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

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells Florian Wimmers 1,2, Nikita Subedi3,4, Nicole van Buuringen1, Daan Heister1, Judith Vivié5, Inge Beeren-Reinieren1, Rob Woestenenk6, Harry Dolstra6, Aigars Piruska7, Joannes F.M. Jacobs8, Alexander van Oudenaarden5, Carl G. Figdor1, Wilhelm T.S. Huck7, I. Jolanda M. de Vries1 & Jurjen Tel 1,3,4

[1]  P. Blanco,et al.  Heat shock protein 70 potentiates interferon alpha production by plasmacytoid dendritic cells: relevance for cutaneous lupus and vitiligo pathogenesis , 2017, The British journal of dermatology.

[2]  Evan W. Newell,et al.  Mapping the human DC lineage through the integration of high-dimensional techniques , 2017, Science.

[3]  A. Abate,et al.  SiC-Seq: Single-cell genome sequencing at ultra high-throughput with microfluidic droplet barcoding , 2017, Nature Biotechnology.

[4]  N. Hacohen,et al.  Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors , 2017, Science.

[5]  F. Klauschen,et al.  CD8+ T Cells Orchestrate pDC‐XCR1+ Dendritic Cell Spatial and Functional Cooperativity to Optimize Priming , 2017, Immunity.

[6]  Xiangyue Zhang,et al.  A distinct subset of plasmacytoid dendritic cells induces activation and differentiation of B and T lymphocytes , 2017, Proceedings of the National Academy of Sciences.

[7]  Mauro J. Muraro,et al.  A Single-Cell Transcriptome Atlas of the Human Pancreas , 2016, Cell systems.

[8]  Özlem Türeci,et al.  Systemic RNA delivery to dendritic cells exploits antiviral defence for cancer immunotherapy , 2016, Nature.

[9]  D. Isenberg,et al.  A Regulatory Feedback between Plasmacytoid Dendritic Cells and Regulatory B Cells Is Aberrant in Systemic Lupus Erythematosus , 2016, Immunity.

[10]  R. Medzhitov,et al.  Tissue biology perspective on macrophages , 2015, Nature Immunology.

[11]  Hans Clevers,et al.  Single-cell messenger RNA sequencing reveals rare intestinal cell types , 2015, Nature.

[12]  M. Colonna,et al.  The multifaceted biology of plasmacytoid dendritic cells , 2015, Nature Reviews Immunology.

[13]  K. Hirata,et al.  Heat shock protein 90 associates with Toll‐like receptors 7/9 and mediates self‐nucleic acid recognition in SLE , 2015, European journal of immunology.

[14]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[15]  Sanjay Tyagi,et al.  Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection , 2015, Science Signaling.

[16]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[17]  V. Hornung,et al.  Self‐priming determines high type I IFN production by plasmacytoid dendritic cells , 2014, European journal of immunology.

[18]  T. Elton,et al.  Regulation of the MIR155 host gene in physiological and pathological processes. , 2013, Gene.

[19]  Wilhelm T S Huck,et al.  Probing cellular heterogeneity in cytokine-secreting immune cells using droplet-based microfluidics. , 2013, Lab on a chip.

[20]  J. Blay,et al.  Tumor promotion by intratumoral plasmacytoid dendritic cells is reversed by TLR7 ligand treatment. , 2013, Cancer research.

[21]  D. Weitz,et al.  Single-cell analysis and sorting using droplet-based microfluidics , 2013, Nature Protocols.

[22]  W. Oyen,et al.  Natural human plasmacytoid dendritic cells induce antigen-specific T-cell responses in melanoma patients. , 2013, Cancer research.

[23]  C. Leclerc,et al.  Neonatal Plasmacytoid Dendritic Cells (pDCs) Display Subset Variation but Can Elicit Potent Anti-Viral Innate Responses , 2013, PloS one.

[24]  Kerstin Pingel,et al.  50 Years of Image Analysis , 2012 .

[25]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[26]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[27]  Thomas Höfer,et al.  Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response , 2012, Molecular systems biology.

[28]  S. Sealfon,et al.  Role of Cell-to-Cell Variability in Activating a Positive Feedback Antiviral Response in Human Dendritic Cells , 2011, PloS one.

[29]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[30]  T. Matsui,et al.  CD2 Distinguishes Two Subsets of Human Plasmacytoid Dendritic Cells with Distinct Phenotype and Functions1 , 2009, The Journal of Immunology.

[31]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[32]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[33]  A. Oudenaarden,et al.  Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.

[34]  R. Coffman,et al.  PI3K is critical for the nuclear translocation of IRF-7 and type I IFN production by human plasmacytoid predendritic cells in response to TLR activation , 2008, The Journal of experimental medicine.

[35]  Hadley Wickham,et al.  Reshaping Data with the reshape Package , 2007 .

[36]  S. Akira,et al.  Nucleic acids of mammalian origin can act as endogenous ligands for Toll-like receptors and may promote systemic lupus erythematosus , 2005, The Journal of experimental medicine.

[37]  D. Golenbock,et al.  Human lupus autoantibody-DNA complexes activate DCs through cooperation of CD32 and TLR9. , 2005, The Journal of clinical investigation.

[38]  J. Dai,et al.  Regulation of IFN Regulatory Factor-7 and IFN-α Production by Enveloped Virus and Lipopolysaccharide in Human Plasmacytoid Dendritic Cells1 , 2004, The Journal of Immunology.

[39]  Akiko Iwasaki,et al.  Recognition of single-stranded RNA viruses by Toll-like receptor 7. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[40]  D. Mason,et al.  The plasmacytoid monocyte/interferon producing cells , 2003, Virchows Archiv.

[41]  H. Gary-Gouy,et al.  Type I interferon production by plasmacytoid dendritic cells and monocytes is triggered by viruses, but the level of production is controlled by distinct cytokines. , 2002, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[42]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[43]  N. Kadowaki,et al.  Distinct CpG DNA and Polyinosinic-Polycytidylic Acid Double-Stranded RNA, Respectively, Stimulate CD11c− Type 2 Dendritic Cell Precursors and CD11c+ Dendritic Cells to Produce Type I IFN1 , 2001, The Journal of Immunology.

[44]  D. Jarrossay,et al.  Plasmacytoid monocytes migrate to inflamed lymph nodes and produce large amounts of type I interferon , 1999, Nature Medicine.

[45]  N. Kadowaki,et al.  The nature of the principal type 1 interferon-producing cells in human blood. , 1999, Science.

[46]  D. Levy,et al.  Differential viral induction of distinct interferon‐α genes by positive feedback through interferon regulatory factor‐7 , 1998, The EMBO journal.

[47]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[48]  L. Glimcher,et al.  Osteopontin expression is essential for interferon-alpha production by plasmacytoid dendritic cells. , 2006, Nature immunology.

[49]  L. Packer Physiological and pathological processes , 1996 .