Integrating gene expression and splicing dynamics across dose-response oxidative modulators | JoVE Visualize

Area of Science:

Toxicology
Transcriptomics
Molecular Biology

Background:

Transcriptomics, including gene expression and alternative splicing, is crucial for toxicological risk assessment, aiding in the determination of chemical's point of departure (POD) and modes of action (MOA).
Alternative splicing, a process generating multiple RNA isoforms from a single gene, plays a vital role in cellular function and response to stimuli.

Purpose of the Study:

To evaluate the role of splicing dysregulation in toxicological assessments.
To explore alternative splicing as a complementary endpoint in toxicological evaluations.
To investigate the potential of intron retention as a biomarker for chemical risk assessment.

Main Methods:

RNA sequencing (RNA-seq) was performed on A549 cells exposed to five oxidative stress modulators at various concentrations.
Differential gene expression (DGE) analysis was conducted to identify changes in gene expression levels.
Alternative splicing analysis focused on intron retention events, and benchmark dose modeling was applied to splicing data.

Main Results:

Differential gene expression analysis revealed limited pathway enrichment, primarily at high chemical concentrations.
Alternative splicing analysis identified significant intron retention events across diverse pathways for all tested chemicals, even without substantial gene expression changes.
Intron retention events increased progressively with chemical exposure, suggesting splicing alterations can precede changes in gene expression, as observed with diazinon.

Conclusions:

Alternative splicing analysis, particularly intron retention, provides a more sensitive measure of chemical toxicity compared to traditional gene expression analysis.
Integrating splicing data into toxicogenomic toolkits offers a more comprehensive understanding of transcriptomic dose-responses and enhances chemical risk assessment.
Splicing-aware toxicogenomics, by evaluating intron retention dynamics, can identify novel biomarkers for improved regulatory decision-making in chemical safety.