Investigating neuroblastoma cell lines to identify mechanisms of resistance to cisplatin and vincristine

Tumour relapse and acquired resistance formation to drugs are major complications in effective cancer treatment. Neuroblastoma is a heterogeneous malignancy of the sympathetic nervous system to which cisplatin and vincristine are two commonly used chemotherapeutic drugs. Many high-risk neuroblastomas are initially sensitive to therapy before acquiring resistance. Analysis of whole exome sequencing data from the MYCN-amplified neuroblastoma cell line UKF-NB-3, its cisplatin-adapted subline UKF-NB-3rCDDP1000, and its vincristine-adapted subline UKF-NB-3rVCR10 was performed with the aim of identifying and comparing resistance formation between

these two drugs that substantially differ in their mechanisms of action. 2,038 variants present only in the cisplatin-adapted subline, 122 variants present only in the vincristine-adapted subline and 50 variants overlapping the two drug-adapted sublines were identified as likely to have a functional effect on gene structure, function or expression. An over-representation analysis to identify enrichment of mutated genes in signalling pathways and gene ontology categories revealed several resistance mechanisms overlapping the drug-adapted sublines, related to prevention of the drugs from reaching their targets, through mutations in the extracellular matrix proteins, ABC transporters and solute carrier transporters. Nucleoporins, which regulate transport across the nuclear membrane, and calcium voltage-gated ion channel subunits, which are important in calcium homeostasis, were also highly mutated in the cisplatin-adapted subline, indicating possible roles in resistance formation. Mutations in MAP3K1, NOTCH2 and TP53 in the vincristine-adapted subline could confer resistance through evading pro-apoptotic signals. Several mechanisms related to olfactory receptors, mucin production and decreased contact inhibition overlapped the three cell lines, which could be due to the underlying genetics of the parental UKF-NB-3 cell line.