Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA268181 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We hypothesized that DKK3 may exert oncogenic function supecifically in head and neck squamous cell carcinoma (HNSCC). DKK3 knockdown in HNSCC cell resulted in decreased cellular proliferation, migration, invasion and in vivo tumor growth.
2018-11-30 | GSE107403 | GEO
Project description:The involvement of microRNAs (miRNAs) in cancer and their potential as biomarkers of diagnosis, prognosis and response to therapy is becoming increasingly appreciated. The etiology of head and neck squamous cell carcinoma (HNSCC) is predominantly associated with the synergistic effects of tobacco and alcohol use, as well as Human Papilloma Virus (HPV) infection, which embodies a distinct clinical and biological phenotype. We sought to examine whether the profile of miRNAs in HNSCC varies based on HPV status, and to identify specific miRNAs altered in head and neck carcinogenesis. Total RNA was isolated from 16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines. The miRNA profile of 662 individual miRNAs in these tissues was examined by microarray. 18 miRNAs are significantly altered in their expression between normal tissues and HNSCC tumors and 5 miRNAs are identified as significantly differentially expressed between HPV-positive (HPV+) and HPV-negative (HPV-) tumors. A striking difference in expression pattern of miRNA was also observed between primary tissues and cell lines. These data suggest that the pattern of miRNA expression may be reflective of disease etiology, and may be useful in the realm of diagnostic biomarkers defining broadly responsive prevention and treatment strategies for HNSCC. These data also suggest that cultured tumor cell lines may be inappropriate for novel miRNA biomarker identification. Keywords: miRNA; Disease-state analysis Expression of 662 individual miRNA was assessed in16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines were arrayed
2010-05-19 | E-GEOD-11163 | biostudies-arrayexpress
Project description:Chromosomal instability is a hallmark of cancer and genes that display abnormal expression in chromosomally aberrant regions are likely to be key players in tumor progression. Identifying such driver genes from high-throughput data requires computational methods that are capable of integrating data from several sources and thereby enhance the reliability of driver gene identification. Hence, several algorithms that integrate copy number and expression data have been developed but their relative performance has not been assessed so far. We have compared 10 algorithms that integrate high-throughput copy number and transcriptomics data using simulated, cancer cell line and primary tumor data. Our results show that there are significant differences between the methods and their performance decreases significantly with small sample sets. Head and neck squamous cell carcinoma (HNSCC) cell lines from the tongue (UT-SCC-21,UT-SCC-24B, UT-SCC-30, UT-SCC-67, UT-SCC-73, UT-SCC-76A, UT-SCC-81, UT-SCC-87,UT-SCC-95) and larynx (UT-SCC-8, UT-SCC-11, UT-SCC-75) were provided by the Department of Otorhinolaryngology-Head and Neck Surgery at the Turku University Central Hospital (Turku, Finland). HNSCC cell lines SCC-4, SCC-9, SCC-25 and human skin keratinocyte HPV-16 E6/E7 transformed cell line CCD1106 KERTr was ordered from American Type Culture Collection (ATCC; Manassas, VA) and cultured according to the ATCC recommendations.
2012-02-10 | E-MEXP-3415 | biostudies-arrayexpress
Project description:We collected HNSCC primary tumor from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for single cell RNA seq analysis.
2023-03-24 | GSE185965 | GEO
Project description:We collected HNSCC primary tumor sections from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for 10x Genomics Visium analysis.
2022-08-29 | GSE181300 | GEO
Project description:Gene expression analysis of a unique HNSCC (Head and Neck Squamous Cell Carcinoma) localization, the hypopharynx. Four normal and 34 tumor samples were analysed using Affymetrix HG-U95A microarrays containing probe sets representing ~12650 distinct transcription features. Keywords = HNSCC Hypopharynx Keywords: ordered
2005-03-09 | GSE2379 | GEO
Project description:Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis due to the development of locoregional recurrences, distant metastases and second primary tumors. There is an urgent need for biomarkers that enable detection and monitoring of the disease to provide adequate therapeutic strategies. In this study we have investigated markers in peripheral blood cells (PBC) of 28 HNSCC patients who underwent surgery by means of expression profiling. Our hypothesis is that nucleated blood cells circulate continuously, also passing the tumor, and might change their expression profiles in response to tumor cell factors. For comparison, we enrolled a control group of 11 patients who underwent surgery in the head and neck region for non-HNSCC reasons. A set of 2,349 genes was found to be statistically different between the groups (p<0.05, false discovery rate-corrected) and the most prominently different pathways were EIF2 and mTOR signaling. These preliminary results are promising and warrant further studies on the definitive role of PBC gene expression as a biomarker for HNSCC detection and monitoring. Two-color experiment with each individual sample in a single channel. RNA of nucleated blood cells of humans was analysed. Case-control analysis, with 28 cases, patients with head and neck squamous cell carcinoma and 11 controls, without squamous cell carcinoma
2012-09-03 | E-GEOD-39400 | biostudies-arrayexpress
Project description:Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer and is major cause of cancer mortality and morbidity. It emerges within oral cavity, lip, tongue, floor of the mouth, nasopharynx, palate, gingival and larynx, is common cancer worldwide especially in Southeast Asia and Southern China. Despite of the advancements in the understanding of the HNSCC as the disease, the 5 year survival rate remains unchanged at 50% since last three decades. Factors such as advanced stage presentation of the patient and consequent delay in diagnosis contributes to the bleak scenario. Thus, therefore there is dire need of useful biomarkers that can predict HNSCC in early stages and can serve as prognostic indicators or targets for treatment. In the present study, We used iTRAQ (isobaric tags for relative and absolute quantitation)-based quantitative proteomic approach followed by liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential proteins from head and neck cancer cell lines.
2015-01-29 | PXD000737 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE25083: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue GSE25089: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC GSE25091: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: blood controls Refer to individual Series
2011-10-27 | E-GEOD-25093 | biostudies-arrayexpress
Project description:We hypothesized that DKK3 may exert oncogenic function supecifically in head and neck squamous cell carcinoma (HNSCC). DKK3 overexpression in HNSCC cell resulted in elevated cellular proliferation, migration, invasion and in vivo tumor growth. This elevated malignant properties was not driven by Wnt/beta-catenin pathway.
2017-07-22 | GSE84725 | GEO