A1818
Title: NicheScope: Identifying multicellular niches and niche-regulated cell states in spatial transcriptomics
Authors: Jiashun Xiao - Sun Yat-sen University (China) [presenting]
Abstract: The functional state of a Cell is intricately linked to its local microenvironment, or Cell niche, composed of multiple interacting Cell types. Deciphering how these Multicellular Niches regulate Cell States is fundamental to understanding tissue biology and disease mechanisms, yet remains challenging with current computational approaches. NicheScope, a unified framework for identifying Multicellular Niches (MCNs) and their corresponding NicheRegulated Cell States (NRCSs) from spatial transcriptomics (ST) data, is introduced. NicheScope builds on the principle that a Cell's transcriptional state is influenced by its local Multicellular composition. By jointly modeling the neighborhood cellular composition and the gene expression profile of a target Cell type, NicheScope enables the discovery of MCNs defined by specific neighboring Cell type combinations and their associated NRCSs characterized by distinct gene programs. NicheScope's power and versatility are demonstrated across diverse tissues and ST platforms. The results establish NicheScope as a robust, scalable, and interpretable framework for dissecting the spatial and functional organization of complex tissues, providing new insights into Multicellular coordination in health and disease.
