SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data

MotivationRecent advances in spatial proteomics technologies have enabled the profiling of dozens of proteins in thousands of single cells in situ. This has created the opportunity to move beyond quantifying the composition of cell types in tissue, and instead probe the spatial relationships between cells. However, most current methods for clustering data from these assays only consider the expression values of cells and ignore the spatial context. Furthermore, existing approaches do not account for prior information about the expected cell populations in a sample.ResultsTo address these shortcomings, we developed SpatialSort, a spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge. Our method is able to account for the affinities of cells of different types to neighbour in space, and by incorporating prior information about expected cell populations, it is able to simultaneously improve clustering accuracy and perform automated annotation of clusters. Using synthetic and real data, we show that by using spatial and prior information SpatialSort improves clustering accuracy. We also demonstrate how SpatialSort can perform label transfer between spatial and nonspatial modalities through the analysis of a real world diffuse large B-cell lymphoma dataset.

Automated summary

Recent advances in spatial proteomics technologies have allowed for the profiling of multiple proteins in single cells, creating the opportunity to explore spatial relationships between cells. However, current clustering methods do not consider spatial context or prior knowledge about cell populations. In response, the authors developed SpatialSort, a Bayesian clustering approach that incorporates spatial awareness and prior biological knowledge to improve clustering accuracy and perform automated annotation.