Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics

Current approaches to inferring cell-cell interactions (CCIs) are largely constrained by predefined ligand-receptor databases, particularly for low-resolution spatial transcriptomics (ST) platforms such as Visium. Due to the difficulties in accurately resolving interacting cells at coarse spatial resolution, other modes of interaction are often overlooked. Low-resolution ST data, however, can serve as an alternative to high-resolution ST, which suffers from low sensitivity, and to image-based ST, which is limited by restricted gene panels. Here, we present CellNeighborEX v2, a database-free framework that directly infers CCI-associated genes from ST data by detecting deviations between observed and expected gene expression at the spot-population level. These deviations are rigorously evaluated through a hybrid statistical framework involving permutation testing and are further refined by considering the abundance of interacting cell-type pairs. Compared with other conventional approaches relying on ligand-receptor databases, CellNeighborEX v2 can capture CCI genes from a broad spectrum of interactions, including both paracrine signaling and contact-dependent communication. Across datasets from hippocampus, liver cancer, colorectal cancer, ovarian cancer, and lymph node infection, CellNeighborEX v2 accurately recapitulated previously identified CCIs. Notably, it uniquely detected interactions absent from existing ligand-receptor databases, enabling detection of context-specific CCIs from Visium data. CellNeighborEX v2 is a tool that expands the analytical spectrum of Visium data and deepens our understanding of the molecular language of intercellular communication.