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

TL;DR

This study explores how splicing changes in genes can improve understanding of chemical toxicity, offering new insights beyond traditional gene expression analysis.

Contribution

The novel contribution is demonstrating that splicing dysregulation, particularly intron retention, can reveal toxicological effects even when gene expression changes are minimal.

Findings

Alternative splicing analysis revealed intron retention events across all chemicals tested, even without significant gene expression changes.

Intron retention data identified relevant pathways missed by traditional gene expression analysis.

Splicing alterations, such as intron retention, may serve as early biomarkers for chemical toxicity.

Abstract

Toxicological risk assessment increasingly utilizes transcriptomics to derive point of departure (POD) and modes of action (MOA) for chemicals. One essential biological process that allows a single gene to generate several different RNA isoforms is called alternative splicing. To comprehensively assess the role of splicing dysregulation in toxicological evaluation and elucidate its potential as a complementary endpoint, we performed RNA-seq on A549 cells treated with five oxidative stress modulators across a wide dose range. Differential gene expression (DGE) showed limited pathway enrichment except at high concentrations. However, alternative splicing analysis revealed variable intron retention events affecting diverse pathways for all chemicals in the absence of significant expression changes. For instance, diazinon elicited negligible gene expression changes but progressive increase in the number of intron retention events, suggesting splicing alterations precede expression responses. Benchmark dose modeling of intron retention data highlighted relevant pathways overlooked by expression analysis. Systematic integration of splicing datasets should be a useful addition to the toxicogenomic toolkit. Combining both modalities paint a more complete picture of transcriptomic dose-responses. Overall, evaluating intron retention dynamics afforded by toxicogenomics may provide biomarkers that can enhance chemical risk assessment and regulatory decision making. This work highlights splicing-aware toxicogenomics as a possible additional tool for examining cellular responses.

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