A heterogeneous cellular response to ionizing radiation revealed by single cell transcriptome sequencing.

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• Bulk sequencing limits understanding of individual tumor cell responses to ionizing radiation (IR).
• Tumor heterogeneity obscures how single cells transcriptionally adapt to DNA damage.
• The role of ATM (Ataxia-Telangiectasia Mutated) in mediating heterogeneous IR responses remains unclear.

Purpose of the Study:

• To investigate the heterogeneity of transcriptional responses in breast cancer cells following ionizing radiation (IR) exposure at the single-cell level.
• To elucidate the role of ATM kinase in mediating these heterogeneous cellular responses to DNA damage.
• To identify potential biomarkers for predicting radiation sensitivity.

Main Methods:

• Utilized barcoded Smart-seq2 single-cell transcriptome sequencing on the MDA-MB-231 breast cancer cell line.
• Performed experiments with and without IR treatment, including ATM gene knockdown.
• Analyzed single-cell transcriptomic data using t-SNE to identify distinct cell clusters.

Main Results:

• Identified four distinct clusters of cells with heterogeneous transcriptional responses to IR.
• Observed that ATM kinase deficiency significantly reduced transcriptional changes post-IR.
• Found that a major responsive cell cluster (Cluster 4) was absent in ATM-knockdown cells.
• Validated the importance of selected IR-induced genes in radiation sensitivity across two breast cancer cell lines.

Conclusions:

• Single-cell transcriptome sequencing reveals significant heterogeneity in breast cancer cell responses to ionizing radiation.
• ATM kinase plays a critical role in orchestrating the transcriptional adaptation of individual cells to DNA damage.
• The identified IR-induced genes and cellular response patterns may serve as potential biomarkers for radiation sensitivity.