Evidence map›Paper›PMID 38279874›Full record

ArticleClinical and translational medicine2024

Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma.

Shengming Xu, Chaoji Shi, Rong Zhou, Yong Han, NianNian Li, Chuxiang Qu, Ronghui Xia, Chunye Zhang, Yuhua Hu, Zhen Tian and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical and translational medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
2.6field-weighted citation impact, top 11% of its field
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

9 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Review
  6. HPV Infection and Oral Microbiota: Interactions and Future Implications.International journal of molecular sciences · 2025
    Review
  7. Review
  8. Review
  9. 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

14 authors at 2 institutions in 1 country.

Shengming XuDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Chaoji ShiDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Rong ZhouDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Yong HanDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
NianNian LiDepartment of Bioinfomatics, Sequanta, Shanghai, China.
Chuxiang QuCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Ronghui XiaCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Chunye ZhangCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Yuhua HuCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Zhen TianCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Shuli LiuDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.ORCID 0000-0002-8988-8899
Lizhen WangCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Jiang LiCollege of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
Zhiyuan ZhangDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.ORCID 0000-0003-3845-7420
Shanghai Jiao Tong University · CNShanghai Center For Bioinformation Technology · CN

Funding

CAMS Innovation Fund for Medical Sciences 2019-I2M-5-037Cross-research Fund Project of Shanghai Ninth People's Hospital and Shanghai University of Science and Technology JYJC202121National Natural Science Foundation of China 82273017Shanghai Clinical Research Center for Oral Diseases 19MC1910600Shanghai Municipal Key Clinical Specialty shslczdzk01601Shanghai's Top Priority Research Center 2022ZZ01017
6 · The paper itself

Abstract

backgroundHuman papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND

methodsHigh-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing.

resultsHPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process.

conclusionsHPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.

Indexed as

Head and Neck NeoplasmsPapillomavirus InfectionsCarcinogenesisDNA Copy Number VariationsHuman Papillomavirus VirusesHumansPapillomaviridaePapillomavirus E7 ProteinsSquamous Cell Carcinoma of Head and NeckPapillomavirus E7 Proteinshost genomic alterationsHPVoropharyngeal squamous cell carcinomaviral integration

Identifiers

PMID38279874
PMCPMC10819103
OpenAlexW4391278300

What OpenQuestion holds

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LicenceCC BY
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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 OpenQuestion graph.