Culture of Cancer Cells at Physiological Oxygen Levels Affects Gene Expression in a Cell-Type Specific Manner

Standard cell culture is routinely performed at supraphysiological oxygen levels (~18% O₂). Conversely, O₂ levels in most mammalian tissues range from 1-6% (physioxia). Such hyperoxic conditions in cell culture can alter reactive oxygen species (ROS) production, metabolism, mitochondrial networks, and response to drugs and hormones. The aim of this study was to investigate the transcriptional response to different O₂ levels and determine whether it is similar across cell lines, or cell line-specific. Using RNA-seq, we performed differential gene expression and functional enrichment analyses in four human cancer cell lines, LNCaP, Huh-7, PC-3, and SH-SY5Y cultured at either 5% or 18% O₂ for 14 days. We found that O₂ levels affected transcript abundance of thousands of genes, with the affected genes having little overlap between cell lines. Functional enrichment analysis also revealed different processes and pathways being affected by O₂ in each cell line. Interestingly, most of the top differentially expressed genes are involved in cancer biology, which highlights the importance of O₂ levels in cancer cell research. Further, we observed several hypoxia-inducible factor (HIF) targets, HIF-2α targets particularly, upregulated at 5% O₂, consistent with a role for HIFs in physioxia. O₂ levels also differentially induced the transcription of mitochondria-encoded genes in most cell lines. Finally, by comparing our transcriptomic data from LNCaP and PC-3 with datasets from the Prostate Cancer Transcriptome Atlas, a correlation between genes upregulated at 5% O₂ in LNCaP cells and the in vivo prostate cancer transcriptome was found. We conclude that the transcriptional response to O₂ over the range from 5-18% is robust and highly cell-type specific. This latter finding indicates that the effects of O₂ levels are difficult to predict and thus highlights the importance of regulating O₂ in cell culture.