Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LncRNA expression profiles in areca nut chewing induced Tongue Squamous Cell Carcinoma (TSCC) and matched paracancerous tissues

ABSTRACT: Chewing betel nut is an important risk factor for the carcinogenesis of tongue squamous cell carcinoma (TSCC), but the mechanism is still unknown.To screen the lncRNAs associated with betel nut chewing-induced TSCC and identify potential biomarkers for the TSCC, we collected 5 pairs of TSCC and paracancerous tissues and monitored the resultant lncRNA and mRNA expression profiles using an lncRNA microarray. All 5 patients have a history of areca nut chewing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE139869 | GEO | 2020/10/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

LncRNA expression profiles in areca nut chewing induced Tongue Squamous Cell Carcinoma (TSCC) and matched paracancerous tissues

Project description:LncRNA expression profiles in areca nut chewing induced Tongue Squamous Cell Carcinoma (TSCC) and matched paracancerous tissues

| PRJNA587415 | ENA

Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.

2018-05-31 | E-MTAB-4654 | biostudies-arrayexpress

Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

2018-05-31 | E-MTAB-4653 | biostudies-arrayexpress

Development and application of mass spectrometric molecular networking for analyzing ingredients of areca nut

Project description:Areca nut(Areca catechu L.) is commonly consumed as a chewing food in the Asian region. However, the investigations into the components of areca nut are limited. In this study, we have developed an approach that combines mass spectrometry with feature-based molecular network to explore the chemical characteristics of the areca nut. In comparison to the conventional method, this technique demonstrates a superior capability in annotating unknown compounds present in areca nut. We annotated a total of 52 compounds, including one potential previously unreported alkaloids, one carbohydrate, and one phenol and confirmed the presence of 6 of them by comparing with commercial standards. The validated method was used to evaluate chemical features of areca nut at different growth stages, annotating 25 compounds as potential biomarkers for distinguishing areca nut growth stages. Therefore, this approach offers a rapid and accurate method for the component analysis of areca nut.

2023-11-10 | MSV000093351 | MassIVE

Role of areca nut induced TGF-β and epithelial mesenchymal interaction in pathogenesis of precancerous Oral submucous fibrosis

Project description:To understand the role of areca nut and TGF-β induced gene expression changes in fibroblasts and its contibution in the manifestation of Oral submucous fibrosis, we studied gene expression profile in primary human gingival fibroblast (hGF) cells following treatment with areca nut, TGF-β and both together. Control Vs Areca nut 5 µg/ml water extract (5H) (2), Contro Vs TGF-β (2), Control Vs Areca nut (5 µg/ml) and TGF-β (5 ng/ml) (5H+T) (2). (2)- Biological duplicates.

2015-07-06 | E-GEOD-59414 | biostudies-arrayexpress

Activation of TGF-beta pathway by areca nut constituents: A possible cause of Oral submucous fibrosis.

2013-05-22 | GSE38227 | GEO

Role of areca nut induced TGF-β and epithelial mesenchymal interaction in pathogenesis of precancerous Oral submucous fibrosis

2015-07-06 | GSE59414 | GEO

Activation of TGF-beta pathway by areca nut constituents: A possible cause of Oral submucous fibrosis.

Project description:To understand the role of areca nut constituents in manifestation of Oral submucous fibrosis, we studied gene expression profile in epithelial cells following areca nut water extract treatment. A comaprison with TGF-beta induced gene expression changes were performed as epithelial cells were predicted to be source of TGF-beta. Control Vs Areca nut 5 ug/ml water extract (5H) (2), Contro Vs TGF-beta (2), Control Vs ALK5 (TbetaRI inhibitor) (2), Control Vs 5H + ALK5 inhibitor (2). (2)- Biological duplicates.

2013-05-22 | E-GEOD-38227 | biostudies-arrayexpress

GNPS - Development and application of mass spectrometric molecular networking for analyzing ingredients of areca nut

2023-11-10 | MSV000093351 | GNPS

Transcriptomic analysis of immortalized oral keratinocytes (n=2) and oral squamous cell carcinoma cells (n=5)

Project description:Due to betel nut chewing habit, oral cancer is the fourth leading cause of cancer death among Taiwanese men. In addition, oral cancer is the most common malignancy observed in men with 25-44 years old, alerting an urgent need to curb this disease. It is hypothesized that betel nut ingredients exhibit carcinogenic effects on the oral epithelium and alter local immune system. As a step to identify potential oncogenic gene fusions in Taiwanese oral cancer cells, total RNAs of two immortalized oral keratinocytes (CGHNK2, -K6) and five oral squamous cell carcinoma cell lines (C9, OC3, OEC-M1, TW2.6) were subjected to RNA-sequencing analysis, followed by an in-house bioinformatic pipeline for fusion gene detection.

2020-07-07 | GSE150469 | GEO

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