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Transcript profiling of normal oral keratinocytes and the tongue squamous cell carcinoma line LK0412

ABSTRACT: The current study analyzed a unique, serum-free medium derived tongue squamous cell carcinoma (TSCC) line termed LK0412 relative to the normal state to elucidate biomarkers at the protein and transcript level. A bioinformatics approach using Gene Ontology categories, gene networks and signature evaluation was applied to combine the protein and transcript data for identification of various gene signatures. The generated signatures were further assessed in public available data sets from normal and tumor tongue tissues. The analysis identified a novel gene signature that may improve the diagnosis and treatment of TSCC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE21866 | GEO | 2014/01/31

SECONDARY ACCESSION(S): PRJNA127051

REPOSITORIES: GEO

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Transcript profiling of normal oral keratinocytes and the tongue squamous cell carcinoma line LK0412

Project description:The current study analyzed a unique, serum-free medium derived tongue squamous cell carcinoma (TSCC) line termed LK0412 relative to the normal state to elucidate biomarkers at the protein and transcript level. A bioinformatics approach using Gene Ontology categories, gene networks and signature evaluation was applied to combine the protein and transcript data for identification of various gene signatures. The generated signatures were further assessed in public available data sets from normal and tumor tongue tissues. The analysis identified a novel gene signature that may improve the diagnosis and treatment of TSCC. Analysis of differential gene expression in LK0412 relative to the normal state. Both normal and LK0412 cells were cultured under a standardized serum-free condition.

2014-01-31 | E-GEOD-21866 | biostudies-arrayexpress

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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.

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Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

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MicroRNA Expression Profiling of Saliva in Tongue Squamous Cell Carcinoma Patients

Project description:41% of all oral carcinomas have been found to localize at tongue, where they were characterized as being aggressive and having capacity to locally invade and relapse frequently. Despite considerable enhancements in the cancer diagnosis and treatment techniques, tongue squamous cell carcinoma (TSCC) still remains to be one of the most common and lethal cancer types in the head and neck region. In this study, we aimed to identify a signature of saliva-specific microRNAs (miRNAs) expression in TSCC patients. To explore putative diagnostic biomarkers, we compared the miRNA profiles of saliva samples obtained from 3 TSCC patients and 4 healthy control individual using Agilent miRNA microarray (V19). Three of the differentially expressed miRNAs were selected for further validation with quantitative reverse-transcription PCR (qRT-PCR) using saliva samples of 25 TSCC patients and 25 healthy control individuals. Microarray analysis demonstrated that 428 miRNA probes were deregulated in TSCC patients when compared to control group and qRT-PCR results validated the reduced expression of miR-139-5p in TSCC saliva. Further analysis of post-operative saliva samples of TSCC patients revealed that miR-139-5p level elevated to normal level after surgery, pointing its diagnostic and prognostic power. As a conclusion, we propose saliva as a feasible source in routine patient examination for early diagnosis of TSCC patients, and our results suggest saliva miR-139-5p as a novel potential diagnostic marker.

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Project description:MicroRNAs play a crucial role in tumorigenesis. However, the value of microRNAs in the diagnosis and treatment of tongue squamous cell carcinoma (TSCC) still await investigations. To identify the microRNAs associated with the metastasis of TSCC, we analyzed the transcriptomic difference between metastatic and the non-metastatic TSCC tissue. We identified a set of metastasis-related microRNAs with potential prognostic value.

2016-12-31 | GSE81821 | GEO

Expression analysis of LncRNA in Tongue Squamous Cell Carcinoma (TSCC) and matched nonmalignant tissues (NC)

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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.

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