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Decoding cellular stress states for toxicology using single-cell transcriptomics.

Imran Shah¹, David Gallegos^1,2, Brian Robinette¹

¹Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency (EPA), Research Triangle Park, NC, USA.

|June 29, 2026

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This summary is machine-generated.

Single-cell transcriptomic profiling of HepaRG cells revealed five distinct cellular stress phenotypes, including homeostasis, adaptive responses, and apoptosis, in response to various chemical exposures. This approach decodes cellular stress states and potential transitions to cell death.

Area of Science:

Cellular biology
Toxicology
Genomics

Background:

Understanding cellular responses to chemical exposure is crucial for toxicology.
Adaptive stress response pathways (SRPs) play a key role in cellular survival and death.
Single-cell transcriptomic (SCTr) profiling offers high resolution for analyzing cellular heterogeneity.

Purpose of the Study:

To characterize cellular stress phenotypes induced by various chemicals using SCTr.
To analyze adaptive stress response pathways (SRPs) at the single-cell level.
To identify dynamic shifts in cellular subpopulations and their transitions to terminal states.

Main Methods:

Applied TempO-LINC® platform for SCTr profiling of ~40,000 HepaRG cells.
Exposed cells to etoposide, brefeldin A, cycloheximide, rotenone, tBHQ, troglitazone, and tunicamycin.

Keywords:

Adaptive stress response HepaRG cell states cell strate transition graph computational toxicology single-cell transcriptomics (SCTr)

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Main Results:

Identified five distinct cellular phenotypic groups: homeostasis, adaptive responses, terminal outcomes, autophagy, and apoptosis.
Observed differential activation of SRPs (UPR, OSR, HSR, DDR) by various chemicals.
Visualized dynamic shifts in cellular subpopulations, revealing early stress responses and transitions towards cell death.

Conclusions:

SCTr is a powerful tool for decoding complex cellular stress states.
The study provides insights into transitions between cellular adaptation and toxicity.
Findings highlight the utility of SCTr in understanding chemical-induced cellular responses and toxicity mechanisms.