, Johannes Hubertus
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2022
Subjects: subject: Neuroblastoma
subject: CRISPR screening
subject: ALK
subject: Resistance
subject: NF1
subject: NRAS
subject: Trametinib
subject: Lorlatinib
subject: Ceritinib
subject: Collateral sensitivity
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background: Development of resistance to targeted therapies has tempered initial optimism that precision oncology would improve poor outcomes for cancer patients. Resistance mechanisms, however, can also confer new resistance-specific vulnerabilities, termed collateral sensitivities. Here we investigated anaplastic lymphoma kinase (ALK) inhibitor resistance in neuroblastoma, a childhood cancer frequently affected by activating ALK alterations. Methods: Genome-wide forward genetic CRISPR-Cas9 based screens were performed to identify genes associated with ALK inhibitor resistance in neuroblastoma cell lines. Furthermore, the neuroblastoma cell line NBLW-R was rendered resistant by continuous exposure to ALK inhibitors. Genes identified to be associated with ALK inhibitor resistance were further investigated by generating suitable cell line models. In addition, tumor and liquid biopsy samples of four patients with ALK-mutated neuroblastomas before ALK inhibitor treatment and during tumor progression under treatment were genomically profiled. Results Both: genome-wide CRISPR-Cas9-based screens and preclinical spontaneous ALKi resistance models identified NF1 loss and activating NRAS(Q61K) mutations to confer resistance to chemically diverse ALKi. Moreover, human neuroblastomas recurrently developed de novo loss of NF1 and activating RAS mutations after ALKi treatment, leading to therapy resistance. Pathway-specific perturbations confirmed that NF1 loss and activating RAS mutations lead to RAS-MAPK signaling even in the presence of ALKi. Intriguingly, NF1 loss rendered neuroblastoma cells hypersensitive to MEK inhibition. Conclusions: Our results provide a clinically relevant mechanistic model of ALKi resistance in neuroblastoma and highlight new clinically actionable collateral sensitivities in resistant cells.