Intra-tumor heterogeneity and temozolomide resistance in Glioblastoma U87MG cell line

The criticality of therapeutic impact arising from tumor heterogeneity is indisputable. Glioblastoma multiforme, an aggressive primary brain tumor, is generally treated with alkylating agent, temozolomide. An authenticated U87MG glioblastoma cell line was investigated to identify a sub-population of neurospheroidal (NSP) cells within the main epithelial population (U87MG). Genomic variability across these two populations, that showed difference in their drug responses, was studied. Exome, the coding part of genome consisting of the complete set of exons, was sequenced using next generation sequencing platform to assess the genomic variability across the two cell types - drug sensitive, U87MG and drug resistant, NSP. With exome sequencing, the data generated is less to analyze and interpret, that forms the important consideration, other than the faster turnaround time and cost effective technology. In order to identify the DNA variants most possibly contributing for the heterogeneity and temozolomide resistance, within the 1% of the genome (protein coding), the genomic DNA of both these cell types were pipelined in the exome sequencing work flow. Ion ProtonTM system (Life technologies Pvt. Ltd., India) was used to obtain the Exome sequences of U87MG and NSP cells. Ion TargetSeqTM Exome kit and Ion ProtonTM sequencer was used for acquiring the Exome data that was further processed through TorrentSuite and Ion Reporter software to identify the variants and for the coverage analysis. The identified variants were considered from the targets with base coverage at 20x with 92.22% recovery in U87MG exome and 95.00% recovery in NSP exome. Exome sequencing indicated 1804 and 795 variants as novel for U87MG and NSP respectively with 20x base coverage. These results should eventually stimulate further works aimed at targeting cancer cell adaptive mechanisms to resistance and relapse.