Single-cell informed metabolic modeling reveals organ-specific metabolic adaptations in breast cancer organotropism

Abstract

Breast cancer organotropism is driven by interactions between tumor cells and organ-specific microenvironments that support metastatic growth. To better understand the metabolic basis of organ-specific metastasis, we integrated single-cell transcriptomics with constraint-based systems biology to generate context-specific metabolic models of breast cancer metastasis to the liver, bone, and brain. Our analysis identified both common and organ-specific metabolic changes, suggesting that metastatic cells share a core metabolic program while also adapting to the metabolic environment of each target organ. Primary tumors with metastatic potential showed early alterations in nucleotide metabolism, transport reactions, and energy-related pathways, indicating metabolic changes before metastatic spread. Metabolic transformation analysis identified key metabolic regulators involved in the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, redox balance, and metabolite transport. Integration with CRISPR gene essentiality data further highlighted metabolically important genes as potential therapeutic targets. In addition, analysis of organ-specific secreted metabolites revealed distinct metabolic signatures associated with metastatic colonization of the liver, bone, and brain. Overall, our single-cell-informed metabolic modeling approach shows that breast cancer organotropism is associated with both shared and organ-specific metabolic adaptations. The study provides a framework for identifying potential metabolic vulnerabilities that could be targeted to treat metastatic breast cancer.