Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Biological systems are inherently 3D, but current spatial transcriptomics methods are limited to 2D tissue sections.
• This limitation hinders the resolution of cellular organization and microenvironments within intact tissue volumes.

Purpose of the Study:

• To develop a scalable, optics-free method for spatial transcriptome profiling directly within intact biological specimens.
• To enable the reconstruction of three-dimensional spatial relationships for comprehensive tissue analysis.

Main Methods:

• Developed volumetric DNA microscopy, encoding spatial information into DNA molecules within an intermolecular network.
• Detailed workflow: in situ cDNA synthesis, DNA nanoball formation for spatial encoding, proximity bridging, and 3D reconstruction via geodesic spectral embedding.
• Utilizes routine molecular biology reagents and a benchtop sequencer for library generation and computational analysis.

Main Results:

• Successfully established a complete workflow for volumetric spatial transcriptome profiling in intact tissues.
• Demonstrated the capability to reconstruct three-dimensional spatial relationships through DNA encoding and short-read sequencing.
• Workflow is efficient, with sequencing libraries generated in 7-8 days.

Conclusions:

• Volumetric DNA microscopy offers a versatile platform for exploring genetic and morphological features in intact tissues.
• Overcomes limitations of 2D tissue sectioning, providing deeper insights into tissue architecture and cellular interactions.
• Accessible technology for researchers using standard molecular biology techniques and equipment.