RNA-Seq of oral squamous cell carcinomas and matched normal tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tuch BB
PROVIDER: S-ECPF-GEOD-20116 | biostudies-other | 2010
REPOSITORIES: biostudies-other
Similar Datasets
Project description:RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance.
2010-02-25 | GSE20116 | GEO
Project description:RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance. Oral squamous cell carcinomas (OSCC) and matched normal tissue from 3 patients.
2010-02-25 | E-GEOD-20116 | biostudies-arrayexpress
Project description:Abnormal expression of non-coding circular RNAs (circRNAs) have been reported in many types of tumors. circRNA have been suggested to be an ideal candidate biomarker for diagnostic and therapeutic implications in cancers. The aim of this study was to assess the circRNA expression profile of laryngeal squamous cell carcinomas (LSCC). The biopsy samples from patients with LSCC were obtained intra-operatively. The circRNA expression was performed using secondary sequencing. Among 10 patients with LSCC, 2 were well differentiated, 3 were moderately differentiated and 5 were adjunctive samples with normal and LSCC tissues. A total of 21,444 distinct circRNA candidates were detected. Among them, we defined the statistical criteria for selecting aberrant-expressed circRNA using a q-value of < 0.001 with a fold change of > 2.0 or < 0.5. A total of 29 circRNA were upregulated and 19 circRNA were downregulated significantly in the LSCC tissues. The intersection of these dysregulated circRNAs of normal-well differentiated set and normal-moderately differentiated set was then assessed to narrow the upregulated and downregulated circRNAs down to 18 and 5 respectively. Furthermore, an association of the circRNA-miRNA-mRNA was investigated, showing that 20 dysregulated circRNA successfully predicted an interaction with several cancer-related miRNAs. Finally, a further KEGG analysis showed that PPAR, Axon guidance, Wnt and Cell cycle signaling pathway were key putative pathways in the process of LSCC. hsa_circ:chr20:31876585-31,897,648 was found to be able to differentiate most of LSCC from the matching normal tissues. This observational study demonstrated dysregulation of circRNA in LSCC, which may have an impact on development of potential biomarkers in this disease. Validation of down-regulation of hsa_circ:chr20:31876585-31,897,648 in LSCC compared to each adjunctive tissue by Q-RT-PCR, indicating that hsa_circ:chr20:31876585-31,897,648 may be a novel promising tumor suppresser in LSCC.
| S-EPMC5930968 | biostudies-literature
Project description:Nearly 50% of patients with oral squamous cell carcinoma (OSCC) die of metastases or locoregional recurrence. Metastasis is mediated by cancer cell adhesion, migration, and invasion. Osteoactivin (OA) overexpression plays a role in metastases in several malignancies. The aims were to determine how integrin interactions modulate OA-induced OSCC cell migration; and to investigate OA effects on cell survival and proliferation. We confirmed OA mRNA and protein overexpression in OSCC cell lines. We assessed OA's interactions with integrins using adhesion inhibition assays, fluorescent immunocytochemistry and co-immunoprecipitation. We investigated OA-mediated activation of mitogen-activated protein kinases (MAPKs) and cell survival. Integrin inhibition effects on OA-mediated cell migration were determined. We assessed effects of OA knock-down on cell migration and proliferation. OA is overexpressed in OSCC cell lines, and serves as a migration-promoting adhesion molecule. OA co-localized with integrin subunits, and co-immunoprecipitated with the subunits. Integrin blocking antibodies, especially those directed against the β1 subunit, inhibited cell adhesion (P = 0.03 for SCC15 cells). Adhesion to OA activated MAPKs in UMSCC14a cells and OA treatment promoted survival of SCC15 cells. Integrin-neutralizing antibodies enhanced cell migration with OA in the extracellular matrix. OA knock-down resulted in decreased proliferation of SCC15 and SCC25 cells, but did not inhibit cell migration. OA in the extracellular matrix promotes OSCC cell adhesion and migration, and may be a novel target in the prevention of HNSCC spread. J. Cell. Physiol. 231: 1761-1770, 2016. © 2015 Wiley Periodicals, Inc.
