title: Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
abstract: High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.
authors.affiliation: 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [4].
authors.forename: Alex K
authors.initials: AK
authors.lastname: Shalek
authors.affiliation: 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2].
authors.forename: Rahul
authors.initials: R
authors.lastname: Satija
authors.affiliation: 1] Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA [2].
authors.forename: Joe
authors.initials: J
authors.lastname: Shuga
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: Trombetta
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Gennert
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Lu
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Peilin
authors.initials: P
authors.lastname: Chen
authors.affiliation: 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA.
authors.forename: Rona S
authors.initials: RS
authors.lastname: Gertner
authors.affiliation: 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA.
authors.forename: Jellert T
authors.initials: JT
authors.lastname: Gaublomme
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Yosef
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Schraga
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Fowler
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Weaver
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wang
authors.affiliation: 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA.
authors.forename: Ruihua
authors.initials: R
authors.lastname: Ding
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.affiliation: School of Computer Science and Engineering, Hebrew University, 91904 Jerusalem, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.affiliation: 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Center for Immunology and Inflammatory Diseases & Department of Medicine, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.affiliation: 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Hongkun
authors.initials: H
authors.lastname: Park
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: May
authors.affiliation: 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D000956:Antigens, Viral / Q000494:pharmacology; D001483:Base Sequence; D002450:Cell Communication; D003713:Dendritic Cells / Q000187:drug effects / Q000276:immunology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000276:immunology*; D007109:Immunity / Q000235:genetics*; D016899:Interferon-beta / Q000235:genetics; D051379:Mice; D046210:Microfluidic Analytical Techniques; D019899:Paracrine Communication; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D059010:Single-Cell Analysis
chemical_list: D000956:Antigens, Viral; D012333:RNA, Messenger; D016899:Interferon-beta