Learning cell communication from spatial graphs of cells

Abstract

Tissue niches are sources of cellular variation and key to understanding both single-cell and tissue phenotypes. The interaction of a cell with its niche can be described through cell communication events. These events cannot be directly observed in molecular profiling assays of single cells and have to be inferred. However, computational models of cell communication and variance attribution defined on data from dissociated tissues suffer from multiple limitations with respect to their ability to define and to identify communication events. We address these limitations using spatial molecular profiling data with node-centric expression modeling (NCEM), a computational method based on graph neural networks which reconciles variance attribution and communication modeling in a single model of tissue niches. We use these models in varying complexity across spatial assays, such as immunohistochemistry and MERFISH, and biological systems to demonstrate that the statistical cell–cell dependencies discovered by NCEM are plausible signatures of known molecular processes underlying cell communication. We identify principles of tissue organisation as cell communication events across multiple datasets using interpretation mechanisms. In the primary motor cortex, we found gene expression variation that is due to niche composition variation across cortical depth. Using the same approach, we also identified niche-dependent cell state variation in CD8 T cells from inflamed colon and colorectal cancer. Finally, we show that NCEMs can be extended to mixed models of explicit cell communication events and latent intrinsic sources of variation in conditional variational autoencoders to yield holistic models of cellular variation in spatial molecular profiling data. Altogether, this graphical model of cellular niches is a step towards understanding emergent tissue phenotypes.