Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA expression in tongue squamous cell carcinoma, tumour free tongue tissue and control tongue

ABSTRACT: Tongue squamous cell carcinoma is a tumour type with rather low five year survival, around 60%. The poor survival rate has been ascribed to late detection, a high frequency of locoregional recurrence, the occurrence of secondary primary tumours and death due to comorbidity. One reason for development of recurrence is thought to be the existence of transformed cells in areas adjacent to the primary tumour, cancerization field effect. The aim of this study was to map the changes in the tumour free tongue tissue adjacent to tongue tumours compared with healthy control tongue tissue to better understand the cancerization field effect. Tissue biopsies were collected from tumour (T) and tumour free tissue adjacent to the tumour (TF) from patients with tongue squamous cell carcinoma. Control tissue was collected from latter border of the tongue of tumour free healthy volunteers (C). All samples were homogenized and RNA was extracted. The RNA was biotin labelled and run on Illumina HT-12 bead chip array.

ORGANISM(S): Homo sapiens

SUBMITTER: Linda Boldrup

PROVIDER: E-MTAB-4678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA expression in squamous cell carcinoma of the tongue and normal tissue adjacent to squamous cell carcinoma of the tongue

Project description:Increasing incidence of squamous cell carcinoma of the tongue (SCCT) in young patients has been reported. In this study, we aimed to investigate the transcriptional profiles in tumour and matched tumour-free tissue from patients with SCCT. Particularly, transcriptional profiles of young patients (< 40 years) were compared with those of old patients (> 50 years), in order to know whether young patients are transcriptionally different to old patients. A total of 12 patients with SCCT treated at The University hospital of Umeå (NUS) were recruited. Three patients were younger than 40 years old at diagnosis (young patient), and the other 9 patients were older than 50 years old (old patient). Biopsies of tumour and tumour-free tissues were fresh-frozen in liquid nitrogen and stored at -80°C until nuclear acid extraction.

2019-03-30 | E-MTAB-5534 | biostudies-arrayexpress

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

Project description:DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. 83 FFPE primary OTSCC tumour samples were analysed in one experimental run.

2016-07-18 | E-GEOD-79556 | biostudies-arrayexpress

Tongue tissue gene profile in 4NQO induced tongue carcinogenesis before and after IL-1Ra interference

Project description:Nine groups of rat tongue tissue RNA samples, including three from normal control, three from 4NQO induced tongue tissue, and three from 4NQO induced and IL-1Ra interference tongue tissue (3 rats per group) were collected for gene microarray hybridization.

2017-02-11 | GSE42855 | GEO

Gene expression profiling of archival tongue carcinoma and normal tongue tissue

Project description:This SuperSeries is composed of the following subset Series: GSE34105: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples) GSE34106: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset) Refer to individual Series

2012-05-10 | E-GEOD-34115 | biostudies-arrayexpress

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

2016-07-18 | GSE79556 | GEO

Analysis of differentially expressed long noncoding RNAs, circular RNAs and the associated TF‐mRNA network in tongue squamous cell carcinoma

Project description:Purpose: The purpose of this study was to identify aberrantly expressed lncRNAs, circular RNAs and the associated TF‐mRNA network in TSCC. Methods: Tongue tumor noncoding and mRNA profiles of tongue squamous cell carcinoma and adjacent noncancerous tissues were generated by deep sequencing, using Illumina HiSeq 4000. Results: Using an optimized data analysis workflow. Conclusions: we found a profile of dysregulated lncRNAs, TFs and mRNAs that could serve as prospective clinical biomarkers because of their tissue specificity and association with the tumorigenesis and progression of TSCC.

2020-08-04 | GSE149008 | GEO

Fasting Cycles Retard Growth of Tumors and Sensitize a Range of Cancer Cell Types to Chemotherapy

Project description:Short-term starvation (STS or fasting) provides protection to normal cells, mice, and possibly patients from a variety of chemotherapy drugs, but the possibility that it may also protect tumor cells renders its translational potential uncertain. Here we show that fasting cycles can be as effective as toxic chemotherapy drugs, and increase chemotherapy efficacy in the treatment of melanoma, glioma, breast cancer, and neuroblastoma. In vitro, STS sensitizes to chemotherapy 15 of the 17 cancer cell lines tested. In combination with chemotherapy STS results in a synergistic 20-fold increase in DNA damage, increased phosphorylation of pro-aging genes AKT and S6 kinase, reduced expression of stress resistance transcription factors FOXO3a and NFkB, elevated superoxide, and activated caspase-3; all changes not observed in normal tissues. Several of these effects are linked to the activity of heme oxygenase 1 (HO-1), whose modulation was sufficient to regulate chemotherapy-dependent cell death in breast cancer cells. These studies suggest that multiple fasting cycles have the potential to replace certain toxic chemotherapy drugs and to sensitize a wide range of tumors to chemotherapy. To obtain an unbiased view of the gene expression changes occurring in cancer cells in response to fasting, we performed genome-wide microarray analyses, using Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA), on the subcutaneous 4T1 breast cancer tumor mass, heart, muscle and liver tissues from balb-c mice that were either fasted for 48 hours or fed an ad lib diet. Three mice from each of the starvation and the ad lib fed groups were used for the array studies.

2012-03-21 | E-GEOD-28556 | biostudies-arrayexpress

RNA-seq of intestinal cancer GEMMs

Project description:Intestinal tumours from genetically engeenierd mouse modesl (GEMMs), of various gentopyes, were isolated at endpoint and RNA was isolated. In an additional experiment, epithelial tumour organoids were isolated at end point and grown in vitro. These organoids were harvested 72 hours after seeding and RNA was isolated.

2019-09-16 | E-MTAB-6363 | biostudies-arrayexpress

Tongue immune compartment analysis reveals spatial macrophage heterogeneity [bulk RNA-Seq]

Project description:The tongue is a unique muscular organ situated in the oral cavity where it is involved in taste sensation, mastication and articulation. As a barrier organ, which is constantly exposed to environmental pathogens,the tongue isexpected to host animmune cell network ensuringlocal immune defence. However, the composition and the transcriptional landscape of the tongue immune system are currently not completely defined. Here we characterised the tissue-resident immune compartment of the murine tongue during development, health anddisease, combining single cell RNA-sequencing with in situ immunophenotyping. We identified distinct local immune cell populations and described two specific subsets of tongue-resident macrophages occupying discrete anatomical niches. Cx3cr1+macrophages were located specifically in the highly innervated lamina propria beneath the tongue epidermis and at times in close proximity to fungiform papillae.Folr2+ macrophages were detected in deeper muscular tissue. The two macrophage subsets originate from a common proliferative precursor during early postnatal development and responded differently to systemic LPSin vivo. Our description of the under-investigated tongue immune system sets a starting point to facilitate research on tongue immune-physiology and pathology including cancer and taste disorders.

2022-06-29 | GSE205158 | GEO

Tongue immune compartment analysis reveals spatial macrophage heterogeneity [bulk RNA-Seq]

2022-06-29 | GSE205157 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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