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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
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
HepaRGadaptive stress responsecell statescell strate transition graphcomputational toxicologysingle-cell transcriptomics (SCTr)

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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.