Hidden long-range memories of growth and cycle speed correlate cell cycles in lineage trees

  1. Erika E Kuchen
  2. Nils B Becker
  3. Nina Claudino
  4. Thomas Höfer  Is a corresponding author
  1. German Cancer Research Center (DKFZ), Germany

Abstract

Cell heterogeneity may be caused by stochastic or deterministic effects. The inheritance of regulators through cell division is a key deterministic force, but identifying inheritance effects in a systematic manner has been challenging. Here we measure and analyze cell cycles in deep lineage trees of human cancer cells and mouse embryonic stem cells and develop a statistical framework to infer underlying rules of inheritance. The observed long-range intra-generational correlations in cell-cycle duration, up to second cousins, seem paradoxical because ancestral correlations decay rapidly. However, this correlation pattern is naturally explained by the inheritance of both cell size and cell-cycle speed over several generations, provided that cell growth and division are coupled through a minimum-size checkpoint. This model correctly predicts the effects of inhibiting cell growth or cycle progression. In sum, we show how fluctuations of cell cycles across lineage trees help understand the coordination of cell growth and division.

Data availability

Data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1 and 4.

The following previously published data sets were used

Article and author information

Author details

  1. Erika E Kuchen

    Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Nils B Becker

    Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Nina Claudino

    Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Thomas Höfer

    Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
    For correspondence
    t.hoefer@dkfz.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3560-8780

Funding

Bundesministerium für Bildung und Forschung (0316076A)

  • Thomas Höfer

Bundesministerium für Bildung und Forschung (01ZX1307)

  • Thomas Höfer

Bundesministerium für Bildung und Forschung (031L0087A)

  • Thomas Höfer

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2020, Kuchen et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,136
    views
  • 322
    downloads
  • 23
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Erika E Kuchen
  2. Nils B Becker
  3. Nina Claudino
  4. Thomas Höfer
(2020)
Hidden long-range memories of growth and cycle speed correlate cell cycles in lineage trees
eLife 9:e51002.
https://doi.org/10.7554/eLife.51002

Share this article

https://doi.org/10.7554/eLife.51002

Further reading

    1. Computational and Systems Biology
    2. Neuroscience
    Cesare V Parise, Marc O Ernst
    Research Article

    Audiovisual information reaches the brain via both sustained and transient input channels, representing signals’ intensity over time or changes thereof, respectively. To date, it is unclear to what extent transient and sustained input channels contribute to the combined percept obtained through multisensory integration. Based on the results of two novel psychophysical experiments, here we demonstrate the importance of the transient (instead of the sustained) channel for the integration of audiovisual signals. To account for the present results, we developed a biologically inspired, general-purpose model for multisensory integration, the multisensory correlation detectors, which combines correlated input from unimodal transient channels. Besides accounting for the results of our psychophysical experiments, this model could quantitatively replicate several recent findings in multisensory research, as tested against a large collection of published datasets. In particular, the model could simultaneously account for the perceived timing of audiovisual events, multisensory facilitation in detection tasks, causality judgments, and optimal integration. This study demonstrates that several phenomena in multisensory research that were previously considered unrelated, all stem from the integration of correlated input from unimodal transient channels.

    1. Computational and Systems Biology
    Franck Simon, Maria Colomba Comes ... Herve Isambert
    Tools and Resources

    Live-cell microscopy routinely provides massive amounts of time-lapse images of complex cellular systems under various physiological or therapeutic conditions. However, this wealth of data remains difficult to interpret in terms of causal effects. Here, we describe CausalXtract, a flexible computational pipeline that discovers causal and possibly time-lagged effects from morphodynamic features and cell–cell interactions in live-cell imaging data. CausalXtract methodology combines network-based and information-based frameworks, which is shown to discover causal effects overlooked by classical Granger and Schreiber causality approaches. We showcase the use of CausalXtract to uncover novel causal effects in a tumor-on-chip cellular ecosystem under therapeutically relevant conditions. In particular, we find that cancer-associated fibroblasts directly inhibit cancer cell apoptosis, independently from anticancer treatment. CausalXtract uncovers also multiple antagonistic effects at different time delays. Hence, CausalXtract provides a unique computational tool to interpret live-cell imaging data for a range of fundamental and translational research applications.