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Updated: Jun 27, 2025

Longitudinal Measurement of Extracellular Matrix Rigidity in 3D Tumor Models Using Particle-tracking Microrheology

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Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis.

Wen Wang¹, Shiwei Zheng¹, Sujung Crystal Shin¹

¹Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Biorxiv : the Preprint Server for Biology

|May 7, 2024

Summary

This summary is machine-generated.

We developed ONTraC, a novel computational tool for analyzing spatial variations in tissue microenvironments. ONTraC reconstructs niche trajectories, offering a powerful new method for understanding tissue organization and function.

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Area of Science:

Computational biology
Spatial transcriptomics
Single-cell analysis

Background:

Technological advancements enable single-cell resolution mapping of tissue spatial organization.
Existing computational methods are insufficient for analyzing continuous spatial variations in tissue microenvironments.

Purpose of the Study:

To introduce ONTraC, a novel strategy for constructing niche trajectories.
To provide a computational framework for analyzing spatial variations in the tissue microenvironment.

Main Methods:

Utilized a graph neural network-based modeling framework.
Developed ONTraC for reconstructing spatial trajectories.
Benchmarked ONTraC against existing trajectory reconstruction methods.

Main Results:

ONTraC demonstrated superior performance compared to existing methods in benchmark analyses.
Applied ONTraC to spatial transcriptomics datasets, successfully recapitulating anatomical structures.
Identified tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interactions during embryonic development.

Conclusions:

ONTraC is an effective and broadly applicable tool for characterizing tissue microenvironments.
The strategy enables systematic analysis of both structural and functional organization within tissues.
Facilitates the discovery of microenvironment-driven biological processes.