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

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 multimodal 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 multimodal analyses provide for studying tissue injury especially in pharmacological contexts, and delivers a modular, accessible workflow for data integration

INSTRUMENT(S): MS Imaging -

PROVIDER: MTBLS13445 | MetaboLights | 2025-12-03

REPOSITORIES: MetaboLights

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			Action	DRS
	a_MTBLS13445_MSImaging___metabolite_profiling.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS13445_MSImaging___metabolite_profiling_v2_maf.tsv	Tabular
	s_MTBLS13445.txt	Txt

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

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