Mapping human tissues with highly multiplexed RNA in situ hybridization

Area of Science:

• Molecular Biology
• Genomics
• Neuroscience

Background:

• In situ transcriptomic techniques offer insights into tissue organization and cell interactions.
• Existing multiplexed RNA in situ mapping methods have limitations for large human tissues, including size, quality, and autofluorescence.

Purpose of the Study:

• To develop a novel in situ transcriptomic technology for profiling large human tissue sections.
• To overcome limitations of existing methods for analyzing human tissue at the RNA level.

Main Methods:

• Developed DART-FISH (Digital Analysis of RNA by Fluorescence In Situ Hybridization), a padlock probe-based technology.
• Introduced an omni-cell type cytoplasmic stain for improved cell body segmentation.
• Utilized an enzyme-free isothermal decoding procedure for rapid gene imaging.

Main Results:

• Successfully profiled hundreds to thousands of genes in centimeter-sized human tissue sections.
• Mapped 121 genes in large human neocortex sections in under 10 hours, recapitulating 20 neuronal and non-neuronal subclasses.
• Mapped 300 genes in diseased human kidney tissue, identifying over 20 healthy and pathological cell states and diseased niches.

Conclusions:

• DART-FISH enables high-throughput gene profiling in large human tissues, overcoming previous technical barriers.
• The technology accurately maps cellular architecture and identifies distinct cell states in both healthy and diseased human organs.
• This advancement facilitates deeper understanding of human tissue biology and disease mechanisms.