Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FN1 expression is a marker of radioresistance in head and neck squamous cell carcinoma

ABSTRACT: The goal of this project was to analyze differential expression in head and neck cancer cells with various intrinsic radiosensitivity. The gene expression profiles of the cell lines were determined using the Human Genome U133 plus 2.0 Arrays (Affymetrix, Santa Clara, CA).

ORGANISM(S): Homo sapiens

PROVIDER: GSE21644 | GEO | 2011/06/09

SECONDARY ACCESSION(S): PRJNA127093

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

FN1 expression is a marker of radioresistance in head and neck squamous cell carcinoma

Project description:The goal of this project was to analyze differential expression in head and neck cancer cells with various intrinsic radiosensitivity. The gene expression profiles of the cell lines were determined using the Human Genome U133 plus 2.0 Arrays (Affymetrix, Santa Clara, CA). The UTSCC cells were cultured in DMEM (Gibco) supplemented with 2mM glutamine, 1% non-essential amino acids, 100 IU/ml penicillin-G, 50ug/ml streptomycin, and 5% fetal bovine serum (all from Gibco, Paisley, UK). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany). The study included a total of 10 samples with 2 seperate experiments from 5 cell lines respectivley.

2011-06-09 | E-GEOD-21644 | biostudies-arrayexpress

Isolation and genomic characterization of cancer stem cells in head and neck cancer

Project description:This study investigated the use of three different established cell sorting strategies to isolate and characterize stem cells from head and neck cancer cell lines. Five low passage cell lines were subjected to cell sorting based on Hoechst side population, Aldefluor and CD44 expression. Isolated cell populations were studied for gene expression, radiosensitivity and chemosensitivity to cis-platin and paclitaxel Each sorting method identified a different set of genes associated with different Gene Ontology categories with mitosis being the only common category. CD44 associated gene changes were almost exclusively associated with cell cycle and in particular mitosis. There were no significant differences in radiosensitivity or cis-platin sensitivity of stem or non-stem cells but CD44 isolated stem cells were more resistant to paclitaxel Five head and neck cell lines were used to isolate cancer stem cells by 3 isolation methods. For each isolation method, cancer stem cell enriched populations (n=5) were compared to cancer stem cell depleted populations (n=5). The resulting gene expression patterns were compared among the 3 isolation methods.

2014-03-02 | E-GEOD-55487 | biostudies-arrayexpress

Isolation and genomic characterization of cancer stem cells in head and neck cancer

2014-03-02 | GSE55487 | GEO

FN1 promotes prognosis and radioresistance in head and neck squamous cell carcinoma: From radioresistant HNSCC cell line to integrated bioinformatics methods.

Project description:Background: Radioresistance in head and neck squamous cell carcinoma (HNSCC) patients means response failure to current treatment. In order to screen radioresistant biomarkers and mechanisms associated with HNSCC, differentially expressed genes (DEGs) associated with radioresistance in HNSCC were investigated. Methods: The HNSCC cell line with radioresistance, Hep2-R, was established and detected the radiosensitivity using MTT, colony formation assay and flow cytometry analysis. Clariom™ D chip was applied to compare DEGs between Hep2 and Hep2-R groups and build the differential gene expression profiles associated with radioresistance in HNSCC. Bioinformatic analysis were used to find biological functions and pathways that related to radioresistance in HNSCC, including cell adhesion, cytochrome P450 and drug metabolism. Gene Expression Omnibus (GEO) datasets were selected to verify DEGs between HNSCC radioresistant cells and tissues. The representation of DEGs were validated between HNSCC patients with complete response and post-operative radiation therapy failure. In addition, we evaluated the clinical prognosis of DEGs using The Cancer Genome Atlas (TCGA) database. Results: 2,360 DEGs (|Fold Change|>1.5, p < 0.05) were identified between Hep2 and Hep2-R, including 1,144 upregulated DEGs and 1,216 downregulated DEGs. They were further verified by HNSCC radioresistant cells and tissues in GEO. 13 radioresistant DEGs showed same difference in expression level between cells and tissues. By comparing 13 DEGs with HNSCC patients, upregulations of FN1, SOX4 and ETV5 were found identical with above results. Only FN1 was a prognostic indicator of HNSCC in TCGA. Conclusion: FN1 is the potential novel biomarker for predicting poor prognosis and radioresistance in HNSCC patients. Overexpression of FN1 plays an important role in the tumorigenesis, prognosis and radioresistance of HNSCC.

| S-EPMC9533212 | biostudies-literature

Gene expression data from head and neck cancer patient derived xenografts

Project description:Head and neck cancer is a hetergeneous disease. Based on previoulsy defined molecular subtypes we associated gene expression with response to different compounds. We used microarry gene expression for molecular subtyping Cetuximab is the single targeted therapy approved for the treatment of head and neck cancer (SCCHN). Predictive biomarkers have not been established in the clinical setting and patient stratification based on molecular tumor profiles has not been possible. Since EGFR pathway activation is pronounced in basal subtype, we hypothesized this activation could be a predictive signature for an EGFR directed treatment. From our patient derived xenograft platform of head and neck cancer, 28 models were subjected to Affymetrix gene expression studies on HG U133+ 2.0. Based on the expression of 821 genes, the subtype of each of the 28 models was determined by integrating gene expression profiles through centroid-clustering with previously published gene expression data by Keck et al.,CCR 2015. Response was evaluated by comparing tumor volume at treatment initiation and after three weeks of treatment (RTV).

2016-10-01 | GSE84713 | GEO

Development of Transcriptomic Biomarker Signature in Human Saliva to Detect Lung Cancer

Project description:Affymetrix HG U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) was used to profile transcriptomes and discover altered gene expression in saliva supernatant. Salivary transcriptomic biomarker discovery was performed on 10 lung cancer patients and 10 matched controls. Seven messenger RNA biomarkers were discovered and pre-validated

2013-01-11 | GSE32175 | GEO

Head and neck squamous cell carcinoma

Project description:Quantitative (iTRAQ 4-plex) proteomic analysis of progressive head and neck cancers

2022-03-01 | PXD001438 | Pride

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas. The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 18 normal head and neck samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25083 | biostudies-arrayexpress

Loss of SOX2 expression induces cell migration via Vimentin up-regulation and serves as unfavourable risk factor for poor survival of head and neck squamous cell carcinoma patients

Project description:Transcriptional profiling of patient derived HNSCC (head and neck squamous cell carcinoma) cell line HNO223 comparing control cells transfected with shRNA against luciferase (shLuci) with cells transfected with two different shRNAs targeting SOX2. The goal was to determine the effects of SOX2 knockdown on global gene expression. Total RNA was extracted from stably transfected HNSCC cells with shLuci (control) and two different SOX2 shRNAs (shSOX2#1 and shSOX2#2), comparing the control with each of the two SOX2 shRNAs (replicate1: shLuci vs. shSOX2#1 and replicate2: shLuci vs. shSOX2#2). The biological replicates were from two independent transfection experiments (transfection 1 and transfection 2). Gene expression profiling was performed using the Human GE 4x44K v2 Microarray according to manufacturer`s instructions (Agilent, Santa Clara, CA).

2014-09-23 | E-GEOD-61599 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

2011-10-28 | GSE25083 | GEO