Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA‐seq and VirTect

Autor: Xuelian Chen, Kai Wang, Jiang F. Zhong, Qian Liu, Xi Zhang, Parish P. Sedghizadeh, Andres Stucky, Atlas Khan, Daniel Adelpour
Rok vydání: 2019
Předmět:
Gene Expression Regulation
Viral
Male
0301 basic medicine
Cancer Research
viral detection
Genes
Viral
Carcinogenesis
RNA-Seq
head and neck squamous cell carcinoma
medicine.disease_cause
lcsh:RC254-282
Effective solution
03 medical and health sciences
0302 clinical medicine
Prediction methods
Genetics
medicine
Humans
Human papillomavirus
human papillomavirus
Papillomaviridae
VirTect
Gene
Research Articles
Cervical cancer
Base Sequence
Sequence Analysis
RNA
Squamous Cell Carcinoma of Head and Neck
business.industry
Papillomavirus Infections
High-Throughput Nucleotide Sequencing
General Medicine
lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens
medicine.disease
Head and neck squamous-cell carcinoma
3. Good health
030104 developmental biology
Oncology
030220 oncology & carcinogenesis
Cancer research
RNA‐seq
Molecular Medicine
Female
business
Signal Transduction
Research Article
Zdroj: Molecular Oncology
Molecular Oncology, Vol 13, Iss 4, Pp 829-839 (2019)
ISSN: 1878-0261
1574-7891
DOI: 10.1002/1878-0261.12435
Popis: Next‐generation sequencing provides an opportunity to detect viral species from RNA‐seq data of human tissues, but existing computational approaches do not perform optimally on clinical samples. We developed a bioinformatic method called VirTect for detecting viruses in neoplastic human tissues using RNA‐seq data. Here, we used VirTect to analyze RNA‐seq data from 363 head and neck squamous cell carcinoma (HNSCC) patients and identified 22 human papillomavirus (HPV)‐induced HNSCCs. These predictions were validated by manual review of pathology reports on histopathologic specimens. VirTect showed better performance in recall and accuracy compared to the two existing prediction methods, VirusFinder and VirusSeq, in identifying viral sequences from RNA‐seq data. The majority of HPV carcinogenesis studies thus far have been performed on cervical cancer and generalized to HNSCC. Our results suggest that carcinogenesis of HPV‐induced HNSCC and other cases of HNSCC involve different genes, so understanding the underlying molecular mechanisms will have a significant impact on therapeutic approaches and outcomes. In summary, RNA‐seq together with VirTect can be an effective solution for the detection of viruses from tumor samples and can facilitate the clinicopathologic characterization of various types of cancers with broad applications for oncology.
Databáze: OpenAIRE
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