Beta human papillomavirus 8E6 promotes alternative end-joining

  1. Changkun Hu
  2. Taylor Bugbee
  3. Rachel Palinski
  4. Ibukun A Akinyemi
  5. Michael T McIntosh
  6. Thomas MacCarthy
  7. Sumita Bhaduri-McIntosh
  8. Nicholas Wallace  Is a corresponding author
  1. Fred Hutchinson Cancer Research Center, United States
  2. Kansas State University, United States
  3. University of Florida, United States
  4. Stony Brook University, United States

Abstract

Double strand breaks (DSBs) are one of the most lethal DNA lesions in cells. The E6 protein of beta-human papillomavirus (HPV8 E6) impairs two critical DSB repair pathways; homologous recombination (HR) and non-homologous end-joining (NHEJ). However, HPV8 E6 only delays DSB repair. How DSBs are repaired in cells with HPV8 E6 remains to be studied. We hypothesize that HPV8 E6 promotes a less commonly used DSB repair pathway, alternative end-joining (Alt-EJ). Using CAS9 based Alt-EJ reporters, we show that HPV8 E6 promotes Alt-EJ. Further, using small molecule inhibitors, CRISPR/CAS9 gene knockout, and HPV8 E6 mutant, we find that HPV8 E6 promotes Alt-EJ by binding p300, an acetyltransferase that facilitates DSB repair by HR and NHEJ. At least some of this repair occurs through a subset of Alt-EJ known as polymerase theta dependent end joining. Finally, whole genome sequencing analysis showed HPV8 E6 caused an increased frequency of deletions bearing the microhomology signatures of Alt-EJ. This study fills the knowledge gap of how DSB is repaired in cells with HPV8 E6 and the mutagenic consequences of HPV8 E6 mediated p300 destabilization. Broadly, this study supports the hypothesis that beta-HPV promotes cancer formation by increasing genomic instability.

Data availability

Sequences have been deposited in the NCBI SRA database with accession number (PRJNA 856469).

The following data sets were generated

Article and author information

Author details

  1. Changkun Hu

    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4407-7144
  2. Taylor Bugbee

    Division of Biology, Kansas State University, Manhattan, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Rachel Palinski

    Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ibukun A Akinyemi

    Department of Pediatrics, University of Florida, Gainesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Michael T McIntosh

    Department of Pediatrics, University of Florida, Gainesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Thomas MacCarthy

    Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Sumita Bhaduri-McIntosh

    Department of Pediatrics, University of Florida, Gainesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Nicholas Wallace

    Division of Biology, Kansas State University, Manhattan, United States
    For correspondence
    nwallac@ksu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3971-716X

Funding

National Institute of General Medical Sciences (P20GM130448)

  • Nicholas Wallace

NIH Research Enhancement Award (NCI R15 CA242057 01A1)

  • Nicholas Wallace

U.S. Department of Defense (CMDRP PRCRP CA160224 (NW))

  • Nicholas Wallace

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

Copyright

© 2023, Hu 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

  • 1,160
    views
  • 140
    downloads
  • 5
    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. Changkun Hu
  2. Taylor Bugbee
  3. Rachel Palinski
  4. Ibukun A Akinyemi
  5. Michael T McIntosh
  6. Thomas MacCarthy
  7. Sumita Bhaduri-McIntosh
  8. Nicholas Wallace
(2023)
Beta human papillomavirus 8E6 promotes alternative end-joining
eLife 12:e81923.
https://doi.org/10.7554/eLife.81923

Share this article

https://doi.org/10.7554/eLife.81923

Further reading

    1. Cancer Biology
    Han V Han, Richard Efem ... Richard Z Lin
    Research Article

    Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Now, we show that implantation of Pik3ca−/− KPC (named αKO) cancer cells induces clonal enrichment of cytotoxic T cells infiltrating the pancreatic tumors. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression, and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with clonally enriched CD8+ T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated these clonally enriched T cells infiltrating p-αKO tumors, leading to slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic cancers and this understanding may lead to improvement in immunotherapy for this difficult-to-treat cancer.

    1. Cancer Biology
    2. Immunology and Inflammation
    Almudena Mendez-Perez, Andres M Acosta-Moreno ... Esteban Veiga
    Short Report

    In this study, we present a proof-of-concept classical vaccination experiment that validates the in silico identification of tumor neoantigens (TNAs) using a machine learning-based platform called NAP-CNB. Unlike other TNA predictors, NAP-CNB leverages RNA-seq data to consider the relative expression of neoantigens in tumors. Our experiments show the efficacy of NAP-CNB. Predicted TNAs elicited potent antitumor responses in mice following classical vaccination protocols. Notably, optimal antitumor activity was observed when targeting the antigen with higher expression in the tumor, which was not the most immunogenic. Additionally, the vaccination combining different neoantigens resulted in vastly improved responses compared to each one individually, showing the worth of multiantigen-based approaches. These findings validate NAP-CNB as an innovative TNA identification platform and make a substantial contribution to advancing the next generation of personalized immunotherapies.