Spatial Nucleus Barcoding Integrates Cellular Genomics and Tissue Architecture in Normal and Malignant Breast Tissues

The expression programs of cell types and their spatial organization are critical for understanding hemostat of normal tissues, and progressions of diseases such as cancer. Here we present SnuBar-RNAseq, a spatially-resolved single nucleus RNA sequencing (snRNA-seq) technology that enable provide expression programs and spatial information on single cells in their native tissue context for studying cell types, cell programming states spatial colocalization and interaction between their microenvironment. SnuBar shows high efficiency and accuracy to index multiplex samples and eliminate multiplets for snRNA-seq in validation experiments. We further applied SnuBar to identify multiple major cell types, cell programming states and their spatial colocalizations of 36 regions in a normal breast tissues, and of 15 regions in a malignant breast tissue. We found the spatial microenvironment of cells has strong effect on the reprogramming of expressions. Our method establishes a framework to delineate cell type, cell states and their spatial colocalization and interactions among their specific microenvironment.