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Published on: November 21, 2025
Dynamics of the transcriptome response of cultured human embryonic stem cells to ionizing radiation exposure
Mykyta V Sokolov1, Irina V Panyutin, Igor G Panyutin
1Nuclear Medicine Division, Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States.
Abstract:
One of the key consequences of exposure of human cells to genotoxic agents is the activation of DNA damage responses (DDR). While the mechanisms underpinning DDR in fully differentiated somatic human cells have been studied extensively, molecular signaling events and pathways involved in DDR in pluripotent human embryonic stem cells (hESC) remain largely unexplored. We studied changes in the human genome-wide transcriptome of H9 hESC line following exposures to 1Gy of gamma-radiation at 2h and 16h post-irradiation. Quantitative real-time PCR was performed to verify the expression data for a subset of genes. In parallel, the cell growth, DDR kinetics, and expression of pluripotency markers in irradiated hESC were monitored. The changes in gene expression in hESC after exposure to ionizing radiation (IR) are substantially different from those observed in somatic human cell lines. Gene expression patterns at 2h post-IR showed almost an exclusively p53-dependent, predominantly pro-apoptotic, signature with a total of only 30 up-regulated genes. In contrast, the gene expression patterns at 16h post-IR showed 354 differentially expressed genes, mostly involved in pro-survival pathways, such as increased expression of metallothioneins, ubiquitin cycle, and general metabolism signaling. Cell growth data paralleled trends in gene expression changes. DDR in hESC followed the kinetics reported for human somatic differentiated cells. The expression of pluripotency markers characteristic of undifferentiated hESC was not affected by exposure to IR during the time course of our analysis. Our data on dynamics of transcriptome response of irradiated hESCs may provide a valuable tool to screen for markers of IR exposure of human cells in their most naive state; thus unmasking the key elements of DDR; at the same time, avoiding the complexity of interpreting distinct cell type-dependent genotoxic stress responses of terminally differentiated cells.
Insights
Human embryonic stem cells (hESC) exhibit unique DNA damage responses (DDR) to radiation compared to somatic cells. Early responses are p53-dependent and pro-apoptotic, shifting to pro-survival pathways later, without affecting pluripotency markers.
Area of Science:
- Genomics
- Stem Cell Biology
- Radiation Biology
Background:
- DNA damage responses (DDR) are crucial for cell survival upon genotoxic exposure.
- DDR mechanisms in differentiated somatic cells are well-understood, but remain largely unexplored in pluripotent human embryonic stem cells (hESC).
Purpose of the Study:
- To investigate the genome-wide transcriptome changes in hESC following gamma-radiation exposure.
- To compare DDR in hESC with that of somatic cells and understand the role of p53.
- To assess the impact of radiation on hESC pluripotency markers and cell growth.
Main Methods:
- Genome-wide transcriptome analysis of H9 hESC line at 2h and 16h post-1Gy gamma-irradiation.
- Quantitative real-time PCR for gene expression verification.
- Monitoring of cell growth, DDR kinetics, and pluripotency marker expression.
Main Results:
- Gene expression changes in hESC post-irradiation differ significantly from somatic cells.
- At 2h post-irradiation, a p53-dependent, pro-apoptotic signature with 30 upregulated genes was observed.
- At 16h post-irradiation, 354 differentially expressed genes, primarily involved in pro-survival pathways (e.g., metallothioneins, ubiquitin cycle), were identified.
- Cell growth trends mirrored gene expression changes, and DDR kinetics were similar to somatic cells.
- Pluripotency markers remained unaffected throughout the study.
Conclusions:
- The dynamic transcriptome response of irradiated hESC provides insights into DDR in pluripotent cells.
- These findings may aid in developing tools to screen for radiation exposure markers in naive human cells.
- Understanding hESC-specific DDR avoids the complexity of interpreting cell type-dependent responses in differentiated cells.
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