Modulation of Gene Expression in Human Lung Carcinoma Cells by Hypoxia and Exposure to Ionizing Radiation

Abstract

Carbon ion (C-ion) therapy is a relatively new alternative to classical X-ray treatment in cancer radiation therapy. It has multiple benefits from causing less damage to the surrounding tissues to lowering metastatic responses and being more effective against hypoxic tumors, where classical X-ray therapy often struggles. While the physical differences of these radiation therapy settings are well understood, knowledge about changes in gene regulation after exposure to these two radiation types is incomplete, especially concerning the radiation exposure under hypoxic conditions. To tackle this problem, A549 human lung carcinoma cells were exposed to these two different radiations under normoxia and hypoxia. RNA was extracted four hours after exposure and gene expression was then performed by RNA sequencing. In this work, a comprehensive bioinformatic analysis of the obtained data was performed, including the following steps: Running it through a DeSeq2 pipeline, then identification and removal of outliers. This process was followed by data exploration to assess the data without outliers. A GSEA analysis was used to identify key GO term groups and interesting core genes, followed with an indebt analysis of the selected gene sets. Three GSEA groups were identified that under all conditions were affected in Cell Cycle Regulation, RNA- and Protein Regulation, Cellular Responses and Development. While these groups were the same between X-ray treated samples and C-ion treated samples, the specific affected genes differ. Twenty genes were identified that in the selected gene sets behaved differently between the radiation types. Among them is a group of genes coding for heat shock proteins (HSP), behaving specifically different after C-ion radiation treatment combined with hypoxia. This points to a connection between these conditions and the regulation of HSP expression. The analysis also revealed that genes involved in the AKT pathway and NF-κB pathway are over-represented in genes that differ between X-rays and C-ions exposure under normoxia and hypoxia, with the AKT pathway being more prevalent. However, genes that differ specifically under hypoxia tend to only be involved in the NF- κB pathway. While lastly identifying potential target candidate genes for combined chemo and C-ion radiation therapy, PVRL4, PDGFRB NEFL, DRAXIN were found to be potentially promising knockdown targets, as well as EPHB3 as a target for enhancement.For best results from the auspicious method of C-ion radiation in cancer treatment, it must be adjusted for its exact biological effects, the discovery of which this thesis provides a baseline point for.