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Single-cell RNA sequencing profiles drug activity within spatially engineered 3D cultures

Spatial transcriptomic techniques provide a wealth of information useful in guiding drug development, while three-dimensional (3D) cell cultures have demonstrated power in accelerating drug approvals. However, techniques for robust spatial analysis of 3D cultures are limited. Here, we present a transfection-based method for constructing cellular spheroids through a layer-by-layer approach, in which DNA barcodes encode the spatial positioning of cells.

Citation:
King JJ, Mowla A, Kretzmann JA, ……. Kadolsky UD, Iqbal M, Saxena A, Amos SE, et al. Single-cell RNA sequencing profiles drug activity within spatially engineered 3D cultures. Nat Commun. 2026;17(1).

Keywords:
Cell culture; three dimensional; methods; HeLa cells; sequence analysis; RNA; gene expression; spatial transcript5omics; spheroids

Abstract:
Spatial transcriptomic techniques provide a wealth of information useful in guiding drug development, while three-dimensional (3D) cell cultures have demonstrated power in accelerating drug approvals. However, techniques for robust spatial analysis of 3D cultures are limited. Here, we present a transfection-based method for constructing cellular spheroids through a layer-by-layer approach, in which DNA barcodes encode the spatial positioning of cells.