Prospective identification of hematopoietic lineage choice by deep learning.

Journal: Nature methods
PMID: 28218899

Abstract

Differentiation alters molecular properties of stem and progenitor cells, leading to changes in their shape and movement characteristics. We present a deep neural network that prospectively predicts lineage choice in differentiating primary hematopoietic progenitors using image patches from brightfield microscopy and cellular movement. Surprisingly, lineage choice can be detected up to three generations before conventional molecular markers are observable. Our approach allows identification of cells with differentially expressed lineage-specifying genes without molecular labeling.

Authors

  • Felix Buggenthin
    Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
  • Florian Buettner
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. Electronic address: buettner@ebi.ac.uk.
  • Philipp S Hoppe
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Max Endele
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Manuel Kroiss
    Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
  • Michael Strasser
    Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
  • Michael Schwarzfischer
    Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
  • Dirk Loeffler
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Konstantinos D Kokkaliaris
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Oliver Hilsenbeck
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Timm Schroeder
    Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
  • Fabian J Theis
    Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany.
  • Carsten Marr
    Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.

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