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Single-cell metabolic profiling of human cytotoxic T cells

Hartmann, Felix J. and Mrdjen, Dunja and McCaffrey, Erin and Glass, David R. and Greenwald, Noah F. and Bharadwaj, Anusha and Khair, Zumana and Verberk, Sanne G. S. and Baranski, Alex and Baskar, Reema and Graf, William and Van Valen, David and Van den Bossche, Jan and Angelo, Michael and Bendall, Sean C. (2021) Single-cell metabolic profiling of human cytotoxic T cells. Nature Biotechnology, 39 (2). pp. 186-197. ISSN 1087-0156.

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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.

Item Type:Article
Related URLs:
URLURL TypeDescription ReadCube access
Hartmann, Felix J.0000-0002-4174-2276
Mrdjen, Dunja0000-0001-9269-2806
McCaffrey, Erin0000-0001-7241-1798
Glass, David R.0000-0001-9924-167X
Greenwald, Noah F.0000-0002-7836-4379
Khair, Zumana0000-0003-3617-2472
Verberk, Sanne G. S.0000-0003-4509-4824
Baskar, Reema0000-0002-3872-0164
Graf, William0000-0003-0460-4605
Van Valen, David0000-0001-7534-7621
Van den Bossche, Jan0000-0002-7852-2891
Angelo, Michael0000-0003-1531-5067
Bendall, Sean C.0000-0003-1341-2453
Additional Information:© 2020 Nature Publishing Group. Received 21 January 2020; Accepted 23 July 2020; Published 31 August 2020. 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.). 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 Code availability: All custom R scripts associated with this manuscript will be made available upon reasonable request. Author Contributions: 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. The authors declare no competing interests.
Funding AgencyGrant Number
European Molecular Biology Organization (EMBO)ALTF 1141-2017
Novartis Foundation16C148
Swiss National Science Foundation (SNSF)P2ZHP3-171741
Subject Keywords:Adaptive immunity; Cancer; Metabolomics; Proteomics; Systems biology
Issue or Number:2
Record Number:CaltechAUTHORS:20200909-073011987
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Official Citation:Hartmann, F.J., Mrdjen, D., McCaffrey, E. et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol 39, 186–197 (2021).
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:105285
Deposited By: Tony Diaz
Deposited On:09 Sep 2020 17:34
Last Modified:11 Feb 2021 21:30

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