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Three and Four-Dimensional Visualization and Analysis Approaches to Study Vertebrate Axial Elongation and Segmentation

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INSIHGT: an accessible multi-scale, multi-modal 3D spatial biology platform.

Chun Ngo Yau^1,2, Jacky Tin Shing Hung^1,2, Robert A A Campbell³

¹Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.

Nature Communications

|December 31, 2024

Summary

INSIHGT is a novel 3D spatial biology method enabling deep tissue probing for comprehensive molecular mapping. This technique preserves diverse biological molecules, advancing systems biology and multi-omics research.

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Area of Science:

Molecular Biology
Cell Biology
Biotechnology

Background:

Biological systems exhibit complex spatial, molecular, and functional interdependencies.
Existing methodologies face limitations in extracting comprehensive biological information.
Advanced techniques are needed for deep, high-resolution molecular profiling within intact tissues.

Purpose of the Study:

To develop a non-destructive, accessible 3D spatial biology method for deep tissue molecular mapping.
To enable simultaneous visualization of diverse biomolecules at centimeter scales.
To facilitate advanced spatial multi-omics and systems biology studies.

Main Methods:

Developed INSIHGT (in situ imaging and hybridization) utilizing superchaotropes and host-guest chemistry.
Achieved homogeneous, deep penetration of macromolecular probes up to centimeter scales.
Enabled multi-round, highly multiplexed 3D molecular probing compatible with downstream analyses.

Main Results:

Demonstrated preservation and simultaneous visualization of diverse antigens, mRNAs, neurotransmitters, and post-translational modifications.
Successfully mapped microfilaments in mouse glomeruli and inclusion bodies in the human cerebellum.
Identified NPY-proximal cell types via spatial morpho-proteomics in the mouse hypothalamus.

Conclusions:

INSIHGT provides a robust platform for deep 3D spatial molecular profiling.
The method supports simultaneous detection of multiple molecular species and is compatible with existing workflows.
INSIHGT is poised to advance 3D spatial multi-omics and holistic systems biology research.