title: Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.
abstract: In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a "simple" program that all cells execute identically but results from the dynamical behavior of the underlying molecular network.
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
authors.forename: Angélique
authors.identifier: http://orcid.org/0000-0002-5440-8656
authors.initials: A
authors.lastname: Richard
authors.affiliation: Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France.|Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France.|Département de Mathématiques et de statistiques de l'Université de Montréal, Pavillon André-Aisenstadt, 2920, chemin de la Tour, Montréal (Québec) H3T 1J4 Canada.
authors.forename: Loïs
authors.initials: L
authors.lastname: Boullu
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.|Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France.|Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France.
authors.forename: Ulysse
authors.identifier: http://orcid.org/0000-0002-0972-385X
authors.initials: U
authors.lastname: Herbach
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.|Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France.|The CoSMo company. 5 passage du Vercors - 69007 LYON - France.
authors.forename: Arnaud
authors.identifier: http://orcid.org/0000-0003-0472-0761
authors.initials: A
authors.lastname: Bonnafoux
authors.affiliation: Univ Lyon, Univ Claude Bernard, CNRS UMR 5310 - INSERM U1217, Institut NeuroMyoGène, F-69622 Villeurbanne-Cedex, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Morin
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Vallin
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
authors.forename: Anissa
authors.initials: A
authors.lastname: Guillemin
authors.affiliation: Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.|Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne Switzerland.
authors.forename: Nan
authors.initials: N
authors.lastname: Papili Gao
authors.affiliation: Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.|Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne Switzerland.
authors.forename: Rudiyanto
authors.identifier: http://orcid.org/0000-0002-6480-7976
authors.initials: R
authors.lastname: Gunawan
authors.affiliation: Genethon - Institut National de la Santé et de la Recherche Médicale - INSERM, Université d'Evry-Val-d'Essone - 1 rue de l'internationale 91000 Evry, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Cosette
authors.affiliation: RIKEN - Center for Life Science Technologies (Division of Genomic Technologies)-CLST (DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Ophélie
authors.initials: O
authors.lastname: Arnaud
authors.affiliation: INSERM, Centre Cavaillès, Ecole Normale Supérieure, F-75005 Paris, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Kupiec
authors.affiliation: Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: Espinasse
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Gonin-Giraud
authors.affiliation: Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.|Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France.
authors.forename: Olivier
authors.identifier: http://orcid.org/0000-0002-3676-6513
authors.initials: O
authors.lastname: Gandrillon
mesh_terms: D002454:Cell Differentiation; D019277:Entropy; D020869:Gene Expression Profiling; D008954:Models, Biological; D059010:Single-Cell Analysis; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism