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STdGCN: accurate cell-type deconvolution using graph convolutional networks in spatial transcriptomic data

Yawei Li, Yuan Luo
bioRxiv (2023)


Spatially resolved transcriptomics performs high-throughput measurement of transcriptomes while preserving spatial information about the cellular organizations. However, many spatially resolved transcriptomic technologies can only distinguish spots consisting of a mixture of cells instead of working at single-cell resolution. Here, we present STdGCN, a graph neural network model designed for cell type deconvolution of spatial transcriptomic (ST) data that can leverage abundant single-cell RNA sequencing (scRNA-seq) data as reference. STdGCN is the first model incorporating the expression profiles from single cell data as well as the spatial localization information from the ST data for cell type deconvolution. Extensive benchmarking experiments on multiple ST datasets showed that STdGCN outperformed 13 published state-of-the-art models. Applied to a human breast cancer Visium dataset, STdGCN discerned spatial distributions between stroma, lymphocytes and cancer cells for tumor microenvironment dissection. In a human heart ST dataset, STdGCN detected the changes of potential endothelial-cardiomyocyte communications during tissue development. Our results demonstrate that STdGCN can serve as a robust and versatile tool for cell type deconvolution across multiple ST platforms and tissues. STdGCN is available as open source Python software at https://github.com/luoyuanlab/stdgcn.