GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE122512 Query DataSets for GSE122512
Status Public on Nov 15, 2018
Title Gene expression analysis of head and neck squamous cell carcinoma (HNSCC) cell lines.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design RNAseq from individual cell lines grown under standard tissue culture conditions.

***Pleaes note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact the submitter for the sequence data***
Contributor(s) Pickering CR, Johnson FM, Myers JN
Citation(s) 30626753, 33108350
Submission date Nov 14, 2018
Last update date Dec 15, 2020
Contact name Curtis Pickering
Organization name The University of Texas MD Anderson Cancer Center
Department Head and Neck Surgery
Lab Pickering Lab
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (74)
GSM3473050 Ca922
GSM3473051 FaDu
GSM3473052 UMSCC1
BioProject PRJNA505441

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE122512_rnaseq_hn_rawcount-Data.csv.gz 3.2 Mb (ftp)(http) CSV
GSE122512_rnaseq_hn_voom-Data.csv.gz 8.2 Mb (ftp)(http) CSV
Raw data not provided for this record
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap