Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Florian Wimmers; Nikita Subedi; Nicole van Buuringen; Daan Heister; Judith Vivié; Inge Beeren-Reinieren; Rob Woestenenk; Harry Dolstra; Aigars Piruska; Joannes F M Jacobs; Alexander van Oudenaarden; Carl G Figdor; Wilhelm T S Huck; I Jolanda M de Vries; Jurjen Tel

doi:10.1038/s41467-018-05784-3

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Florian Wimmers
, Nikita Subedi
, Nicole van Buuringen
, Daan Heister
, Judith Vivié
, Inge Beeren-Reinieren
, Rob Woestenenk
, Harry Dolstra
, Aigars Piruska
, Joannes F M Jacobs
, Alexander van Oudenaarden
, Carl G Figdor
, Wilhelm T S Huck
, I Jolanda M de Vries
, Jurjen Tel

Hubrecht Institute

Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, 94305, CA, USA.
Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands.
Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 HP, The Netherlands.
Department of Laboratory Medicine, Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands. [email protected].

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

120 Citations (Scopus)

Abstract

Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level.

Original language	English
Pages (from-to)	3317
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-05784-3
Publication status	Published - 20 Aug 2018

Keywords

Cellular Microenvironment
Cross-Priming
Dendritic Cells/metabolism
Gene Expression Regulation
Humans
Interferon Type I/biosynthesis
Jurkat Cells
Paracrine Communication
Sequence Analysis, RNA
Single-Cell Analysis/methods
Stochastic Processes
Toll-Like Receptors/metabolism

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10.1038/s41467-018-05784-3

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Wimmers, F., Subedi, N., van Buuringen, N., Heister, D., Vivié, J., Beeren-Reinieren, I., Woestenenk, R., Dolstra, H., Piruska, A., Jacobs, J. F. M., van Oudenaarden, A., Figdor, C. G., Huck, W. T. S., de Vries, I. J. M., & Tel, J. (2018). Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells. Nature Communications, 9(1), 3317. https://doi.org/10.1038/s41467-018-05784-3

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abstract = "Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level.",

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author = "Florian Wimmers and Nikita Subedi and \{van Buuringen\}, Nicole and Daan Heister and Judith Vivi{\'e} and Inge Beeren-Reinieren and Rob Woestenenk and Harry Dolstra and Aigars Piruska and Jacobs, \{Joannes F M\} and \{van Oudenaarden\}, Alexander and Figdor, \{Carl G\} and Huck, \{Wilhelm T S\} and \{de Vries\}, \{I Jolanda M\} and Jurjen Tel",

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Wimmers, F, Subedi, N, van Buuringen, N, Heister, D, Vivié, J, Beeren-Reinieren, I, Woestenenk, R, Dolstra, H, Piruska, A, Jacobs, JFM, van Oudenaarden, A, Figdor, CG, Huck, WTS, de Vries, IJM & Tel, J 2018, 'Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells', Nature Communications, vol. 9, no. 1, pp. 3317. https://doi.org/10.1038/s41467-018-05784-3

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T1 - Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

AU - Wimmers, Florian

AU - Subedi, Nikita

AU - van Buuringen, Nicole

AU - Heister, Daan

AU - Vivié, Judith

AU - Beeren-Reinieren, Inge

AU - Woestenenk, Rob

AU - Dolstra, Harry

AU - Piruska, Aigars

AU - Jacobs, Joannes F M

AU - van Oudenaarden, Alexander

AU - Figdor, Carl G

AU - Huck, Wilhelm T S

AU - de Vries, I Jolanda M

AU - Tel, Jurjen

PY - 2018/8/20

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N2 - Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level.

AB - Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level.

KW - Cellular Microenvironment

KW - Cross-Priming

KW - Dendritic Cells/metabolism

KW - Gene Expression Regulation

KW - Humans

KW - Interferon Type I/biosynthesis

KW - Jurkat Cells

KW - Paracrine Communication

KW - Sequence Analysis, RNA

KW - Single-Cell Analysis/methods

KW - Stochastic Processes

KW - Toll-Like Receptors/metabolism

U2 - 10.1038/s41467-018-05784-3

DO - 10.1038/s41467-018-05784-3

M3 - Article

C2 - 30127440

SN - 2041-1723

VL - 9

SP - 3317

JO - Nature Communications

JF - Nature Communications

IS - 1

ER -

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Abstract

Keywords

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