Construction of Gene Regulatory Networks Based on Spatial Multi-Omics Data and Application in Tumor-Boundary Analysis.

BACKGROUND/OBJECTIVES: Cell-cell communication (CCC) is a critical process within the tumor microenvironment, governing regulatory interactions between cancer cells and other cellular subpopulations. Aiming to improve the accuracy and completeness of intercellular gene-regulatory network inference, we constructed a novel spatial-resolved gene-regulatory network framework (spGRN).

METHODS

Firstly, the spatial multi-omics data of colorectal cancer (CRC) patients were analyzed. We precisely located the tumor boundaries and then systematically constructed the spGRN framework to study the network regulation. Subsequently, the key signaling molecules obtained by the spGRN were identified and further validated by the spatial-proteomics dataset.

RESULTS

Through the constructed spatial gene regulatory network, we found that in the communication with malignant cells, the highly expressed ligands and and receptors and in fibroblasts can promote tumor proliferation, and the highly expressed ligands in plasma cells play an important role in regulating inflammatory responses. Further, validation of the key signaling molecules by the spatial-proteomics dataset highlighted the role of these genes in mediating the regulation of boundary-related cells. Furthermore, we applied the spGRN to publicly available single-cell and spatial-transcriptomics datasets from three other cancer types. The results demonstrate that ITGB1 and its target genes FOS/JUN were commonly expressed in all four cancer types, indicating their potential as pan-cancer therapeutic targets.

CONCLUSION

the spGRN was proven to be a useful tool to select signal molecules as potential biomarkers or valuable therapeutic targets.