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Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development

Author

Listed:
  • Jinglong Zhang

    (Fudan University
    Fudan University)

  • Jiao Wang

    (Shanghai University)

  • Qiongjie Zhou

    (Obstetrics and Gynecology Hospital of Fudan University)

  • Zixin Chen

    (Shanghai University)

  • Junyi Zhuang

    (Shanghai University)

  • Xingzhong Zhao

    (Fudan University
    Fudan University)

  • Ziquan Gan

    (Fudan University
    Fudan University)

  • Yinan Wang

    (Obstetrics and Gynecology Hospital of Fudan University)

  • Chunxiu Wang

    (Obstetrics and Gynecology Hospital of Fudan University)

  • Robert S. Molday

    (University of British Columbia
    University of British Columbia)

  • Yucheng T. Yang

    (Fudan University
    Fudan University)

  • Xiaotian Li

    (Obstetrics and Gynecology Hospital of Fudan University
    Shenzhen)

  • Xing-Ming Zhao

    (Fudan University
    Fudan University
    Affiliated Central Hospital Huzhou University
    Fudan University)

Abstract

The morphogenesis and cellular interactions in developing retina are incompletely characterized. The full understanding needs a precise mapping of the gene expression with a single-cell spatial resolution. Here, we present a spatial transcriptomic (ST) resource for the developing human retina at six developmental stages. Combining the spatial and single-cell transcriptomic data enables characterization of the cell-type-specific expression profiles at distinct anatomical regions at each developmental stage, highlighting the spatiotemporal dynamics of cellular composition during retinal development. All the ST spots are catalogued into consensus spatial domains, which are further associated to their specific expression signatures and biological functions associated with neuron and eye development. We prioritize a set of critical regulatory genes for the transitions of spatial domains during retinal development. Differentially expressed genes from different spatial domains are associated with distinct retinal diseases, indicating the biological relevance and clinical significance of the spatially defined gene expression. Finally, we reconstruct the spatial cellular communication networks, and highlight critical ligand-receptor interactions during retinal development. Overall, our study reports the spatiotemporal dynamics of gene expression and cellular profiles during retinal development, and provides a rich resource for the future studies on retinogenesis.

Suggested Citation

  • Jinglong Zhang & Jiao Wang & Qiongjie Zhou & Zixin Chen & Junyi Zhuang & Xingzhong Zhao & Ziquan Gan & Yinan Wang & Chunxiu Wang & Robert S. Molday & Yucheng T. Yang & Xiaotian Li & Xing-Ming Zhao, 2025. "Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57625-9
    DOI: 10.1038/s41467-025-57625-9
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    References listed on IDEAS

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