Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Altered Epigenetic Regulation of Homeobox Genes in Human Oral Squamous Cell Carcinoma Cells

ABSTRACT: To gain insight into the molecular changes during OSCC carcinogenesis, we performed unbiased, whole genome deep sequencing (RNA-seq) using RNA isolated from cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51415 | GEO | 2013/10/19

SECONDARY ACCESSION(S): PRJNA222994

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Altered Epigenetic Regulation of Homeobox Genes in Human Oral Squamous Cell Carcinoma Cells

Project description:To gain insight into the molecular changes during OSCC carcinogenesis, we performed unbiased, whole genome deep sequencing (RNA-seq) using RNA isolated from cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells. OKF6-TERT1R cells and SCC-9 cells were plated in 10 cm2 tissue culture plates at the density of 2 × 106 cells/plate and treated with 1 μM RA or vehicle (0.1% ethanol) for 48 hours. Experiment includes 3 independent biological replicates. Note: All samples in SRA were assigned the same sample accession (GSM1245064 1). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2013-10-19 | E-GEOD-51415 | biostudies-arrayexpress

Altered DNA Methylation Patterns in Human Oral Squamous Cell Carcinoma Cells

2014-10-28 | GSE51752 | GEO

Altered DNA Methylation Patterns in Human Oral Squamous Cell Carcinoma Cells

Project description:To gain insight into the DNA methylation changes during OSCC carcinogenesis, we utilized cytosine conversion and next generation sequencing based technique- enhanced reduced representation bisulfite sequencing (ERRBS) - to assess DNA methylation in cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells. OKF6-TERT1R cells and SCC-9 cells were plated in 10 cm2 tissue culture plates at the density of 2 M-CM-^W 106 cells/plate. Total genomic DNA was extracted from OKF6-TERT1R and SCC-9 cells using DNeasy Blood & Tissue Kit (Qiagen, Germantown, MD, USA), including an RNAse treatment step.

2014-10-28 | E-GEOD-51752 | biostudies-arrayexpress

Reductionist approach using primary and metastatic cell-derived extracellular vesicles prospect proteins associated with oral cancer prognosis

Project description:Oral squamous cell carcinoma (OSCC) shows high mortality rates that are largely associated with the presence of lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Here, we used a reductionist approach mapping the proteomic, miRNA, metabolomic and lipidomic profiles of extracellular vesicles (EVs) from human primary tumor (SCC-9 cells) and matched lymph node metastasis (LN1 cells) to explore the role of EV cargo in OSCC metastasis. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites and 64 lipids differentially abundant between LN1 and SCC-9-derived EVs. A multi-omics integration indicated 11 ‘hub proteins’ significantly modulated in the metastatic site when compared to primary site-derived EVs, seven of them correlated with aggressiveness in cancer patients. The multi-omics approach allowed the prospection of proteins transported by EVs that potentially serves as prognostic markers in OSCC.

2021-07-19 | PXD019216 | Pride

Affymetrix SNP array data for oral squamous cell carcinoma and oral dysplasia samples

Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. Oral carcinogenesis is a multifactorial process involving numerous genetic changes that affect the activity of oncogenes, tumor suppressor genes and other classes of disease-related genes.Therefore, to identify the responsive genes for progression of oral dysplasia or OSCC, we here performed CGH analysis to DNA from oral dysplasia and OSCC by microdissection Copy number analysis of Affymetrix 250K SNP arrays was performed for 8 oral dysplasia samples, 8 oral squamous cell carcinoma samples, using microdissection

2013-10-22 | E-GEOD-51265 | biostudies-arrayexpress

Affymetrix SNP array data for oral squamous cell carcinoma and oral dysplasia samples

2013-10-22 | GSE51265 | GEO

Gene expression profilings of normal human oral keratinocyte (HOK) and dysplastic oral keratinocyte cell line from a heavy smoker (DOK)

Project description:In our previous study, we identified global genetic and epigenetic aberrations in the tumors of oral squamous cell carcinoma (OSCC) patients who were habitual smokers. We hypothesized that cigarette smoke might play a role in oral malignant transformation. DOK cell line is a dysplasitc oral keratinocyte derived from a heavy smoker with OSCC. The differentially expressed genes between DOK and normal human oral keratinocytes (HOK) may provide important information about OSCC carcinogenesis mediated by cigarette smoking. Total RNA was collected from DOK and HOK cells followed by gene expression microarray analysis.

2015-12-31 | E-GEOD-54861 | biostudies-arrayexpress

Gene expression profilings of normal human oral keratinocyte (HOK) and dysplastic oral keratinocyte cell line from a heavy smoker (DOK)

2015-12-31 | GSE54861 | GEO

Skin cancer-associated S. aureus downregulates DNA repair mechanisms, and promotes oxidative stress and DNA damage in human keratinocytes

Project description:Actinic keratoses (AK) are premalignant lesions common on photo-damaged skin that, over time, can progress to squamous cell carcinoma (SCC). A high bacterial load of Staphylococcus aureus is associated with AK and SCC but it is unknown whether this has a direct impact on skin cancer development. To determine whether S. aureus is able to trigger pro-tumorigenic skin responses, we performed RNAseq and shotgun proteomics on primary human keratinocytes after challenge with sterile culture supernatant (‘secretome’) from S. aureus clinical strains isolated from AK and SCC. Certain S. aureus secretomes induced keratinocytes to overexpress SCC biomarkers that have been associated with skin carcinogenesis, and upregulate the expression of enzymes linked with reduced skin barrier function. Further, S. aureus secretomes downregulated DNA repair mechanisms and induced oxidative stress markers. Subsequent experiments confirmed that exposure to SCC-derived S. aureus secretomes lead to increased intracellular ROS levels and DNA damage in primary human keratinocytes. Altogether, this study reveal a novel mechanism for the pro-tumorigenic activity of S. aureus. Further studies are required to determine whether S. aureus products promote SCC development in vivo, which would have important implications for the treatment of AK and prevention of SCC.

2022-05-11 | PXD031622 | Pride

Identification of oral carcinoma miRNA involved in Wnt/b-catenin signaling

Project description:MicroRNAs (miRNAs) participate in many biological processes and have emerged as key players in carcinogenesis. In order to identify changes in miRNAs specific for betelquid-associated oral squamous cell carcinoma (OSCC), we investigated the expression profiles of 858 miRNAs in a panel of 40 pairs of OSCC specimens and their matched non-tumorous epithelial counterparts. Eighty-four miRNAs were differentially expressed in the OSCC specimens compared to the matched tissue. Among these miRNAs, 19 downregulated miRNAs located in the chromosome 14q32.2 miRNA cluster region were analyzed. This miRNA cluster resides within a parentally imprinted region known to be important in development and growth. The re-expression of miR-329 and miR-410from this cluster significantly reduced OSCC cell proliferation and invasion and downregulated Wnt-7b, an activator of the Wnt/b-catenin pathway. Furthermore, the expression of those 2 miRNAs was restored by 5-aza-2′-deoxycytidine treatment and the expression levels of the 2 miRNAs were inversely correlated with the hypermethylation of the Meg-3 promoter in OSCC cells. Specifically, arecoline, a major betel nut alkaloid, reduces miR-329 and miR-410 expression. Our results thus provide a novel molecular insight into how betel quid may contribute to oral carcinogenesis through the epigenetic silencing of tumor suppressor miRNAs targeting the Wnt/b-catenin signaling pathway. Total RNA was obtained from 40 pairs of OSCC patients with tumor specimens and their adjacent non-tumorous epithelia.

2015-01-07 | E-GEOD-45238 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data