Screening cell-cell communication in spatial transcriptomics via collective optimal transport.

ABSTRACT: Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell-cell communication (CCC). However, incorporation of the spatial information and complex biochemical processes required in the reconstruction of CCC remains a major challenge. Here, we present COMMOT (COMMunication analysis by Optimal Transport) to infer CCC in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signali

SUBMITTER: Cang Z 

PROVIDER: S-EPMC9911355 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature