ArticleInternational journal of cancer2016
Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.
Article in International journal of cancer, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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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.
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Who cites it
35 citing papers in PubMed, 50 citations in OpenAlex.
- FUBP3 regulates expression and alternative splicing of genes associated with cell proliferation and apoptosis in cancer cells.Oncology letters · 2026Article
- Virus-mediated gene fusion: igniting and sustaining oncogenesis.Trends in cancer · 2025Article
- Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC.iScience · 2025Article
- FGFR3::TACC3 fusions in head and neck carcinomas: a study of nine cases highlighting phenotypic heterogeneity, frequent HPV association, and a morphologically distinct subset in favor of a putative entity.Virchows Archiv : an international journal of pathology · 2025Article
- Identifying Strong Neoantigen MHC-I/II Binding Candidates for Targeted Immunotherapy with SINE.International journal of molecular sciences · 2024Article
- Recurrent UBE3C-LRP5 translocations in head and neck cancer with therapeutic implications.NPJ precision oncology · 2024Article
- OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events.BioMedInformatics · 2023Article
- Article
- The Immune Response Generated against HPV Infection in Men and Its Implications in the Diagnosis of Cancer.Microorganisms · 2023Review
- Human papillomavirus E5 suppresses immunity via inhibition of the immunoproteasome and STING pathway.Cell reports · 2023Article
- HPV-associated oropharyngeal cancer: epidemiology, molecular biology and clinical management.Nature reviews. Clinical oncology · 2022Review
- Susceptibility of cytoskeletal-associated proteins for tumor progression.Cellular and molecular life sciences : CMLS · 2021Review
- A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.Cell systems · 2021Article
- Article
- AKR1C3 is a biomarker and druggable target for oropharyngeal tumors.Cellular oncology (Dordrecht, Netherlands) · 2021Article
- A newERJ open research · 2021Article
- Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models.International journal of cancer · 2020Article
- Article
- Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma.Epigenetics · 2020Article
- HPV16 E5 Mediates Resistance to PD-L1 Blockade and Can Be Targeted with Rimantadine in Head and Neck Cancer.Cancer research · 2020Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
The Cancer Genome Atlas (TCGA) sequencing analysis of head and neck squamous cell carcinoma (HNSCC) recently reported on gene fusions, however, few human papillomavirus (HPV) positive samples were included, and the functional relevance of identified fusions was not explored. We therefore performed an independent analysis of gene fusions in HPV-positive oropharyngeal SCC (OPSCC). RNA sequencing was performed on 47 HPV-positive OPSCC primary tumors and 25 normal mucosal samples from cancer unaffected controls on an Illumina TruSeq platform. MapSplice2 was used for alignment and identification of fusion candidates. Putative fusions with less than five spanning reads, detected in normal tissues, or that mapped to the same gene were filtered out. Selected fusions were validated by RT-PCR and Sanger sequencing. Within 47 HPV-positive OPSCC tumors, 282 gene fusions were identified. Most fusions (85.1%) occurred in a single tumor, and the remaining fusions recurred in 2-16 tumors. Gene fusions were associated with significant up regulation of 16 genes (including EGFR and ERBB4) and down regulation of four genes (PTPRT, ZNF750, DLG2, SLCO5A1). Expression of these genes followed similar patterns of up regulation and down regulation in tumors without these fusions compared to normal tissue. Five of six gene fusions selected for validation were confirmed through RT-PCR and sequencing. This integrative analysis provides a method of prioritizing functionally relevant gene fusions that may be expanded to other tumor types. These results demonstrate that gene fusions may be one mechanism by which functionally relevant genes are altered in HPV-positive OPSCC.
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Registered trials
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.