ProxiNet transfers spatially learned cellular proximity to dissociated single-cell transcriptomes

Abstract

Spatial transcriptomics reveals cellular organization within intact tissues, whereas dissociated single-cell RNA sequencing provides broad transcriptomic coverage but loses information about cellular proximity and neighborhood structure. Here, we developed ProxiNet, a spatially supervised framework that learns transcriptomic signatures of pairwise cellular proximity from spatial reference datasets and transfers these relationships to dissociated single-cell transcriptomes. ProxiNet predicted cellular proximity across brain regions and spatial technologies, including zero-shot cross-technology transfer, and gradient-based attribution identified genes and broader transcriptional programs associated with proximity predictions. In spatial datasets with known coordinates, ProxiNet-derived cellular neighborhoods recovered reproducible tissue organization and anatomical structure, providing independent spatial validation of the inferred proximity relationships. Applying the spatially calibrated model to dissociated scRNA-seq revealed heterogeneous cellular neighborhoods with distinct cell-type compositions and candidate communication programs. In an Alzheimer dataset, ProxiNet further identified age-associated remodeling of inferred neighborhoods, including an AD-associated neighborhood at 8 months characterized by distinct astrocyte and neuronal transcriptional states and candidate intercellular communication programs. Together, these results establish pairwise cellular proximity as an interpretable and transferable representation for extending spatially learned tissue organization to dissociated single-cell transcriptomes.