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

Lafzi, A.; Borrelli, C.; Bach, K.; Kretz, J. A.; Handler, K.; Regan-Komito, D.; Ficht, X.; Frei, A. P.; Moor, A. E.

doi:10.1101/2023.02.13.526554

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bioRxiv · 10.1101/2023.02.13.526554

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

Lafzi, A.·Borrelli, C.·Bach, K.·Kretz, J. A.·Handler, K.·Regan-Komito, D.·Ficht, X.·Frei, A. P.·Moor, A. E.

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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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Lafzi, A., Borrelli, C., Bach, K., Kretz, J. A., Handler, K., Regan-Komito, D., Ficht, X., Frei, A. P., Moor, A. E.. 2023-02-15. Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA). https://doi.org/10.1101/2023.02.13.526554

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