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Analysis of differential gene expression in HPV+ and HPV- HNSCC cell lines

ABSTRACT: Analysis of differential gene expression in HPV+ and HPV- HNSCC cell lines

PROVIDER: PRJNA1053339 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27589600.fastq.gz	Fastqsanger.gz
	SRR27589601.fastq.gz	Fastqsanger.gz
	SRR27589602.fastq.gz	Fastqsanger.gz
	SRR27589603.fastq.gz	Fastqsanger.gz
	SRR27589604.fastq.gz	Fastqsanger.gz

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Project description:HPV+ and HPV- HNSCCs are defined as two aetiologically distinct diseases that are driven by unique risk factors. RNA-seq was used to investigate transcriptional differences based on HPV phenotype.

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Project description:Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESC) cell lines separately, we performed genomic, viral gene expression, and viral integration analyses on 74 cell lines that include all readily-available HPV-positive (9 HNSCC, 8 CESC) and CESC (8 HPV-positive, 2 HPV-negative) cell lines and 55 HPV-negative HNSCC cell lines. We used over 700 human tumors for comparison. Mutation patterns in the cell lines were similar to those of human tumors. We confirmed HPV viral protein and mRNA expression in the HPV-positive cell lines. We found HPV types in three CESC cell lines that are distinct from those previously reported. We found that cell lines and tumors had similar patterns of viral gene expression; there were few sites of recurrent HPV integration. As seen in tumors, HPV integration did appear to alter host gene expression in cell lines. The HPV-positive cell lines had higher levels of p16 and lower levels of Rb protein expression than did the HPV-negative lines. Although the number of HPV-positive cell lines is limited, our results suggest that these cell lines represent suitable models for studying HNSCC and CESC, both of which are common and lethal.

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