Single-Cell Mapping of Malignant Signaling Networks Guides Drug Combinations

Authors

Yavuz, B. R., Jang, H., Nussinov, R.

Abstract

Single-cell breast cancer atlases reveal malignant, immune, and stromal diversity; however, how the recurrent signaling pathways drive untreated malignant-cell states and could inform combination therapy remains unclear. Here, we analyzed 15,753 malignant cells from untreated primary breast tumors using a cell-resolved network framework. Individual transcriptomes were projected onto a protein-protein interaction network, partitioned into Leiden communities, and annotated by pathway enrichment. Pathway recurrence was evaluated against matched null models preserving community size, protein-network degree, and gene detection rate. Before null correction, recurrent pathways included PI3K/AKT, MAPK, JAK/STAT, and HIF-1 (hypoxia-inducible factor 1) signaling. After correction, HIF-1 emerged as the dominant recurrent signal across patients, indicating convergence of diverse upstream pathways on a shared hypoxia- and stress-adaptive malignant-cell program. The recurrent JAK/STAT, cAMP, glucagon, oxytocin, and thyroid hormone signaling suggest inflammatory, metabolic, and endocrine crosstalk. These findings support rational drug combinations targeting HIF-1 together with upstream PI3K/AKT/mTOR, MAPK, or JAK/STAT signaling.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 19 Aug 2026.

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