Spatial context of cellular heterogeneity in triple-negative breast cancer reveals actionable subtypes

Mesrizadeh, Z.; Mukund, K.; Yang, L.; Pillai, R. K.; Frankhouser, D. E.; Schmolze, D.; Neuhausen, S. L.; Zabaleta, J.; Valle, L. D.; Tomsic, J.; Ding, Y. C.; Ochoa, A.; Miele, L.; Seewaldt, V.; Subramaniam, S.

doi:10.64898/2026.10.10.758236

bioRxiv · 10.64898/2026.10.10.758236

Spatial context of cellular heterogeneity in triple-negative breast cancer reveals actionable subtypes

Mesrizadeh, Z.·Mukund, K.·Yang, L.·Pillai, R. K.·Frankhouser, D. E.·Schmolze, D.·Neuhausen, S. L.·Zabaleta, J.·Valle, L. D.·Tomsic, J.·Ding, Y. C.·Ochoa, A.·Miele, L.·Seewaldt, V.·Subramaniam, S.

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Abstract

Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous disease with limited targeted treatment options. Leveraging bulk and spatial transcriptomics and cellular mapping of breast tissue from a large patient cohort, we identified three reproducible TNBC ecosystem subtypes that encode distinct spatial tumor-microenvironment architectures and clinically relevant treatment-response phenotype. Our analyses define: (1) an immune-exhausted subtype associated with immune checkpoint therapy (ICT); (2) a highly fibrotic/hypoxic subtype; and (3) a metabolically reprogrammed subtype characterized by nuclear-receptor and fatty-acid signaling. Spatial profiling further revealed subtype-specific organization of epithelial, immune, and stromal programs across tumor centers and invasive edges. Multiplexed imaging independently supported the contrasting immune-infiltrated and stromal-excluded architectures of the immune-engaged and fibrotic subtypes. The unique markers associated with the subtypes also provide the basis for subtyping and candidate therapeutic vulnerabilities. Our study provides a robust framework for personalized medicine, highlighting that targeting specific spatio-cellular architectures is critical to improving clinical outcomes.

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Mesrizadeh, Z., Mukund, K., Yang, L., Pillai, R. K., Frankhouser, D. E., Schmolze, D., Neuhausen, S. L., Zabaleta, J., Valle, L. D., Tomsic, J., Ding, Y. C., Ochoa, A., Miele, L., Seewaldt, V., Subramaniam, S.. 2026-10-13. Spatial context of cellular heterogeneity in triple-negative breast cancer reveals actionable subtypes. https://doi.org/10.64898/2026.10.10.758236

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