Single-cell metabolic profiling of human cytotoxic T cells

Felix J. Hartmann, Dunja Mrdjen, Erin McCaffrey, David R. Glass, Noah F. Greenwald, Anusha Bharadwaj, Zumana Khair, Sanne G.S. Verberk, Alex Baranski, Reema Baskar, William Graf, David Van Valen, Jan Van den Bossche, Michael Angelo, Sean C. Bendall*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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.

Original languageEnglish
Pages (from-to)186-197
Number of pages12
JournalNature Biotechnology
Issue number2
Publication statusPublished - Feb 2021

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