Analysis of cellular responses to microwave irradiation in E. coli and change of oxygen level and culture medium in human cancer cell lines using RNA-seq based transcriptomic profiling

Abstract

RNA sequencing (RNA-seq) is one of the applications of next-generation sequencing (NGS) with differential gene expression (DGE) analysis at the transcriptomic level as its primary objective. Among the NGS technologies, the Illumina platforms are the current standard for RNA-seq analysis for their best cost efficiency and sequencing accuracy. In this study, we employed Illumina-based RNA-seq to examine the gene expression profile change in E. coli cells after exposure to microwave irradiation (MWI) and in cancer cell lines in response to different culture conditions using breast cancer cell lines (MCF7) and prostate cancer cell lines (PC3) as the models. Our results in examining the gene expression change in E. coli showed that the non-thermal effects of MWI led to E. coli cells entering the stationary phase with most of the downregulated genes involved in metabolic and biosynthesis pathways. MWI also upregulated the expression of genes important for the maintenance of membrane integrity and adhesion associated with bacterial motility. In comparison with other similar studies, our methodology allowed us to observe the impact of non-thermal effects of MWI at 2.45 GHz via simultaneous cooling. Our results in examining the transcriptomic profile of MCF7 and PC3 cells in response to oxygen level and culture medium change showed that gene expression in MCF7 is highly affected by oxygen level and culture medium changes when compared to PC3, especially in DMEM at 18% O2. DNA replication, cell-cycle, and viral carcinogenesis are the most affected pathways observed from different culture conditions in both cell lines. In PC3, only the legionellosis seems to be most impacted by culture medium changes at 5% O2, involving 8 differentially expressed genes (DEGs), important for cancer cell development. DGE analysis also provides the transcriptomic profile of MCF7 and PC3, showing that different nutrient composition (between DMEM and Plasmax) and oxygen levels (5% O2 and 18% O2) changes the metabolism and various signaling pathways in both cell lines differently suggesting that the oxygen level and culture medium are important factors impacting the outcome of cell culture-based experiments in cell type-specific fashion.