Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq.

ABSTRACT: Cell-cell interactions are the fundamental building blocks of tissue organization and multicellular life. We developed Neighbor-seq, a method to identify and annotate the architecture of direct cell-cell interactions and relevant ligand-receptor signaling from the undissociated cell fractions in massively parallel single cell sequencing data. Neighbor-seq accurately identifies microanatomical features of diverse tissue types such as the small intestinal epithelium, terminal respiratory tract, and splenic white pulp. It also captures the differing topologies of cancer-immune-stromal cell communications in pancreatic and skin tumors, which are consistent with the patterns observed in spatial transcriptomic data. Neighbor-seq is fast and scalable. It draws inferences from routine single-cell

SUBMITTER: Ghaddar B 

PROVIDER: S-EPMC9371920 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature