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Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign

Author

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  • Biao Zhang

    (Fudan University)

  • Shuqin Zhang

    (Fudan University
    Fudan University, Ministry of Education
    Fudan University)

  • Shihua Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences, Chinese Academy of Sciences)

Abstract

The increasing utilization of mouse models in human neuroscience research places higher demands on computational methods to translate findings from the mouse brain to the human one. In this study, we develop BrainAlign, a self-supervised learning approach, for the whole brain alignment of spatial transcriptomics (ST) between humans and mice. BrainAlign encodes spots and genes simultaneously in two separated shared embedding spaces by a heterogeneous graph neural network. We demonstrate that BrainAlign could integrate cross-species spots into the embedding space and reveal the conserved brain regions supported by ST information, which facilitates the detection of homologous regions between humans and mice. Genomic analysis further presents gene expression connections between humans and mice and reveals similar expression patterns for marker genes. Moreover, BrainAlign can accurately map spatially similar homologous regions or clusters onto a unified spatial structural domain while preserving their relative positions.

Suggested Citation

  • Biao Zhang & Shuqin Zhang & Shihua Zhang, 2024. "Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50608-2
    DOI: 10.1038/s41467-024-50608-2
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