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Updated: Jun 21, 2026
05:54
Generation of High-Throughput Three-Dimensional Tumor Spheroids for Drug Screening
Published on: September 5, 2018
Single-cell RNA sequencing profiles drug activity within spatially engineered 3D cultures
Jessica J King1, Alireza Mowla2,3, Jessica A Kretzmann1,4
1School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
Nature Communications
|June 19, 2026
Summary
Researchers developed a new method to map gene expression and drug responses in 3D cell cultures using DNA barcoding. This spatial transcriptomic technique aids drug development by analyzing cellular assemblies in three-dimensional (3D) cultures.
Area of Science:
- Biotechnology
- Genomics
- Drug Development
Background:
- Spatial transcriptomic techniques offer valuable insights for drug development.
- Three-dimensional (3D) cell cultures accelerate drug approvals but lack robust spatial analysis methods.
- Existing spatial analysis techniques for 3D cultures are limited.
Purpose of the Study:
- To present a novel transfection-based method for constructing spatially barcoded cellular spheroids.
- To enable multiplex single-cell RNA sequencing for spatial mapping of gene expression and drug response in 3D cultures.
- To facilitate correlative imaging for quantifying local tissue elasticity and cell population locations.
Main Methods:
- Layer-by-layer construction of cellular spheroids.
- Incorporation of DNA barcodes to encode cell spatial positions.
- Multiplex single-cell RNA sequencing and correlative imaging.
Main Results:
- Demonstrated heterogeneous drug responses in model HeLa 3D spheroids.
- Identified potential causes for heterogeneous responses, including diffusion gradients and metabolic differences.
- Generated spatial maps of gene expression and drug response within 3D culture models.
Conclusions:
- The developed technique provides spatial maps of gene expression and drug response in 3D cultures.
- Spatially encoded cellular assemblies can reveal spatial variations in gene expression.
- This method may advance drug development by enabling detailed analysis of 3D cell culture models.
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