Abstract
Lymph node metastasis correlates with breast cancer prognosis; however, the cellular mechanisms underlying the earliest metastatic events remain unclear. In spatial transcriptomic analysis of a patient with breast cancer at single-cell resolution, we identified 30 tumor cells representing the initial metastatic seeding in a lymph node. These cells originated from multiple epithelial–mesenchymal (EM) transition status and included six distinct subpopulations with biological significance. Only cells exhibiting a metabolic shift toward fatty acid metabolism successfully established lymph node colonies, implicating this shift in metastatic fitness. The tumor microenvironment surrounding these cells showed immunosuppressive and tumor-promoting features, supporting metastasis establishment. Cross-referencing these expression profiles with public datasets revealed that poor prognosis correlated not with fully mesenchymal or metastatic populations, but with hybrid EM cells exhibiting epithelial and mesenchymal traits. These findings highlight the metabolic and phenotypic plasticity of metastatic cells and serve as translational bridges between the spatial evolution of tumor cells in the extremely early stages of lymph node metastasis and clinical prognosis in breast cancer.
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Data availability
The Xenium and bulk multi-omics data supporting the findings of this study are available at the DDBJ Japanese Genotype-phenotype Archive (https://gr-sharingdbs.dbcls.jp) under accession number JGAD000946. The single-cell RNA-seq dataset from Guan et al.4 was downloaded from Gene Expression Omnibus (GSE180286). METABRIC transcriptome and clinical data were downloaded from cBioPortal (https://www.cbioportal.org). Additional data are available from the corresponding authors upon reasonable request.
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Acknowledgements
We thank K. Imamura, K. Abe, M. Satake, J. Zenkou, E. Sekimori, R. Fujinaga, and A. Gouda for their technical assistance. The authors would like to thank Enago (www.enago.jp) for the English language review. This work was supported by the Japan Agency for Medical Research and Development (AMED) grant number JP21ck0106700 (to S.N.), the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI Grants) Number JP16H06279 (PAGS), JP22H04925 (PAGS), JP24K11738(to S.N.), JP23K27160 (to M.S.), as well as by Nikon Corporation. The supercomputing resource was provided by the Human Genome Center, the University of Tokyo (http://sc.hgc.jp/shirokane.html). Computational resources were also supplied by Kashiwa-no-ha Omics Gate (https://www.kog.or.jp/en/server.html).
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S.N. and K.K collected the human samples, performed experiments and computational analyses, and generated all figures and tables. A.M., T.I., T.O., and K.T. aided in human sample collection. T.O. generated Fig. 2a.E.I. performed computational analyses. M.K. and M.N. assisted in the Xenium experiments. A.H., I.M., and J.K. conducted the pathological review. A.M. and K.T. developed viewer software. A.K. and A.S. offered advice and reviewed the manuscript. S.N., M.S., and Y.S. designed the project and wrote the manuscript. All authors read and approved the final manuscript.
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A.M. and K.T. are employees of Nikon Corporation. The other authors do not have a competing interest.
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Nagasawa, S., Kajiya, K., Ishikawa, E. et al. Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer. npj Breast Cancer (2026). https://doi.org/10.1038/s41523-026-00897-1
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DOI: https://doi.org/10.1038/s41523-026-00897-1
