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Single-cell metabolic profiling of human cytotoxic T cells

Abstract

Cellular metabolism regulates immune cell activation, differentiation and effector functions, but current metabolic approaches lack single-cell resolution and simultaneous characterization of cellular phenotype. In this study, we developed an approach to characterize the metabolic regulome of single cells together with their phenotypic identity. The method, termed single-cell metabolic regulome profiling (scMEP), quantifies proteins that regulate metabolic pathway activity using high-dimensional antibody-based technologies. We employed mass cytometry (cytometry by time of flight, CyTOF) to benchmark scMEP against bulk metabolic assays by reconstructing the metabolic remodeling of in vitro-activated naive and memory CD8+ T cells. We applied the approach to clinical samples and identified tissue-restricted, metabolically repressed cytotoxic T cells in human colorectal carcinoma. Combining our method with multiplexed ion beam imaging by time of flight (MIBI-TOF), we uncovered the spatial organization of metabolic programs in human tissues, which indicated exclusion of metabolically repressed immune cells from the tumor–immune boundary. Overall, our approach enables robust approximation of metabolic and functional states in individual cells.

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Fig. 1: Single-cell metabolic regulomes organize the human immune system.
Fig. 2: Single-cell metabolic regulome profiles of T cell activation dynamics.
Fig. 3: Integrative modeling of metabolic rewiring reveals determinants of human T cell activation.
Fig. 4: Cytotoxic T cell metabolic states reflect tissue of residence.
Fig. 5: Imaging-based scMEP analysis reveals spatial influences on the organization of metabolic features.
Fig. 6: Metabolic polarization at the tumor–immune boundary in human colorectal carcinoma.

Data availability

Single-cell mass cytometry data sets for metabolic analysis of human whole blood populations, in vitro T cell activation and analysis of metabolic states in human tissues as well as MIBI-TOF imaging data of colorectal carcinoma and healthy colon are publicly available at https://doi.org/10.5281/zenodo.3951613.

Code availability

All custom R scripts associated with this manuscript will be made available upon reasonable request.

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Acknowledgements

We thank L. Keren for insightful discussions and invaluable feedback as well as the Nakamura lab at the Gladstone Institutes for access to their Seahorse XF analyzer. Further, we thank A. Tsai for advice and help with clinical samples. This study was supported by an EMBO Long-Term Fellowship ALTF 1141–2017 (to F.J.H.), the Novartis Foundation for Medical-Biological Research 16C148 (to F.J.H.) and the Swiss National Science Foundation SNF Early Postdoc Mobility P2ZHP3-171741 (to F.J.H.). In addition, we received support from National Institutes of Health 1DP2OD022550-01 (to S.C.B.), 1R01AG056287-01 (to S.C.B.), 1R01AG057915-01 (to S.C.B.) and 1U24CA224309-01 (to S.C.B.).

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F.J.H. conceived and conceptualized the study, performed the mass cytometry and imaging experiments, validated reagents, analyzed mass cytometry and imaging data, acquired funding and wrote the manuscript. D.M. helped with imaging experiments. E.M. performed the spatial enrichment analysis. D.R.G. and R.B. helped to analyze mass cytometry data. N.F.G. performed cell segmentation. A. Bharadwaj and Z.K. performed IHC stainings and analysis to validate antibodies. S.G.S.V. and J.V.d.B. performed human macrophage polarizations and their extracellular flux analysis. A. Baranski helped to analyze imaging data. W.G. and D.V.V. wrote software for cell segmentation. M.A. provided resources and helped with all aspects of imaging acquisition and analysis. S.C.B. conceptualized and supervised the study, provided resources, acquired funding and wrote the manuscript.

Corresponding author

Correspondence to Sean C. Bendall.

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Supplementary Figs. 1–13

Reporting Summary

Supplementary Table 1

Antibody clones evaluated for this study and antibody panels used in each figure

Supplementary Table 2

Basic information on all human samples used in this study

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Hartmann, F.J., Mrdjen, D., McCaffrey, E. et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol 39, 186–197 (2021). https://doi.org/10.1038/s41587-020-0651-8

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