Comparative gene expression in cells competent in or lacking DNA-PKcs kinase activity following etoposide exposure reveal differences in gene expression associated with histone modifications, inflammation, cell cycle regulation, Wnt signaling, and differentiation

Abstract

Maintenance of the genome is essential for cell survival, and impairment of the DNA damage response is associated with multiple pathologies including cancer and neurological abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical nonhomologous end-joining pathway, but it may have roles in modulating gene expression and thus, the overall cellular response to DNA damage. Using cells producing either wild-type (WT) or kinase-inactive (KR) DNA-PKcs, we assessed global alterations in gene expression in the absence or presence of DNA damage. We evaluated differential gene expression in untreated cells and observed differences in genes associated with cellular adhesion, cell cycle regulation, and inflammation-related pathways. Following exposure to etoposide, we compared how KR versus WT cells responded transcriptionally to DNA damage. Downregulation of pathways involved in biosynthesis were observed in both genotypes, but upregulated biological pathways were divergent, again with KR cells manifesting a more robust inflammatory response compared to WT cells. To determine what major transcriptional regulators are controlling the differences in gene expression noted, we used pathway analysis and found that many master regulators of histone modifications, proinflammatory pathways, cell cycle regulation, Wnt/β-catenin signaling, and cellular development and differentiation were impacted by DNA-PKcs status. Overall, our results indicate that DNA-PKcs, in a kinase-dependent fashion, decreases proinflammatory signaling following genotoxic insult. As multiple DNA-PK kinase inhibitors are in clinical trial as cancer therapeutics utilized in combination with DNA damaging agents, understanding the transcriptional response when DNA-PKcs cannot phosphorylate downstream targets will inform the overall patient response to combined treatment.

XRCC4 and MRE11 Roles and Transcriptional Response to Repair of TALEN-Induced Double-Strand DNA Breaks

“…Depletion of another DNA repair enzyme, DNA-PKcs is previously shown to cause alteration in the metabolic pathway and P53 expression levels [ 50 ]. Enhanced p53 activity is a critical cellular signal for DNA damage.…”

Robust Transcriptional Regulatory Response Upon Blocking NHEJ

“…Depletion of another DNA repair enzyme, DNA-PKc is previously shown to cause alteration in metabolic pathway and TP53 levels 33 . Enhanced p53 activity is a critical cellular signal for DNA damage.…”