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New prognostic factor identification by screening changes in differentially expressed genes during oral squamous cell carcinoma progression

ABSTRACT: New prognostic factor identification by screening changes in differentially expressed genes during oral squamous cell carcinoma progression

PROVIDER: PRJNA685414 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13255621.fastq.gz	Fastqsanger.gz
	SRR13255622.fastq.gz	Fastqsanger.gz
	SRR13255623.fastq.gz	Fastqsanger.gz
	SRR13255624.fastq.gz	Fastqsanger.gz
	SRR13255625.fastq.gz	Fastqsanger.gz

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New prognostic factor identification by screening changes in differentially expressed genes during oral squamous cell carcinoma progression

Project description:Identification of differentially expressed genes in human oral squamous cell carcinoma cell line UPCI-SCC-040 after TGF-ß1 treatment compared to untreated controls

2021-05-18 | GSE163241 | GEO

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.

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Differentially expressed miRNAs in human cutaneous squamous cell carcinoma

Project description:To determine the differentially expressed miRNAs in human cutaneous squamous cell carcinoma biopsies versus normal skin samples using microarray analysis.

2015-05-11 | E-MTAB-3409 | biostudies-arrayexpress

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

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

Genetic expression of stage IV oral squamous cell carcinoma according to the recurrence

Project description:To characterize differential gene expression patterns and their actual expression in tissues for recurrent and non-recurrent tumors to identify independent prognostic markers for oral squamous cell carcinoma (OSCC).

2019-09-30 | GSE87593 | GEO

Identification of differentially expressed genes in oral squamous cell carcinoma TCA8113 cells.

Project description:Previous studies have demonstrated that cancer cells with increased levels of aldehyde dehydrogenase 'bright' activity (ALDHbr) exhibit stem cell properties compared with cells exhibiting decreased ALDH activity (ALDHlow). To screen possible biomarkers of cancer stem cells in tongue squamous cell carcinoma, ALDHbr and ALDHlow cells were isolated from the tongue squamous cell carcinoma TCA8113 cell line, and suppression subtractive hybridization was performed to identify differentially expressed genes in the two subpopulations. A total of 240 positive clones were randomly selected for sequencing and were functionally characterized using bioinformatical tools. The results of the present study identified the differential expression of 104 clones, 62 of which corresponded to known genes and 42 of which corresponded to unknown genes. Cluster analysis revealed that the known genes were involved in the regulation of the cell cycle and cell differentiation. In addition, analysis of 10 signaling pathways revealed that genes were markedly altered in the ALDHbr cell subpopulation. Additional study is required to identify the function that these genes serve in the biomolecular regulatory mechanisms of cancer stem cells and to assist in explaining the biological behavior of oral squamous cell carcinoma.

| S-EPMC5754908 | biostudies-literature

Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa.

Project description:Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.

| S-EPMC5458226 | biostudies-literature

A Prognostic Gene Expression Signature for Oropharyngeal Squamous Cell Carcinoma

Project description:A Prognostic Gene Expression Signature for Oropharyngeal Squamous Cell Carcinoma

| PRJNA721375 | ENA

Surface proteoglycans expressions in oral squamous cell carcinoma

Project description:In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2, were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells In situ distributional analysis of these PGs on a total of 149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs.

2013-11-01 | GSE33788 | GEO

Comparative sera proteomics analysis of differentially expressed proteins in oral squamous cell carcinoma.

Project description:BackgroundOral squamous cell carcinoma (OSCC) has increased in incidence from 1990 to 2017, especially in South and Southeast Asia. It is often diagnosed at an advanced stage with a poor prognosis. Therefore, early detection of OSCC is essential to improve the prognosis of OSCC. This study aims to identify the differentially expressed serum proteins as potential biomarkers for oral squamous cell carcinoma (OSCC).MethodsComparative proteomics profiling of serum samples from OSCC patients, oral potentially malignant disorder (OPMD) patients, and healthy individuals were performed using two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry (MS) (n = 60) and bioinformatics analysis. The enzyme-linked immunosorbent assay (ELISA) (n = 120) and immunohistochemistry (IHC) (n = 70) were used to confirm our findings.ResultsThe 2-DE analysis revealed that 20 differentially expressed proteins were detected in OPMD and OSCC (p < 0.05). Bioinformatics analysis indicated that the activation of classical complement, liver X receptor/retinoid X receptor (LXR/RXR) activation, and acute phase response signaling pathway are associated with the development and progression of OSCC. Most of the detected proteins are acute-phase proteins and were related to inflammation and immune responses, including apolipoprotein A-I (APOA1), complement C3 (C3), clusterin (CLU), and haptoglobin (HP). The expression levels of CLU and HP in ELISA are consistent with the findings from the 2-DE analysis, except for the mean serum level of HP in OPMD, whereby it was slightly higher than that in control. IHC results demonstrated that CLU and HP are significantly decreased in OSCC tissues.ConclusionDecreased expression of CLU and HP could serve as complementary biomarkers of OSCC. These proteins may assist in predicting the outcomes of OSCC patients. However, a larger cohort is needed for further investigation.

| S-EPMC8199918 | biostudies-literature

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