Transcriptomic analysis to identify genes associated with chloroquine-mediated radiosensitization of glioblastoma stem cells

Tumour suppressor p53 regulates hundreds of genes by either activating or repressing their transcription. p53-dependent transcription is activated by stress factors such as DNA damage, reactive oxygen species, hypoxia or oncogenic signaling. Lysosomotropic agent and DNA intercalating agent chloroquine has been implicated in sensitizing glioblastoma to radiation via p53 pathway. This study evaluates the effects of chloroquine in glioblastoma stem cells differing for the status of TP53 by using an integrated approach encompassing in vitro, in vivo and in silico methodologies to characterize the impacts of chloroquine on cell vitality, tumor-propagating capacity and gene expression. We used microarrays to identify the genes whose expression is influenced by DNA intercalator chloroquine (ClQ) in glioblastoma stem cells expressing wild type p53 (line #993), mutant p53 (line G112) or a p53 null line #1095. To compare chloroquine-associated transcriptomic changes with those induced by ionizing radiation (IR), samples of IR-treated line #993 ("#993_IR") were analyzed in parallel with ClQ-treated samples ("993_ClQ"). Gene expression was analyzed in three lines of glioblastoma stem cell lines (#993, #1095 and G112) either untreated or treated with chloroquine (ClQ). In addition to ClQ-associated gene expression, transcriptomic changes associated with exposure to ionizing radiation (IR) were also analyzed in line #993. For each line and each condition (treated or untreated), 3 replicates were analyzed (re1, rep2 and rep3).