Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity

Schueddig, E.; Kochat, V.; Arslan, E.; Dallas, Y.; Yang, P.; Pedron, W.; Li, Z.; Henry, R.; Lin, J.; Mattohti, M.; Madan, R.; Fields, T.; Khan, S.; Golem, S.; Wagner, J. L.; Larson, K. E.; Balanoff, C.; Aripoli, A.; Huppe, A.; Winblad, O.; Peterson, J.; Hill, M.; Smith, C.; Jeffers, E. E.; Kilgore, L. J.; Navin, N.; Zang, C.; Wei, P.; Fabian, C.; Lewis, M. T.; Zhu, Q.; Thompson, A. M.; Godwin, A. K.; Koestler, D. C.; Rai, K.; Behbod, F.

doi:10.64898/2026.05.13.724882

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bioRxiv · 10.64898/2026.05.13.724882

Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity

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Abstract

Ductal carcinoma in situ (DCIS) exhibits substantial heterogeneity in its risk of progression to invasive breast cancer, yet the cellular and molecular determinants of high-risk lesions remain incompletely defined. Using spatially resolved single-cell transcriptomic and epigenomic profiling of 43 patient-derived DCIS and DCIS/invasive ductal carcinoma (IDC) samples, we delineate cellular programs, spatial organization, and epigenetic regulatory mechanisms associated with invasive potential. We identify an epithelial population with stemness features within luminal hormone-responsive (LumHR) cells that progressively expands from benign tissue to DCIS and IDC, and is strongly associated with invasive progression and recurrence-linked transcriptional programs. Spatial mapping reveals discrete DCIS niches enriched for stem-like LumHR cells, characterized by elevated CEACAM6 expression and enhanced ligand-receptor interactions, including CEACAM6-EGFR signaling between epithelial and stromal compartments, including cancer-associated fibroblasts, macrophages (APOC1-positive) and perivascular cells. These niches define a microenvironmental context that supports stemness and invasive potential. Epigenomic analyses implicate FOXA1 as a key regulator of these stem-like transcriptional states. Pharmacologic disruption of FOXA1-regulatory network using LSD1 inhibition suppresses stemness-associated transcriptional programs in vitro and significantly restrains tumor growth in vivo. Collectively, these findings define high-risk DCIS as a stemness-driven disease embedded within specialized microenvironments, and identify associated regulatory networks as candidate biomarkers and therapeutic vulnerabilities.

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Schueddig, E., Kochat, V., Arslan, E., Dallas, Y., Yang, P., Pedron, W., Li, Z., Henry, R., Lin, J., Mattohti, M., Madan, R., Fields, T., Khan, S., Golem, S., Wagner, J. L., Larson, K. E., Balanoff, C., Aripoli, A., Huppe, A., Winblad, O., Peterson, J., Hill, M., Smith, C., Jeffers, E. E., Kilgore, L. J., Navin, N., Zang, C., Wei, P., Fabian, C., Lewis, M. T., Zhu, Q., Thompson, A. M., Godwin, A. K., Koestler, D. C., Rai, K., Behbod, F.. 2026-05-16. Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity. https://doi.org/10.64898/2026.05.13.724882

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