Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
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.
Authors
- Azam Hamidinekoo (ORCID: https://orcid.org/0000-0002-2962-6010)
- Irina Mohorianu
- Grégory Hamm (ORCID: https://orcid.org/0000-0002-0769-9411)
- Steven Oag (ORCID: https://orcid.org/0009-0004-3663-4168)
- Martina Olsson Lindvall (ORCID: https://orcid.org/0000-0002-8609-5607)
- Lívia S. Eberlin (ORCID: https://orcid.org/0000-0002-3885-3215)
- Jorrit J. Hornberg (ORCID: https://orcid.org/0000-0001-8853-1532)
- Lovisa Franzén (ORCID: https://orcid.org/0000-0003-3755-718X)
- Muntasir Mamun Majumder (ORCID: https://orcid.org/0000-0002-5550-2951)
- Laura Setyo (ORCID: https://orcid.org/0000-0002-0677-6382)
- Patrik L. Ståhl (ORCID: https://orcid.org/0000-0002-2207-7370)
- Jennifer Y. Tan (ORCID: https://orcid.org/0000-0003-1064-1162)
- Aleksandr Zakirov (ORCID: https://orcid.org/0009-0007-5552-5129)
- Javier Escudero Morlanes (ORCID: https://orcid.org/0009-0004-2885-2456)
- James Denholm
- Trevor M. Godfrey (ORCID: https://orcid.org/0000-0001-5864-6048)
- Joakim Lundeberg
- Eleanor C. Williams
- Marco Vicari
- Anna Ollerstam
- Marianna Stamou
Institutions
- AstraZeneca (United Kingdom) (GB)
- Baylor College of Medicine (US)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- University of Cambridge (GB)
- Science for Life Laboratory (SE)
- Karolinska Institutet (SE)
- AstraZeneca (Australia) (AU)
- AstraZeneca (Finland) (FI)
- AstraZeneca (Sweden) (SE)
- KTH Royal Institute of Technology (SE)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-01-07
- DOI
- https://doi.org/10.1038/s41467-025-68003-w
- Citations
- 1
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 22.24