Etoposide-induced DNA damage affects multiple cellular pathways in addition to DNA damage response

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• DNA damage response (DDR) is crucial for repairing DNA lesions and activating checkpoints.
• The interplay between DDR and gene transcription is complex and not fully understood.
• Etoposide is a known inducer of DNA double-strand breaks, commonly used to study DDR.

Purpose of the Study:

• To investigate the impact of etoposide-induced DNA damage on gene expression.
• To identify specific genes and pathways affected by DDR.
• To characterize the dynamic transcriptional changes during DDR.

Main Methods:

• RNA sequencing (RNA-seq) was performed on MCF7 cells treated with etoposide.
• Differential gene expression analysis was conducted using stringent statistical cutoffs (FDR ≤ 0.001, FDR < 0.05, or p < 0.05).
• Metabolic labeling with 4-thiouridine was used to assess dynamic transcriptional changes in RABL6, RFTN2, FAS-AS1, and TCEB3CL genes.

Main Results:

• Etoposide treatment induced significant alterations in the expression of numerous genes, affecting processes like metabolism, cell motility, and signal transduction.
• Specific pathways, including Ras GTPase activity and RNA binding, were upregulated, while others, like coated vesicle and microtubule-based movement, were downregulated.
• RABL6 and FAS-AS1 were identified as novel DDR-affected genes with dynamic transcriptional changes observed upon etoposide treatment in MCF7 and T47D cells.

Conclusions:

• Etoposide-induced DNA damage triggers dynamic alterations in gene transcription.
• These transcriptional changes impact a wide range of cellular processes.
• The study identifies new genes involved in the DDR pathway and their dynamic transcriptional regulation.