SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and...

Area of Science:

• Spatial omics
• Multi-omics integration
• Bioinformatics

Background:

• Existing spatial omics tools struggle with integrated transcriptomics and metabolomics analysis.
• In-depth biological interpretation and user-friendly operation are often lacking.

Purpose of the Study:

• To introduce SMIntegration, a novel web-based graphical platform for integrated spatial metabolomics and transcriptomics analysis.
• To provide a user-friendly, zero-code solution for exploring gene-metabolite interactions in microenvironments.

Main Methods:

• Developed SMIntegration using R/Shiny and Docker containerization.
• Implemented automated spatial registration, cross-modal pattern recognition, flexible differential analysis, and network construction.
• Utilized adjacent mouse brain sections with Stereo-seq transcriptomics and AFADESI-MS metabolomics data.

Main Results:

• SMIntegration successfully identified specific brain regions missed by single-modality clustering.
• Revealed associations between astrocyte GABA metabolism and Slc6a11.
• Dissected glutamatergic and cannabinoid signaling pathways by comparing distinct brain regions.

Conclusions:

• SMIntegration offers a comprehensive workflow for integrated spatial omics analysis.
• The platform empowers researchers to investigate complex gene-metabolite interactions in various biological contexts.