In-depth organic mass cytometry reveals differential contents of 3-hydroxybutanoic acid at the single-cell level

Shaojie Qin, Yi Zhang, Mingying Shi, Daiyu Miao, Jiansen Lu, Lu Wen and Yu Bai ()
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Shaojie Qin: Peking University
Yi Zhang: Peking University
Mingying Shi: Peking University
Daiyu Miao: Peking University
Jiansen Lu: Peking University
Lu Wen: Peking University
Yu Bai: Peking University

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract Comprehensive single-cell metabolic profiling is critical for revealing phenotypic heterogeneity and elucidating the molecular mechanisms underlying biological processes. However, single-cell metabolomics remains challenging because of the limited metabolite coverage and inability to discriminate isomers. Herein, we establish a single-cell metabolomics platform for in-depth organic mass cytometry. Extended single-cell analysis time guarantees sufficient MS/MS acquisition for metabolite identification and the isomers discrimination while online sampling ensures the high-throughput of the method. The largest number of identified metabolites (approximately 600) are achieved in single cells and fine subtyping of MCF-7 cells is first demonstrated by an investigation on the differential levels of 3-hydroxybutanoic acid among clusters. Single-cell transcriptome analysis reveals differences in the expression of 3-hydroxybutanoic acid downstream antioxidative stress genes, such as metallothionein 2 (MT2A), while a fluorescence-activated cell sorting assay confirms the positive relationship between 3-hydroxybutanoic acid and target proteins; these results suggest that the heterogeneity of 3-hydroxybutanoic acid provides cancer cells with different ability to resist surrounding oxidative stress. Our method paves the way for deep single-cell metabolome profiling and investigations on the physiological and pathological processes that occur during cancer.

Date: 2024
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DOI: 10.1038/s41467-024-48865-2

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