title: Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.
abstract: Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell. Our results identify multiple, distinct cytokine expression patterns that are correlated with NF-κB activation dynamics, establishing a functional role for NF-κB dynamics in determining cellular phenotypes. Applications of this approach to other model systems and single-cell sequencing technologies have significant potential for discovery, as it is now possible to trace cellular behavior from the initial stimulus, through the signaling pathways, down to genome-wide changes in gene expression, all inside of a single cell.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Keara
authors.initials: K
authors.lastname: Lane
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: David
authors.initials: D
authors.lastname: Van Valen
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Mialy M
authors.initials: MM
authors.lastname: DeFelice
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Derek N
authors.initials: DN
authors.lastname: Macklin
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Takamasa
authors.initials: T
authors.lastname: Kudo
authors.affiliation: Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Ariel
authors.initials: A
authors.lastname: Jaimovich
authors.affiliation: Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Ambrose
authors.initials: A
authors.lastname: Carr
authors.affiliation: Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Tobias
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Program in Computational and Systems Biology, Sloan Kettering Institute, New York, NY 10065, USA.
authors.forename: Dana
authors.initials: D
authors.lastname: Pe'er
authors.affiliation: R&D Department, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA.
authors.forename: Stéphane C
authors.initials: SC
authors.lastname: Boutet
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: mcovert@stanford.edu.
authors.forename: Markus W
authors.initials: MW
authors.lastname: Covert
mesh_terms: D000818:Animals; D016207:Cytokines / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics; D008070:Lipopolysaccharides / Q000276:immunology; D051379:Mice; D018448:Models, Immunological; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D000067996:RAW 264.7 Cells; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D059010:Single-Cell Analysis; D015533:Transcriptional Activation; D059467:Transcriptome
chemical_list: D016207:Cytokines; D008070:Lipopolysaccharides; D016328:NF-kappa B
keywords: NF-κB; RNA-seq; gene expression; live-cell imaging; signaling dynamics; single-cell heterogeneity