Molecular Cancer (Jun 2022)

Mutations in ALK signaling pathways conferring resistance to ALK inhibitor treatment lead to collateral vulnerabilities in neuroblastoma cells

  • Mareike Berlak,
  • Elizabeth Tucker,
  • Mathurin Dorel,
  • Annika Winkler,
  • Aleixandria McGearey,
  • Elias Rodriguez-Fos,
  • Barbara Martins da Costa,
  • Karen Barker,
  • Elicia Fyle,
  • Elizabeth Calton,
  • Selma Eising,
  • Kim Ober,
  • Deborah Hughes,
  • Eleni Koutroumanidou,
  • Paul Carter,
  • Reda Stankunaite,
  • Paula Proszek,
  • Neha Jain,
  • Carolina Rosswog,
  • Heathcliff Dorado-Garcia,
  • Jan Jasper Molenaar,
  • Mike Hubank,
  • Giuseppe Barone,
  • John Anderson,
  • Peter Lang,
  • Hedwig Elisabeth Deubzer,
  • Annette Künkele,
  • Matthias Fischer,
  • Angelika Eggert,
  • Charlotte Kloft,
  • Anton George Henssen,
  • Michael Boettcher,
  • Falk Hertwig,
  • Nils Blüthgen,
  • Louis Chesler,
  • Johannes Hubertus Schulte

DOI
https://doi.org/10.1186/s12943-022-01583-z
Journal volume & issue
Vol. 21, no. 1
pp. 1 – 19

Abstract

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Abstract 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 NRASQ61K 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.

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