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Updated: Aug 13, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Screening cell-cell communication in spatial transcriptomics via collective optimal transport.

Zixuan Cang¹, Yanxiang Zhao², Axel A Almet^3,4

¹Department of Mathematics and Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA.

|January 23, 2023

Summary

We developed COMMOT, a new method to analyze cell-cell communication in spatial transcriptomics. It considers ligand-receptor competition and cell proximity, advancing our understanding of biological signaling.

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Published on: April 25, 2011

Area of Science:

Single-cell biology
Systems biology
Bioinformatics

Background:

Spatial transcriptomics and single-cell RNA sequencing enable cell-cell communication (CCC) studies.
Integrating spatial data and complex biochemical interactions for CCC inference remains challenging.

Purpose of the Study:

To present COMMOT (COMMunication analysis by Optimal Transport), a novel computational framework for inferring CCC in spatial transcriptomics.
To address the limitations of existing methods by incorporating ligand-receptor competition and spatial proximity.

Main Methods:

Developed a collective optimal transport method to model complex molecular interactions and spatial constraints.
Introduced downstream machine learning tools for inferring spatial signaling directionality and target genes.
Validated COMMOT on simulation data and eight diverse spatial transcriptomic datasets.

Main Results:

COMMOT effectively infers spatial CCC across datasets with varying resolutions and gene coverages.
Demonstrated robustness and accuracy in identifying known and novel CCC interactions.
Identified previously unknown CCCs involved in human skin morphogenesis.

Conclusions:

COMMOT provides a robust and effective approach for dissecting spatial cell-cell communication.
The method enhances the analysis of complex biological signaling in spatial contexts.
COMMOT offers valuable insights into developmental processes like skin morphogenesis.