Dynamic single-cell metabolomics reveals cell-cell interaction between tumor cells and macrophages

Yi Zhang, Mingying Shi, Mingxuan Li, Shaojie Qin, Daiyu Miao and Yu Bai ()
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Yi Zhang: Peking University
Mingying Shi: Peking University
Mingxuan Li: Peking University
Shaojie Qin: Peking University
Daiyu Miao: Peking University
Yu Bai: Peking University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Single-cell metabolomics reveals cell heterogeneity and elucidates intracellular molecular mechanisms. However, general concentration measurement of metabolites can only provide a static delineation of metabolomics, lacking the metabolic activity information of biological pathways. Herein, we develop a universal system for dynamic metabolomics by stable isotope tracing at the single-cell level. This system comprises a high-throughput single-cell data acquisition platform and an untargeted isotope tracing data processing platform, providing an integrated workflow for dynamic metabolomics of single cells. This system enables the global activity profiling and flow analysis of interlaced metabolic networks at the single-cell level and reveals heterogeneous metabolic activities among single cells. The significance of activity profiling is underscored by a 2-deoxyglucose inhibition model, demonstrating delicate metabolic alteration within single cells which cannot reflected by concentration analysis. Significantly, the system combined with a neural network model enables the metabolomic profiling of direct co-cultured tumor cells and macrophages. This reveals intricate cell-cell interaction mechanisms within the tumor microenvironment and firstly identifies versatile polarization subtypes of tumor-associated macrophages based on their metabolic signatures, which is in line with the renewed diversity atlas of macrophages from single-cell RNA-sequencing. The developed system facilitates a comprehensive understanding single-cell metabolomics from both static and dynamic perspectives.

Date: 2025
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DOI: 10.1038/s41467-025-59878-w

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