Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

Recent developments in spatially resolved -omics have enabled studies linking gene expression and metabolite levels to tissue morphology, offering new insights into biological pathways. By capturing multiple modalities on matched tissue sections, one can better probe how different biological entities interact in a spatially coordinated manner. However, such cross-modality integration presents experimental and computational challenges.

To align multimodal datasets into a shared coordinate system and facilitate enhanced integration and analysis, we proposeMAGPIE(Multi-modalAlignment ofGenes andPeaks forIntegratedExploration), a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections.

We illustrate the generalisability and scalability ofMAGPIEon spatial multi-omics data from multiple tissues, combining Visium with both MALDI and DESI mass spectrometry imaging.MAGPIEwas also applied to newly generated multimodal datasets created using specialised experimental sampling strategy to characterise the metabolic and transcriptomic landscape in anin vivomodel of drug-induced pulmonary fibrosis, to showcase the linking of small-molecule co-detection with endogenous responses in lung tissue.

MAGPIEhighlights the refined resolution and increased interpretability of spatial multimodal analyses in studying tissue injury, particularly in pharmacological contexts, and offers a modular, accessible computational workflow for data integration.