Evidence map›Paper›PMID 38147693›Full record

ArticleVirology2024

Computational and AI-driven 3D structural analysis of human papillomavirus (HPV) oncoproteins E5, E6, and E7 reveal significant divergence of HPV E5 between low-risk and high-risk genotypes.

Riley N Jones, Sayuri Miyauchi, Souvick Roy, Nathalie Boutros, Jyoti S Mayadev, Loren K Mell, Joseph A Califano, Aldo Venuti, Andrew B Sharabi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Role of E5 from HPV16 in the Evasion of the Immune Response.International journal of molecular sciences · 2026
    Review
  2. Article
  3. Review
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  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Riley N JonesDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA.
Sayuri MiyauchiDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA.
Souvick RoyDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA.
Nathalie BoutrosDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA.
Jyoti S MayadevDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA.
Loren K MellDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
Joseph A CalifanoMoores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, CA, USA.
Aldo VenutiHPV-UNIT-UOSD Tumor Immunology and Immunotherapy, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Andrew B SharabiDepartment of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA. Electronic address: sharabi@ucsd.edu.

Funding

Role of B-cell mediated anti-tumor antibodies in responses to radiation and immunotherapy in HNSCCR01DE028563 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHARABI, ANDREW B. · 2019 to 2023
$1.8M
NIDCR NIH HHS R01 DE028563
6 · The paper itself

Abstract

There are over 220 identified genotypes of Human papillomavirus (HPV), and the HPV genome encodes 3 major oncogenes, E5, E6, and E7. Conservation and divergence in protein sequence and function between low-risk versus high-risk oncogenic HPV genotypes has not been fully characterized. Here, we used modern computational and structural folding algorithms to perform a comparative analysis of HPV E5, E6, and E7 between multiple low risk and high risk genotypes. We first identified significantly greater sequence divergence in E5 between low- and high-risk genotypes compared to E6 and E7. Next, we used AlphaFold to model the structure of papillomavirus proteins and complexes with high confidence, including some with no established consensus structure. We observed that HPV E5, but not E6 or E7, had a dramatically different 3D structure between low-risk and high-risk genotypes. To our knowledge, this is the first comparative analysis of HPV proteins using Alphafold artificial intelligence (AI) system. The marked differences in E5 sequence and structure in high-risk HPVs may contribute in important and underappreciated ways to the development of HPV-associated cancers.

Indexed as

Oncogene Proteins, ViralPapillomavirus InfectionsArtificial IntelligenceGenotypeHuman Papillomavirus VirusesHumansPapillomaviridaePapillomavirus E7 ProteinsOncogene Proteins, ViralPapillomavirus E7 ProteinsAIAlphafoldDivergenceE5E6E7HomologyHPVOncoproteinPapillomavirusStructural analysis

Identifiers

PMID38147693
PMCPMC12983986

What Socratic holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.