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Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics
Imran Shah1, David Gallegos1, Brian Robinette1
1Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA.
Biorxiv : the Preprint Server for Biology
|August 6, 2025
Summary
Single-cell transcriptomics revealed diverse cellular stress responses to chemicals, identifying five distinct cell states from homeostasis to apoptosis. This approach aids in understanding toxicological pathways and adaptive cellular transitions.
Area of Science:
- Toxicology
- Cell Biology
- Genomics
Background:
- Understanding cellular responses to chemical exposure is crucial for toxicology.
- Adaptive stress response pathways (SRPs) play a key role in cell survival and death.
- Single-cell transcriptomic (SCTr) analysis offers high resolution for studying cellular heterogeneity.
Purpose of the Study:
- To characterize adaptive stress response pathways (SRPs) in HepaRG cells using SCTr.
- To investigate cellular responses to various chemical stressors at the single-cell level.
- To identify distinct cellular phenotypic states and transitions during chemical exposure.
Main Methods:
- Applied the TempO-LINC® platform for SCTr profiling of ~40,000 HepaRG cells.
- Exposed cells to etoposide, brefeldin A, cycloheximide, rotenone, tBHQ, troglitazone, and tunicamycin.
- Scored cells using SRP gene signatures and clustered phenotypes using a generalized Jaccard metric.
Main Results:
- Identified five distinct phenotypic groups: homeostasis, adaptive responses, terminal outcomes, autophagy, and apoptosis.
- Observed heterogeneous responses to chemicals, with specific pathways like UPR, OSR, HSR, and DDR activated.
- Troglitazone upregulated lipid metabolism and HSR/UPR; Brefeldin A/Tunicamycin induced UPR; Rotenone triggered mitochondrial stress responses.
Conclusions:
- SCTr is valuable for decoding cellular stress states and heterogeneity.
- The study provides insights into transitions between cellular adaptation and toxicity.
- This methodology can elucidate mechanisms underlying chemical-induced cell death.
