bioRxiv preprint doi: https://doi.org/10.1101/673707; this version posted June 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 Title:
2 Gene expression-based identification of antigen-responsive CD8+ T cells on a single-cell
3 level
4
5 Authors:
6 Yannick F. Fuchs1‡*; Virag Sharma1,2‡*; Anne Eugster1; Gloria Kraus1; Robert Morgenstern1; 7 Andreas Dahl3, Susanne Reinhardt3, Andreas Petzold3, Annett Lindner1; Doreen Löbel1 and 8 Ezio Bonifacio1,2,4*
9 1 DFG Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische 10 Universität Dresden, Dresden, Germany.
11 2 Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD), 12 Technische Universität Dresden, Dresden, Germany.
13 3 DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering, 14 Technische Universität Dresden, Dresden, Germany.
15 4 Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center 16 for Environmental Health, Munich-Neuherberg, Germany.
17 ‡these authors contributed equally to the work
18 *Corresponding authors. Email: [email protected], yannick.fuchs@tu- 19 dresden.de, [email protected]
20
21 One-sentence summary:
22 Identification of genes, gene sets, and development of a machine learning-based classifier
23 that distinguishes antigen-responsive CD8+ T cells on a single-cell level. bioRxiv preprint doi: https://doi.org/10.1101/673707; this version posted June 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
24 Abstract
25 CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors and self
26 antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their
27 receptors could be identified in unselected single-cell gene expression data. Single-cell RNA
28 sequencing and qPCR of dye-labelled antigen-specific cells identified large gene sets that
29 were congruently up- or downregulated in virus-responsive CD8+ T cells under different
30 antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and
31 CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using
32 transcriptomic data, we developed a machine learning-based classifier that provides
33 sensitive and specific detection of virus-responsive CD8+ T cells from unselected
34 populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific
35 glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific
36 cells. These findings provide single-cell gene expression parameters for comprehensive
37 identification of rare antigen-responsive cells and T cell receptors.
38 bioRxiv preprint doi: https://doi.org/10.1101/673707; this version posted June 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
39 Introduction
40 CD8+ T cells are integral to the clearance of virus-infected cells and the control of cell
41 transformation. These attributes are exploited by therapies, such as vaccination against
42 infection and immune therapies targeting cancer. CD8+ T cells are also involved in the
43 destruction of cells in some autoimmune diseases, such as type 1 diabetes, and in graft-
44 versus-host disease. In active immune responses, CD8+ T cells undergo rapid clonal
45 expansion and this expansion of activated CD8+ T cells can be a marker of ongoing infection
46 in immune