Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

Atefeh Lafzi; Costanza Borrelli; Simona Baghai Sain; Karsten Bach; Jonas A. Kretz; Kristina Handler; Daniel Regan-Komito; Xenia Ficht; Andreas P. Frei; Andreas E. Moor

doi:10.1038/s44320-023-00006-5

Systems BiologyMolecular Systems BiologyJan 15, 2024

Peer-reviewed journal article

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

Atefeh Lafzi iD, Costanza Borrelli iD, Simona Baghai Sain iD, Karsten Bach iD, Jonas A. Kretz iD, Kristina Handler iD, Daniel Regan-Komito iD, Xenia Ficht iD, Andreas P. Frei iD, Andreas E. Moor iD

Abstract

Spatial transcriptomics techniques are able to chart the distribution and localization of cell types and RNA molecules across a tissue. Here, we generated matched sequencing-based (Visium) and hybridization-based (Molecular Cartography) spatial transcriptomics data of human IBD samples. We then developed ISCHIA (Identifying Spatial Co-occurrence in Healthy and InflAmed tissues), a computational framework to analyze the spatial co-occurrence of cell types and transcript species in the tissue environment. ISCHIA revealed tightly associated cellular networks, ligand-receptor interactions enriched in the inflamed human colon, and their associated gene signatures, highlighting the hypothesis-generating power of co-occurrence analysis on spatial transcriptomics data.

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