Generation, characterization and drug sensitivities of twelve patient-derived IDH1 mutant glioma cell cultures
Authors: Verheul Cassandra , Ntafoulis Ioannis , Kers Trisha V. , Hoogstrate Youri , Mastroberardino Pier G. , Barnhoorn Sander , Payán-Gómez César , Yen Romain Tching Chi , Struys Eduard A. , Koolen Stijn L.W. , Dirven Clemens M.F. , Leenstra Sieger , French Pim J. , Lamfers Martine L.M. 
Published: April 2021

Background

Mutations of the isocitrate dehydrogenase (IDH) gene occur in over 80% of low-grade gliomas and secondary glioblastomas. Despite considerable efforts, endogenousin vitro IDH-mutated glioma models remain scarce. Availability of these models is key for the development of new therapeutic interventions.

Methods

Cell cultures were established from fresh tumor material and expanded in serum-free culture media. D-2-Hydroxyglutarate levels were determined by mass-spectrometry. Genomic and transcriptomic profiling were carried out on the Illumina Novaseq platform, methylation profiling was performed with the Infinium MethylationEpic BeadChip array. Mitochondrial respiration was measured with the Seahorse XF24 Analyzer. Drug screens were performed with an NIH FDA-approved anti-cancer drug set and two IDH-mutant specific inhibitors.

Results

A set of twelve patient-derived IDHmt cell cultures was established. We confirmed high concordance in driver mutations, copy number and methylation profiles between the tumors and derived cultures. Homozygous deletion ofCDKN2A/Bwas observed in all cultures. IDH-mutant cultures had lower mitochondrial reserve capacity. IDH-mutant specific inhibitors did not affect cell viability or global gene expression. Screening of 107 FDA-approved anti-cancer drugs identified nine compounds with potent activity against IDHmt gliomas, including three compounds with favorable pharmacokinetic characteristics for CNS penetration: teniposide, omacetaxine mepesuccinate, and marizomib.

Conclusions

Our twelve IDH-mutant cell cultures show high similarity to the parental tissues and offer a unique tool to study the biology and drug sensitivities of high-grade IDHmt gliomasin vitro. Our drug screening studies reveal lack of sensitivity to IDHmt inhibitors, but sensitivity to a set of nine available anti-cancer agents.

Key points

IDHmt glioma cultures closely resemble their parental tumors

Microscopic monitoring of early passages and colony isolation increases IDH1mt culture success

Drug screening identified nine candidate repurposed drugs for IDHmt glioma

Importance of the study

IDH-mutations are highly prevalent in low grade and secondary high-grade gliomas. Despite this high frequency however, very fewin vitromodels have been reported for IDH-mutated gliomas. In this manuscript we describe and characterize in detail twelve primary cultures from IDH-mutant astrocytomas. We show that these cultures retain most of the genetic, epigenetic and metabolic features of their respective parental tumors. Because of these similarities, these independent model systems will not only help understand the molecular defects driven by the mutation, but are also vital to identify means to target these tumors. Screening of 107 FDA-approved anti-cancer agents on these cultures identified a set of highly effective agents that may offer candidates for either systemic or assisted delivery treatment of this tumor subtype.