Evidence map›Paper›PMID 39896613›Full record

ArticlebioRxiv : the preprint server for biology2025

HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes.

Shiting Li, Shaomiao Xia, Maria Lawas, Aishani Kulshreshtha, Bailey F Garb, Aa Chamila Perera, Chen Li, Tingting Qin, Joshua D Welch, Nisha J D'Silva and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Shiting LiDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Shaomiao XiaDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Maria LawasDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Aishani KulshreshthaDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Bailey F GarbDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Aa Chamila PereraDepartment of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
Chen LiDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Tingting QinDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Joshua D WelchDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Nisha J D'SilvaDepartment of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.
Laura S RozekGeorgetown University, Oncology Department, School of Medicine, Washington DC, USA.
Maureen A SartorDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Funding

Strategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Dana Dolinoy · 2011 to 2026
$21.3M
Strategies to Overcome Immune Resistance in Head and Neck CancersP01CA240239 · NCI · YALE UNIVERSITY · PI SARTOR, MAUREEN AGNES · 2019 to 2023
$8.4M
Proteogenomics of Cancer Training ProgramT32CA140044 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI RAO, ARVIND, SARTOR, MAUREEN AGNES · 2010 to 2024
$3.9M
Downstream effects of HPV integration on survival/metastasis in oropharyngeal cancerR01CA250214 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI D'SILVA, NISHA J, ROZEK, LAURA · 2020 to 2024
$3.1M
NCI NIH HHS P01 CA240239NCI NIH HHS R01 CA250214NCI NIH HHS T32 CA140044NIEHS NIH HHS P30 ES017885
6 · The paper itself

Abstract

HPV integration (HPVint) is associated with carcinogenesis and tumor progression in HPV-associated cancers, including head and neck squamous cell carcinomas (HNSCC). While its impact on human DNA has been well characterized, its relationship with clinical outcomes remains unconfirmed. Here we investigate the consequences of HPVint both with respect to human and HPV characteristics by analyzing 261 HPV-associated HNSCC bulk and single-cell RNA-seq samples from five cohorts, and DNA HPVint events from 102 HPV+ participants in two of the cohorts. By leveraging this large meta-cohort, we first reveal an oncogenic network based on the recurrent HPV integration locations in HNSCC. We then classify HPVint-positive (HPVint(+)) participants by HPV RNA features, specifically based on spliced HPV-human fusion transcripts and ratios of HPV gene transcripts, showing that subsets of participants have worse clinical outcomes. Our analyses, focused mainly on RNA instead of DNA, expand our understanding of the carcinogenic mechanisms of HPVint, partially addressing the conflicting findings of whether HPVint is associated with aggressive phenotypes and worse clinical consequences, and provide potential biomarkers to advance precision oncology in HPV-associated HNSCC.

Identifiers

PMID39896613
PMCPMC11785119

What OpenQuestion holds

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Registered trials

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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.