Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9

  1. Hyung Suk Oh
  2. Werner M Neuhausser  Is a corresponding author
  3. Pierce Eggan
  4. Magdalena Angelova
  5. Rory Kirchner
  6. Kevin C Eggan
  7. David M Knipe  Is a corresponding author
  1. Harvard Medical School, United States
  2. Harvard University, United States
  3. Harvard T H Chan School of Public Health, United States

Abstract

Herpes simplex virus (HSV) establishes lifelong latent infection and can cause serious human disease, but current antiviral therapies target lytic but not latent infection. We screened for sgRNAs that cleave HSV-1 DNA sequences efficiently in vitro and used these sgRNAs to observe the first editing of quiescent HSV-1 DNA. The sgRNAs targeted lytic replicating viral DNA genomes more efficiently than quiescent genomes, consistent with the open structure of lytic chromatin. Editing of latent genomes caused short indels while editing of replicating genomes produced indels, linear molecules and large genomic sequence loss around the gRNA target site. The HSV ICP0 protein and viral DNA replication increased the loss of DNA sequences around the gRNA target site. We conclude that HSV, by promoting open chromatin needed for viral gene expression and by inhibiting the DNA damage response, makes the genome vulnerable to a novel form of editing by CRISPR-Cas9 during lytic replication.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

The following previously published data sets were used
    1. Miga KH
    2. Newton Y
    3. Jain M
    4. Altemose N
    5. Willard HF
    6. Kent WJ
    (2014) hg38
    Genome Reference Consortium, Human GRCh38.p12 (GCA_000001405.27).

Article and author information

Author details

  1. Hyung Suk Oh

    Department of Microbiology, Harvard Medical School, Boston, United States
    Competing interests
    Hyung Suk Oh, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1739-0389
  2. Werner M Neuhausser

    Department of Obstetrics and Gynecology, Harvard Medical School, Boston, United States
    For correspondence
    wneuhaus@bidmc.harvard.edu
    Competing interests
    Werner M Neuhausser, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5092-2658
  3. Pierce Eggan

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
  4. Magdalena Angelova

    Department of Microbiology, Harvard Medical School, Boston, United States
    Competing interests
    Magdalena Angelova, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
  5. Rory Kirchner

    Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, United States
    Competing interests
    No competing interests declared.
  6. Kevin C Eggan

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
    Competing interests
    Kevin C Eggan, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
  7. David M Knipe

    Department of Microbiology, Harvard Medical School, Boston, United States
    For correspondence
    david_knipe@hms.harvard.edu
    Competing interests
    David M Knipe, Reviewing editor, eLifeWe have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1554-6236

Funding

National Institutes of Health (P01 AI098681)

  • David M Knipe

National Institutes of Health (R21 AI135423)

  • Kevin C Eggan

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

Reviewing Editor

  1. Sara L Sawyer, University of Colorado Boulder, United States

Version history

  1. Received: September 6, 2019
  2. Accepted: December 1, 2019
  3. Accepted Manuscript published: December 2, 2019 (version 1)
  4. Version of Record published: December 17, 2019 (version 2)

Copyright

© 2019, Oh 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

  • 7,365
    views
  • 532
    downloads
  • 27
    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. Hyung Suk Oh
  2. Werner M Neuhausser
  3. Pierce Eggan
  4. Magdalena Angelova
  5. Rory Kirchner
  6. Kevin C Eggan
  7. David M Knipe
(2019)
Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9
eLife 8:e51662.
https://doi.org/10.7554/eLife.51662

Share this article

https://doi.org/10.7554/eLife.51662

Further reading

    1. Cancer Biology
    2. Genetics and Genomics
    Kevin Nuno, Armon Azizi ... Ravindra Majeti
    Research Article

    Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.

    1. Computational and Systems Biology
    2. Genetics and Genomics
    Weichen Song, Yongyong Shi, Guan Ning Lin
    Tools and Resources

    We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS–trait associations with a significance of p < 5 × 10−8. Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis. HFS-based enrichment analysis uncovered 727 pathway–trait associations and 153 tissue–trait associations with strong biological interpretability, including ‘circadian pathway-chronotype’ and ‘arachidonic acid-intelligence’. Lastly, we applied least absolute shrinkage and selection operator (LASSO) regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1–39.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.