Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
Year: 2026
Type: article
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.
Source: Nature Communications
Authors: Eleanor C. Williams, Lovisa Franzén, Martina Olsson Lindvall, Gregory Hamm, Steven Oag, Muntasir Mamun Majumder, James Denholm, Azam Hamidinekoo, Javier Escudero Morlanes, Marco Vicari, Joakim Lundeberg, Laura Setyo, Trevor M. Godfrey, Livia S. Eberlin, Aleksandr Zakirov, Jorrit J. Hornberg, Marianna Stamou, Patrik L. Ståhl, Anna Ollerstam, Jennifer Y. Tan, Irina Mohorianu
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funder: Medical Research Council
Award: G1981653777
OpenAlex ID: W7118330634