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bioRxiv · 10.1101/2023.08.13.552987

Search and Match across Spatial Omics Samples at Single-cell Resolution

Tang, Z.·Luo, S.·Zeng, H.·Huang, J.·Wu, M.·Wang, X.
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Abstract

Spatial omics technologies characterize tissue molecular properties with spatial information, but integrating and comparing spatial data across different technologies and modalities is challenging. A comparative analysis tool that can search, match, and visualize both similarities and differences of molecular features in space across multiple samples is lacking. To address this, we introduce CAST (Cross-sample Alignment of SpaTial omics), a deep graph neural network (GNN)-based method enabling spatial-to-spatial searching and matching at the single-cell level. CAST aligns tissues based on intrinsic similarities of spatial molecular features and reconstructs spatially resolved single-cell multi-omic profiles. CAST enables spatially resolved differential analysis ({Delta}Analysis) to pinpoint and visualize disease-associated molecular pathways and cell-cell interactions, and single-cell relative translational efficiency (scRTE) profiling to reveal variations in translational control across cell types and regions. CAST serves as an integrative framework for seamless single-cell spatial data searching and matching across technologies, modalities, and disease conditions, analogous to BLAST in sequence alignment.

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Tang, Z., Luo, S., Zeng, H., Huang, J., Wu, M., Wang, X.. 2023-08-15. Search and Match across Spatial Omics Samples at Single-cell Resolution. https://doi.org/10.1101/2023.08.13.552987

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