Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

Area of Science:

• Environmental Science
• Toxicology
• Computational Biology

Background:

• Omics approaches are increasingly used in nanoecotoxicology to study engineered nanomaterials (ENMs).
• A systematic synthesis of common responses and toxicity pathways from these studies is lacking.
• Understanding ENM effects requires a standardized method for analyzing diverse omics data.

Purpose of the Study:

• To develop a computational pipeline for reanalysis and functional analysis of transcriptomic data from nanoecotoxicology studies.
• To identify common molecular mechanisms of nanotoxicity across different organisms and ENM types.
• To provide a comprehensive understanding of the molecular underpinnings of nanotoxicity.

Main Methods:

• Developed an R-scripted computational pipeline for semiautomatic processing of transcriptomic data from various microarray technologies.
• Applied the pipeline to data sets from *Arabidopsis thaliana*, *Caenorhabditis elegans*, and *Danio rerio*.
• Utilized functional analysis to determine common molecular mechanisms of nanotoxicity.

Main Results:

• Identified common nanotoxicity mechanisms including energy generation interference, oxidative stress, DNA synthesis disruption, and DNA repair activation.
• Discovered less-described responses such as DNA/RNA methylation, protein folding, and neurological function interference.
• Visualized toxicological response patterns using radar charts for comparative analysis across organisms and ENM types.

Conclusions:

• The developed pipeline enables consistent analysis of diverse omics data in nanoecotoxicology.
• Common molecular mechanisms of nanotoxicity were identified across different species and ENM types.
• This approach aids in hazard information retrieval and fills knowledge gaps in nanotoxicity mechanisms.