作者：
Yin, WangWan, YouZhou, YuanPeking Univ
Dept Biomed Informat Beijing Peoples R China Peking Univ
Neurosci Res Inst Sch Basic Med Sci Dept Neurobiol Beijing Peoples R China Peking Univ
Sch Basic Med Sci Dept Biomed Informat 38 Xueyuan Rd Beijing 100191 Peoples R China
spatialtranscriptomics (ST) data have emerged as a pivotal approach to comprehending the function and interplay of cells within intricate tissues. Nonetheless, analyses of ST data are restricted by the low spatial re...
详细信息
spatialtranscriptomics (ST) data have emerged as a pivotal approach to comprehending the function and interplay of cells within intricate tissues. Nonetheless, analyses of ST data are restricted by the low spatial resolution and limited number of ribonucleic acid transcripts that can be detected with several popular ST techniques. In this study, we propose that both of the above issues can be significantly improved by introducing a deep graph co-embedding framework. First, we establish a self-supervised, co-graph convolution network-based deep learning model termed spatialcoGCN, which leverages single-cell data to deconvolve the cell mixtures in spatialdata. Evaluations of spatialcoGCN on a series of simulated ST data and real ST datasets from human ductal carcinoma in situ, developing human heart and mouse brain suggest that spatialcoGCN could outperform other state-of-the-art cell type deconvolution methods in estimating per-spot cell composition. Moreover, with competitive accuracy, spatialcoGCN could also recover the spatial distribution of transcripts that are not detected by raw ST data. With a similar co-embedding framework, we further established a spatial information-aware ST datasimulation method, spatialcoGCN-Sim. spatialcoGCN-Sim could generate simulated ST data with high similarity to real datasets. Together, our approaches provide efficient tools for studying the spatial organization of heterogeneous cells within complex tissues.
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