Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines

  1. Elliott D SoRelle
  2. Joanne Dai
  3. Emmanuela N Bonglack
  4. Emma M Heckenberg
  5. Jeffrey Y Zhou
  6. Stephanie N Giamberardino
  7. Jeffrey A Bailey
  8. Simon G Gregory
  9. Cliburn Chan
  10. Micah A Luftig  Is a corresponding author
  1. Duke University School of Medicine, United States
  2. University of Massachusetts Medical School, United States
  3. Brown University, United States

Abstract

Lymphoblastoid Cell Lines (LCLs) are generated by transforming primary B cells with Epstein-Barr Virus (EBV) and are used extensively as model systems in viral oncology, immunology, and human genetics research. In this study, we characterized single-cell transcriptomic profiles of five LCLs and present a simple discrete-time simulation to explore the influence of stochasticity on LCL clonal evolution. Single-cell RNA sequencing (scRNA-seq) revealed substantial phenotypic heterogeneity within and across LCLs with respect to immunoglobulin isotype; virus-modulated host pathways involved in survival, activation, and differentiation; viral replication state; and oxidative stress. This heterogeneity is likely attributable to intrinsic variance in primary B cells and host-pathogen dynamics. Stochastic simulations demonstrate that initial primary cell heterogeneity, random sampling, time in culture, and even mild differences in phenotype-specific fitness can contribute substantially to dynamic diversity in populations of nominally clonal cells.

Data availability

Raw sequencing data for the three previously unpublished samples (LCL_777_B958, LCL_777_M81, and LCL_461_B958) are deposited in the NCBI Sequence Read Archive (SRA) and can be accessed along with processed data from the NCBI Gene Expression Omnibus (GEO, Series Accession: GSE158275).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Elliott D SoRelle

    Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  2. Joanne Dai

    Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
    Competing interests
    Joanne Dai, Joanne Dai is affiliated with Amgen Inc. The author has no financial interests to declare..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9879-4704
  3. Emmanuela N Bonglack

    Molecular Genetics and Microbiology, Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  4. Emma M Heckenberg

    Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  5. Jeffrey Y Zhou

    Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    No competing interests declared.
  6. Stephanie N Giamberardino

    Department of Neurology, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  7. Jeffrey A Bailey

    Department of Pathology and Laboratory Medicine, Brown University, Providence, United States
    Competing interests
    No competing interests declared.
  8. Simon G Gregory

    Department of Neurology, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  9. Cliburn Chan

    Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, United States
    Competing interests
    No competing interests declared.
  10. Micah A Luftig

    Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
    For correspondence
    micah.luftig@duke.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2964-1907

Funding

National Institute of Dental and Craniofacial Research (R01-DE025994)

  • Micah A Luftig

National Cancer Institute (T32-CA009111)

  • Elliott D SoRelle
  • Joanne Dai
  • Micah A Luftig

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

Copyright

© 2021, SoRelle 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

  • 7,155
    views
  • 623
    downloads
  • 32
    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. Elliott D SoRelle
  2. Joanne Dai
  3. Emmanuela N Bonglack
  4. Emma M Heckenberg
  5. Jeffrey Y Zhou
  6. Stephanie N Giamberardino
  7. Jeffrey A Bailey
  8. Simon G Gregory
  9. Cliburn Chan
  10. Micah A Luftig
(2021)
Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines
eLife 10:e62586.
https://doi.org/10.7554/eLife.62586

Share this article

https://doi.org/10.7554/eLife.62586

Further reading

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Xu Zheng, Shi Yu ... Guangxun Meng
    Research Article

    Innate immune responses triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection play pivotal roles in the pathogenesis of COVID-19, while host factors including proinflammatory cytokines are critical for viral containment. By utilizing quantitative and qualitative models, we discovered that soluble factors secreted by human monocytes potently inhibit SARS-CoV-2-induced cell-cell fusion in viral-infected cells. Through cytokine screening, we identified that interleukin-1β (IL-1β), a key mediator of inflammation, inhibits syncytia formation mediated by various SARS-CoV-2 strains. Mechanistically, IL-1β activates RhoA/ROCK signaling through a non-canonical IL-1 receptor-dependent pathway, which drives the enrichment of actin bundles at the cell-cell junctions, thus prevents syncytia formation. Notably, in vivo infection experiments in mice confirmed that IL-1β significantly restricted SARS-CoV-2 spread in the lung epithelium. Together, by revealing the function and underlying mechanism of IL-1β on SARS-CoV-2-induced cell-cell fusion, our study highlights an unprecedented antiviral function for cytokines during viral infection.