HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations

  1. Nir Drayman  Is a corresponding author
  2. Parthiv Patel
  3. Luke Vistain
  4. Savas Tay  Is a corresponding author
  1. University of Chicago, United States

Abstract

Viral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous, where most infected cells give rise to none or few viral progeny while some cells produce thousands. Analysis of HSV-1 infection by population averaged measurements has taught us a lot about the course of viral infection, but has also produced contradictory results, such as the concurrent activation and inhibition of type I interferon signaling during infection. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that they cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming involves the recruitment of b-catenin to the host nucleus and viral replication compartments and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.

Data availability

All sequencing data has been deposited in the Gene Expression Omnibus (GEO) under accession number GSE126042. All the scripts used for data analysis and visualization are available through GitHub at: https://github.com/nirdrayman/single-cell-RNAseq-HSV1.git.

The following data sets were generated

Article and author information

Author details

  1. Nir Drayman

    Institute of Molecular Engineering, University of Chicago, Chicago, United States
    For correspondence
    nirdra@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4460-9558
  2. Parthiv Patel

    Institute of Molecular Engineering, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Luke Vistain

    Institute of Molecular Engineering, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Savas Tay

    Institute of Molecular Engineering, University of Chicago, Chicago, United States
    For correspondence
    tays@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

Human Frontier Science Program (post-doctoral fellowship)

  • Nir Drayman

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

Copyright

© 2019, Drayman 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

  • 7,450
    views
  • 1,119
    downloads
  • 130
    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. Nir Drayman
  2. Parthiv Patel
  3. Luke Vistain
  4. Savas Tay
(2019)
HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations
eLife 8:e46339.
https://doi.org/10.7554/eLife.46339

Share this article

https://doi.org/10.7554/eLife.46339

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.