Abstract
The thymus is the primary site for T cell maturation. While transcriptional profiling of human thymi has been reported, a high-resolution spatial atlas is needed. Here we use Stereo-seq spatial transcriptomics to generate a spatial atlas of the human fetal (13, 14, 17 or 18 weeks post-conception) and pediatric (7 weeks, and 2, 5 or 6 years old) thymi. The architecture of the thymus comprises regions such as the outer cortex, inner medulla, and septa, and contains multiple cell types, including thymic epithelial cells (TEC), thymocytes, dendritic cells, macrophages, and B cells. Utilising this spatial transcriptomics and proteomics information, we further describe lineage-defining transcription factors (TF) that govern molecular signatures of rare mimetic TEC regulation. Our study thus establishes a high-resolution spatial atlas of the human fetal and pediatric thymi to uncover distinct architectural features and TFs regulating these rare cell types, and serves as a resource for further studies.
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Data availability
The scRNA-seq and spatial transcriptomics data of the mouse and human thymi were visualised using a website developed using ShinyCell v2.1.064. The raw spatial and single-cell transcriptomic data are available in the GEO65 repository under https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1045362 and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1213311. The analysed data generated in this study are available at the Zenodo repository https://doi.org/10.5281/zenodo.12595241. Public scRNA-seq data5,17 were obtained from the Zenodo repository (https://doi.org/10.5281/zenodo.5500511) and GEO: GSE220830. The publicly available spatial Visium data9 were obtained from https://cellxgene.cziscience.com/collections/fc19ae6c-d7c1-4dce-b703-62c5d52061b4. All data included in the Supplementary Information are available from the authors. The raw numbers for charts and graphs are available in the Source Data file whenever possible. Source data are provided with this paper.
Code availability
The custom scripts developed and used in this study are made available on GitHub and the Zenodo repository as Jupiter notebooks at https://github.com/UmaSangumathi/mimeTFs.git (https://doi.org/10.5281/zenodo.17851510).
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Acknowledgements
The National Research Foundation, Singapore (NRF) Investigatorship award NRFI2018-02 (Y.-H.L.); National Medical Research Council NMRC/OFIRG21nov-0088 (Y.-H.L.); Singapore Food Story (SFS) R&D Programme W22W3D0007 (Y.-H.L.); A*STAR Biomedical Research Council, Central Research Fund, Use-Inspired Basic Research—CRF UIBR (Y.-H.L.); Competitive Research Programme—CRP NRF-CRP29-2022-0005 (Y.-H.L.); A*STAR Industry Alignment Fund—Prepositioning Programme IAF-PP: H23J2a0095 (Y.-H.L.), EVANTICA IAF-PP: H23J2a0097 (Y.-H.L.). The Singapore Ministry of Education grant MOE-000112 (N.R.J.G.).
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Y.-H.L. conceptualised, designed and supervised this study. U.S.K. conceptualised the computational pipeline and carried out analysis. Y.C. conceptualised, designed and carried out the experimental data generation and analysis. J.L. carried out the computational analysis. P.G., P.H. and C.K.C. generated experimental data. K.W., N.R.J.G., J.C., C.K.M.C., Q.C., Q.L. and L.G.N. analysed the data. U.S.K., C.Y. and Y.-H.L. wrote the manuscript with feedback from all authors. All authors approved and contributed to the final version of the manuscript.
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Kamaraj, U.S., Chen, Y., Lei, J. et al. Spatial cartography of human thymus enables the geopositioning of lineage transcription factors in rare mimetic thymic epithelial cells. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68596-w
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DOI: https://doi.org/10.1038/s41467-026-68596-w
