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A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease

Peter A. Szabo, Hanna Mendes Levitin, Michelle Miron, Mark E. Snyder, Takashi Senda, Jinzhou Yuan, Yim Ling Cheng, Erin C. Bush, Pranay Dogra, Puspa Thapa, Donna L. Farber, Peter A. Sims
doi: https://doi.org/10.1101/555557
Peter A. Szabo
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
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Hanna Mendes Levitin
2Department of Systems Biology, Columbia University Medical Center, New York, NY.
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Michelle Miron
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
3Department of Microbiology and Immunology, Columbia University, New York, NY.
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Mark E. Snyder
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
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Takashi Senda
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
4Department of Surgery, Columbia University, New York, NY.
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Jinzhou Yuan
2Department of Systems Biology, Columbia University Medical Center, New York, NY.
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Yim Ling Cheng
2Department of Systems Biology, Columbia University Medical Center, New York, NY.
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Erin C. Bush
2Department of Systems Biology, Columbia University Medical Center, New York, NY.
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Pranay Dogra
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
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Puspa Thapa
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
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Donna L. Farber
1Columbia Center for Translational Immunology, Columbia University, New York, NY.
3Department of Microbiology and Immunology, Columbia University, New York, NY.
4Department of Surgery, Columbia University, New York, NY.
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  • For correspondence: df2396@cumc.columbia.edu pas2182@cumc.columbia.edu
Peter A. Sims
2Department of Systems Biology, Columbia University Medical Center, New York, NY.
5Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
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  • For correspondence: df2396@cumc.columbia.edu pas2182@cumc.columbia.edu
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ABSTRACT

Human T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied. Here, we used single-cell RNA-seq to define the functional responses of T cells isolated from human lungs, lymph nodes, bone marrow, and blood to TCR-stimulation. We reveal how human T cells in tissues relate to those in blood, and define activation states for CD4+ and CD8+T cells across all sites, including an interferon-response state for CD4+T cells and distinct effector states for CD8+T cells. We further show how profiles of individual tumor-associated T cells can be projected onto this healthy reference map, revealing their functional state.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 20, 2019.
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A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease
Peter A. Szabo, Hanna Mendes Levitin, Michelle Miron, Mark E. Snyder, Takashi Senda, Jinzhou Yuan, Yim Ling Cheng, Erin C. Bush, Pranay Dogra, Puspa Thapa, Donna L. Farber, Peter A. Sims
bioRxiv 555557; doi: https://doi.org/10.1101/555557
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A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease
Peter A. Szabo, Hanna Mendes Levitin, Michelle Miron, Mark E. Snyder, Takashi Senda, Jinzhou Yuan, Yim Ling Cheng, Erin C. Bush, Pranay Dogra, Puspa Thapa, Donna L. Farber, Peter A. Sims
bioRxiv 555557; doi: https://doi.org/10.1101/555557

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