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bioRxiv · 10.1101/2023.03.14.532529

SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models

Wan, X.·Xiao, J.·Tam, S. S. T.·Cai, M.·Sugimura, R.·Wang, Y.·Lin, Z.·Wu, A.·Yang, C.
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Abstract

The rapid emergence of spatial transcriptomics (ST) technologies are revolutionizing our under-standing of tissue spatial architecture and their biology. Current ST technologies based on either next generation sequencing (seq-based approaches) or fluorescence in situ hybridization (image-based approaches), while providing hugely informative insights, remain unable to provide spatial characterization at transcriptome-wide single-cell resolution, limiting their usage in resolving detailed tissue structure and detecting cellular communications. To overcome these limitations, we developed SpatialScope, a unified approach to integrating scRNA-seq reference data and ST data that leverages deep generative models. With innovation in model and algorithm designs, SpatialScope not only enhances seq-based ST data to achieve single-cell resolution, but also accurately infers transcriptome-wide expression levels for image-based ST data. We demonstrate the utility of SpatialScope through comprehensive simulation studies and then apply it to real data from both seq-based and image-based ST approaches. SpatialScope provides a spatial characterization of tissue structures at transcriptome-wide single-cell resolution, greatly facilitating the downstream analysis of ST data, such as detection of cellular communication by identifying ligand-receptor interactions from seq-based ST data, localization of cellular subtypes, and detection of spatially differently expressed genes.

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Wan, X., Xiao, J., Tam, S. S. T., Cai, M., Sugimura, R., Wang, Y., Lin, Z., Wu, A., Yang, C.. 2023-03-15. SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models. https://doi.org/10.1101/2023.03.14.532529

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