High-Throughput Transcriptomics Platform for Screening Environmental Chemicals.

Area of Science:

• Toxicology
• Genomics
• Environmental Health

Background:

• New Approach Methodologies (NAMs) are crucial for accelerating chemical risk assessments without animal testing.
• High-throughput transcriptomics (HTTr) using in vitro assays is a promising NAM for hazard characterization.
• Standardized and scalable methods are needed to evaluate chemical impacts on biological pathways.

Purpose of the Study:

• To evaluate the Templated Oligo with Sequencing Readout (TempO-Seq) assay for HTTr concentration-response screening.
• To develop and validate a robust bioinformatics pipeline for analyzing HTTr data.
• To establish a novel gene signature-based modeling approach for identifying chemical-induced pathway alterations.

Main Methods:

• Utilized the TempO-Seq assay for HTTr in MCF7 cells with reference chemicals and samples.
• Developed a scalable bioinformatics pipeline employing open-source tools for data analysis.
• Implemented a gene expression signature-based concentration-response modeling approach, comparing it with BMDExpress.

Main Results:

• Demonstrated highly reproducible differential gene expression signatures from reference treatments.
• Aggregated gene signals into signatures for concentration-response modeling, yielding biological pathway altering concentrations (BPACs).
• BPACs aligned well with previous ToxCast high-throughput screening assays and identified known chemical molecular targets.

Conclusions:

• The TempO-Seq assay combined with the novel bioinformatics pipeline offers a scalable and reliable in vitro HTTr workflow.
• This workflow is suitable for high-throughput hazard evaluation of environmental chemicals.
• The gene signature-based approach effectively identifies chemical-induced pathway alterations relevant to risk assessment.