Differential expression of oral cancer cell line UM1 and UM2
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE98942 | GEO | 2018/05/16
REPOSITORIES: GEO
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Project description:Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide including the Asian subcontinent. Oral carcinoma exhibits inherent heterogeneity in terms of the sites involved, etiology and pathology. They occur at multiple sites such as tongue, buccal mucosa, maxilla. Effective approaches towards improving survival rates in OSCC patients are primarily focused on early detection of the disease. The early clinical indication of the disease follows the development of potentially malignant lesions (leukoplakia/erythro-leukoplakia) with varied rates of transformation. Currently histopathological evaluation of oral biopsy is generally practiced to evaluate potential malignancy. However, human saliva has been considered to be a valuable medium for discovering biomarker molecules for malignancy. Exfoliated cancer cells may release protein or RNA molecules into the saliva or free molecules may be secreted or leaked from cancer cells representing gene expression changes associated with tumor development. Salivary proteins thus provide a strong option for development of non-invasive, point-of-care assays for screening/early detection of oral cancers. Dysplastic leukoplakia (LP) of the oral cavity is a potentially malignant condition for oral squamous cell carcinoma (OSCC), early detection of which is an unmet clinical need. In an effort to develop non-invasive biomarker based method for early detection of the disease, we have used quantitative mass spectrometry to identify differently abundant salivary proteins in OSCC (buccal mucosa) patients and individuals with potential to develop cancer (oral dysplastic leukoplakia) in comparison to healthy controls (with risk habits such as tobacco chewing or smoking).
2019-11-12 | PXD015722 | Pride
Project description:OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls.
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Project description:Since tobacco abuse have been implicated in oral cancer, we decipher differential saliva proteome profile of tobacco abuser, OSCC and healthy control with the aim of elucidating potential marker in tobacco abuser that might lead to oral cancer.
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Project description:Genome-wide expression array measurements for 9 head and neck squamous cell carcinomas (HNSCC) stratified by worst pattern of invasion (WPOI) Jayakar et al. (2016). Apolipoprotein E promotes invasion in oral squamous cell carcinoma. Li et al. (2013). Validation of the risk model: high-risk classification and tumor pattern of invasion predict outcome for patients with low-stage oral cavity squamous cell carcinoma. Comparison of transcription profiles between OSCC tumors with a more invasive (WPOI 5) versus a less invasive (WPOI 3) pattern of invasion using two independent Illumina platforms.
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Project description:While skin and oral mucosa share many morphological similarities, oral mucosal wounds heal more rapidly than skin wounds. Epithelial cells from oral mucosa exhibit increased migratory and proliferative capacities when compared to cells from skin, suggesting that the improved repair of mucosa may involve intrinsic differences in epithelial cells. This is an exploratory experiment to define the differential microRNA expression of baseline unwounded skin and oral mucosa epithelium.
2019-09-11 | GSE125423 | GEO
Project description:OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls. RNA from 167 OSCC, 17 dysplasia and 45 normal oral tissues were extracted and hybridized to Affymetrix U133 2.0 Plus GeneChip arrays. The differentially expressed genes were identified using GenePlus software and the validation was done using RT-PCR, using independent internal and external datasets.
2011-07-21 | E-GEOD-30784 | biostudies-arrayexpress
Project description:Understanding the dynamics of the immune microenvironment is critical to the development of immuno-prevention strategies for the prevention of oral potentially malignant disorders transformation to oral squamous cell carcinoma (OSCC). We generated gene expression profiles of the microdissected epithelial and stromal compartments normal mucosa, hyperplasia, dysplasia and invasive tumors in the 4-nitroquinolein (4-NQO) murine model of oral carcinogenesis. Most gene expression changes were observed in the stromal compartment and related to immune biological processes. Immune cell deconvolution identified infiltration by the macrophage population as the most important quantitatively especially at the stage of dysplasia. In 86 patients with oral leukoplakia, three M2 macrophages signatures were independently associated and highly predictive of improved oral cancer-free survival.
2022-01-11 | GSE164619 | GEO
Project description:Background: The differential abundance of cell-free RNAs in bodily fluids is emerging as a promising tool for the non-invasive molecular diagnosis of cancer. Human saliva is considered a promising source of non-invasive biomarkers of diagnostic value for oral cancer detection. This study aims to identify diagnostic potent salivary RNAs in oral squamous cell carcinoma (OSCC)-patients by RNA-Sequencing. Method: Unstimulated saliva was collected from 5 normal control (NC) individuals and 9 OSCC patients (PS) with prior consent and ethical committee approvals. Total RNA isolated from cell-free saliva (CFS) supernatant was used to prepare small RNA libraries and sequenced on the Ion Torrent S5 platform. The sequencing reads were aligned to the human genome (hg19) using Bowtie 2, and the differential expression analysis was performed using RUVSeq and DESeq2. Mapped reads were screened across miRBase (v22) annotations for miRNAs and Gencode (v19) annotation for other RNAs. Reads were quantified by the Featurecount (v1.4.6) module of the R-package. The microbial-RNA enrichment analysis was determined using the One Codex platform. Result: RNA-sequencing detected protein-coding transcripts (PCTs), long-intergenic RNAs (lincRNAs), microRNAs (miRNAs), small nuclear RNAs (snRNAs), transfer RNAs (tRNAs) and pseudogenes from the saliva of PS and HC samples. Transcriptome analyses revealed 89 PCTs, 18 lincRNAs and 6 miRNAs differentially expressed between PS and HC with a log2fold change ≥ 1 or ≤ -1 and p-value < 0.05. Gene ontology and pathway enrichment analyses indicated a significant correlation of the identified PCTs and miRNAs to various cancer-related pathways that may have implications in the pathogenesis of OSCC. Interestingly, unmapped non-human reads aligned to the microbial reference genomes. Further analyses of these microbial sequence reads revealed a significant microbial dysbiosis differentiating PS from HC. Metabolic pathways and functional analysis of the identified microbial phylotypes showed gene ontologies associated with inflammation, cell proliferation, ROS generation, and a range of metabolic processes. Conclusion: We report novel panels of differentially expressed PCTs, miRNAs and lincRNAs distinguishing PS from HC. Importantly, our results also provide evidence for oral microbial dysbiosis that appears to have pathological implications in OSCC. Summarily, this study provides a comprehensive landscape of salivary RNAs that can be exploited as non-invasive biomarkers for OSCC detection.
2023-01-30 | GSE176077 | GEO
Project description:Purpose Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder. Experimental Design Discovery phase utilized HumanMethylation27 DNA Analysis BeadChip assay in 18 OLD and 5 control samples. The differently methylated loci and the global DNA methylation surrogate LINE-, were further validated in an independent sample set consisting in 158 OLD and 65 controls. Results DNA methylation profile of the OLD showed only minor significant differences when compared to controls. MGC40178, ADORA1 and LINE-1 were slightly hypomethylated in 23, 40 and 43 % of the OLD samples respectively, while only in 13, 18 and 15% of the controls. Conclusions In summary, our data indicates that the frequency of aberrant DNA alteration is very low in OLD, which support the low rate of malignization of this oral potentially malignant disorder.
2014-04-30 | GSE50608 | GEO
Project description:Genome wide DNA methylation profiling of OSCC tissue samples, oral lichen planus tissue samples and normal controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 15 OSCC, 8 lichen planus and 18 control samples.
2019-04-17 | GSE123781 | GEO