Researchers are constantly working to better understand how cells organize themselves within tissues. One important aspect of this organization is how cells “talk” to each other and respond to their neighbors. A new computational method called SpaGRN, developed by researchers from the BGI Research Institute, offers a powerful way to explore these spatial relationships using RNA sequencing data.

In tissues, different types of cells form patterns and structures, often influenced by signals from nearby cells. Traditional RNA sequencing methods tell us what genes are active in individual cells, but they don’t fully capture how the position of a cell and the surrounding environment influence that activity.

SpaGRN is a statistical tool that connects gene activity within a cell to signals it might be receiving from its neighbors. It creates maps called spatial regulons, which show which genes are turned on or off in specific parts of a tissue, depending on both internal and external signals.

The researchers tested SpaGRN on multiple advanced spatial RNA sequencing platforms—like MERFISH, 10x Visium, and Slide-seq—and found it outperformed existing tools. They applied it to complex cancer samples and even developing fruit fly embryos, where it helped uncover patterns of gene regulation tied to inflammation and organ development.

This tool could help researchers explore how diseases like cancer or chronic inflammation disrupt normal tissue organization. It may also pave the way for future discoveries in regenerative medicine and developmental biology.

Availability – an interactive 3D GRN atlas database for various SRT datasets rendered by VT3D is avaialable at: http://www.bgiocean.com/SpaGRN/. SpaGRN v1.1.0 is available at: https://zenodo.org/records/14925041.