Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis
The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.
Authors
- John T. Chang (ORCID: https://orcid.org/0000-0003-0873-6218)
- Brigid S. Boland (ORCID: https://orcid.org/0000-0002-5360-8816)
- Garry P. Nolan (ORCID: https://orcid.org/0000-0002-8862-9043)
- Mariusz Ferenc (ORCID: https://orcid.org/0000-0003-4252-6986)
- Derek Holman (ORCID: https://orcid.org/0000-0002-3482-832X)
- Elizabeth A. Holman (ORCID: https://orcid.org/0000-0002-5158-4689)
- Stephan Rogalla (ORCID: https://orcid.org/0000-0002-1311-2672)
- Alexander N. Koron
- Samuel J. S. Rubin (ORCID: https://orcid.org/0000-0001-7335-3868)
- Robel Daniel
Institutions
- University of California San Diego (US)
- Stanford Medicine (US)
- Institute of Biocybernetics and Biomedical Engineering (PL)
- Stanford University (US)
- Polish Academy of Sciences (PL)
Publication Details
- Journal
- Scientific Reports
- Published
- 2024-08-15
- DOI
- https://doi.org/10.1038/s41598-024-68397-5
- Citations
- 2
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.47
Funders
- Kenneth Rainin Foundation
- National Institutes of Health
- National Center for Advancing Translational Sciences