Abstract
The cellular interactions that drive the neuropathology of most neuroinvasive viruses remain elusive. We used Japanese encephalitis virus (JEV) to infect female BALB/c mice and applied Stereo-seq to simultaneously capture host and viral transcriptomes in situ, thereby constructing a comprehensive spatiotemporal atlas of Japanese encephalitis (JE) pathogenesis. Our analysis pinpoints Ly6c2+ monocytes as the primary virus carrier, the most abundant infiltrating immune cell type, and a major source of IFN-γ in the infected mouse brain. Following infection, Ackr1+ endothelial cell activation is linked to blood-brain barrier disruption and immune cell chemotaxis, particularly Ly6c2+ monocytes. The crosstalk between these two cell types appears to orchestrate the pronounced inflammation and cell death, including pyroptosis and necroptosis, which radiate from the vasculature to different brain regions. Disrupting the activation and interactions of these two cell types may help mitigate JE progression. This study also provides a technical framework for investigating the pathogenesis of other neurotropic viruses.
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Data availability
All the Stereo-seq data supporting the findings of this study have been deposited in CNGBdb (https://db.cngb.org/cnsa/) under the accession number of STT0000076 (https://db.cngb.org/stomics/). The raw sequencing data have been deposited in the Genome Sequence Archive in National Genomics Data Center129,130, China National Center for Bioinformation under the GSA number of CRA035980 (https://ngdc.cncb.ac.cn/gsa/). The gene expression matrix and associated metadata have been deposited in Zenodo (https://doi.org/10.5281/zenodo.17958448). All the experimental validation data of this study have been deposited in the Figshare database (https://doi.org/10.6084/m9.figshare.30382759) and the Zenodo database (https://doi.org/10.5281/zenodo.18323401). Source data are provided with this paper.
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Acknowledgements
This study was supported by grants from the Science and Technology Project of Southwest United Graduate School of Yunnan (202302AO370010 to G.C.), Shenzhen Medical Research Fund (B2404002 and B2402011 to G.C.), Yunnan Major Scientific and Technological Projects (202502AU100001 to G.C.), the National Key Research and Development Plan of China (2023YFA1801000 to G.C.), the National Natural Science Foundation of China (82341118 and 82341082 to Z.O., 82502710 to Z.W., 32188101 and 82422049 to G.C.), the Shenzhen San Ming Project for Prevention and Research on Vector-borne Diseases (SZSM202211023 to G.C.), the New Cornerstone Science Foundation through the New Cornerstone Investigator Program to G.C., and the XPLORER PRIZE to G.C. We thank China National GeneBank for providing sequencing services for this project. We would also like to thank DCS Cloud (https://cloud.stomics.tech) for providing the computational resources and software support.
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G.C., J.L., Z.O., and Z.W. conceived the study and designed the research. Z.W. constructed the animal models, collected samples, and performed all validation experiments, including flow cytometry, qPCR, and immunofluorescence assays. Y.L. and O.Z. assisted Z.W. with the validation experiments. Z.O., P.R., S.L., A.C., and J.Z. designed and optimized the orthoflavivirus-specific Stereo-seq chips. P.R., Q.C., and Ying’an L. conducted Stereo-seq experiments. Z.P., W.L., and G.H. performed sequencing of Stereo-seq libraries. Z.O., Q.C., X.H., Ying’an L., J.W., D.W., and J.S. carried out bioinformatic analyses. Z.O., Z.W., Q.C., and X.H. wrote and revised the manuscript. G.C., J.L., Z.O., X.X., X.J., and Z.D. supervised the project and revised the manuscript.
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X.X., A.C., and S.L. are the co-inventors of Stereo-seq technology. Employees of BGI have stock holdings in BGI. The other authors declare no competing interests.
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Ou, Z., Wang, Z., Chen, Q. et al. Spatial transcriptomics uncovers vasculature-centered cellular interactions driving Japanese encephalitis progression in a mouse model. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70047-5
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DOI: https://doi.org/10.1038/s41467-026-70047-5
