Language
English
Publication Date
1-7-2026
Journal
Nature Communications
DOI
10.1038/s41467-025-68003-w
PMID
41501078
PMCID
PMC12780049
PubMedCentral® Posted Date
1-7-2026
PubMedCentral® Full Text Version
Post-print
Abstract
Recent developments in spatially resolved -omics have enabled the joint study of gene expression, metabolite levels and tissue morphology, offering greater insights into biological pathways. Integrating these modalities from matched tissue sections to probe spatially-coordinated processes, however, remains challenging. Here we introduce MAGPIE, a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections. We show MAGPIE's generalisability and scalability on spatial multi-omics data from multiple tissues, combining Visium with MALDI and DESI mass spectrometry imaging. MAGPIE was also applied to new multi-modal datasets generated with a specialised sampling strategy to characterise the metabolic and transcriptomic landscape in an in vivo model of drug-induced pulmonary fibrosis and to link small-molecule co-detection with endogenous lung responses. MAGPIE demonstrates the refined resolution and enhanced interpretability that spatial multi-modal analyses provide for studying tissue injury especially in pharmacological contexts, and delivers a modular, accessible workflow for data integration.
Keywords
Metabolomics, Animals, Transcriptome, Lung, Pulmonary Fibrosis, Mice, Gene Expression Profiling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Mice, Inbred C57BL, Metabolome, Male, Software, Computational models, Data integration
Published Open-Access
yes
Recommended Citation
Williams, Eleanor C; Franzén, Lovisa; Olsson Lindvall, Martina; et al., "Spatially Resolved Integrative Analysis of Transcriptomic and Metabolomic Changes in Tissue Injury Studies" (2026). Faculty, Staff and Students Publications. 6151.
https://digitalcommons.library.tmc.edu/baylor_docs/6151