High-throughput RNA-Seq and in-silico analysis of glioblastoma cells treated with cold atmospheric plasma and temozolomide

Abstract Glioblastoma multiforme (GBM) is one of the most common and aggressive forms of malignant brain cancer in adults and is classified based on its isocitrate dehydrogenase (IDH) mutation. Surgery, radiotherapy, and Temozolomide (TMZ) are the standard treatment methods for GBM. Here we present a combination therapy of cold atmospheric plasma (CAP) and TMZ as a key treatment for GBM. CAP works by increasing reactive oxygen and nitrogen species (RONS) and targets the spread of the tumor. In this study, we performed the transcriptomic analysis of U-87MG cells by high throughput deep RNA-Seq analysis to quantify differential gene expression across the genome. Furthermore, we studied various signaling pathways and predicted structural changes of consequential proteins to elucidate the functional changes caused by up or down-regulation of the most altered genes. Our results demonstrate that combination treatment downregulated key genes like p53, histones, DNA damage markers, cyclins, in the following pathways: MAPK, P53, DNA damage and cell cycle. Moreover, in silico studies were conducted for further investigation to verify these results, and the combination of CAP & TMZ showed a significant antitumor effect in the GBM cells leading to apoptosis and damaged key proteins. Further studies of the impact of TMZ on gene expression, biochemical pathways, and protein structure will lead to improved treatment approaches for GBM.