| S-EPMC4836998 | biostudies-literature
Project description:The endothelial-specific receptor, tyrosine kinase with immunoglobulin-like loops and epidermal growth factor homology domains-2 (Tie2) is a member of the tyrosine kinase family and is ubiquitous in normal tissues; however, little is known about the mechanisms and roles of Tie2 in oral squamous cell carcinomas (OSCCs). In the current study, we investigated the expression status of Tie2 in OSCCs by quantitative reverse transcriptase-polymerase chain reaction, immunoblotting, and immunohistochemistry and the functional mechanisms of Tie2 using its overexpressed OSCC (oeTie2) cells and Tie2 blocking by its antibody. We found that Tie2 expression was down-regulated significantly (p < 0.05) in OSCCs compared with normal counterparts in vitro and in vivo. Interestingly, oeTie2 cells showed higher cellular adhesion (p < 0.05) and lower cellular invasion (p < 0.05) compared with control cells; whereas there was similar cellular proliferation in both transfectants. Furthermore, cellular adhesion was inhibited and invasion was activated by Tie2 function-blocking antibody (p < 0.05), indicating that Tie2 directly regulates cellular adhesion and invasion. As expected, among the clinical variables analyzed, Tie2-positivity in patients with OSCC was correlated closely with negative lymph node metastasis. These results suggested for the first time that Tie2 plays an important role in tumor metastasis and may be a potential biomarker for OSCC metastasis.
| S-EPMC4820737 | biostudies-literature
Project description:Esophageal cancer (EC) is the eighth most common cancer globally in 2012 and predominantly occurs in the man (Enzinger and Mayer, 2003; Conteduca et al., 2012). EC is classified mainly into two types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, accounting for 60-70% and 20-30% of all EC cases, respectively. In a previous statistical study it was reported that the numbers of new EC cases and EC-related deaths worldwide in 2008 were estimated to be 482,300 and 406,800, respectively (Jemal et al., 2011). This high mortality rate is largely due to the characteristics of EC such as frequent distant/local metastasis and poor subjective symptoms leading to difficulty with early diagnosis. Patients affected with EC diagnosed at late stages mostly have unsatisfactory prognosis, even though various therapeutic options are available. Therefore, there is an urgent need to develop effective methods that enable the early detection of EC (Orringer, 1993), prompting us to search for novel biomarkers for EC. Here, we provide datasets from RNA-Seq analysis of Het-1A, a normal human esophageal squamous cell line (Stoner et al., 1991), and TE-1, TE-5, and TE-8, which are well-, poorly-, and moderately-differentiated ESCC-derived cell lines, respectively (Nishihira et al., 1993). The raw data of these experiments have been deposited at DNA Data Bank of Japan (DDBJ) under the accession IDs DRR084199, DRR084200, DRR084201, and DRR084202.
| S-EPMC5304241 | biostudies-literature
Project description:Oral squamous cell carcinoma (SCC) is the most common malignant tumor in India with 5-year survival rates totaling <50%. Recently, dysregulation of non-coding RNA was reported as a potential hallmark of carcinogenesis. Colon Cancer Associated Transcript 1 (CCAT1), an lncRNA located in chromosome 8q24, close to the c-Myc gene, has been reported to be overexpressed in many human cancers. In the present study, the authors analyzed the expression of CCAT1, c-Myc and the miRNAs miR155-5p, let7b-5p, miR490-3p and miR218-5p sponged by CCAT1 in 60 oral tumor and 8 normal tissue samples by reverse transcription-quantitative polymerase chain reaction. CCAT1 was significantly overexpressed in 27% (16/60) of oral tumors. Interestingly, a high level of c-Myc expression was observed in all CCAT1 overexpressing cases (P=0.0473). Furthermore, CCAT1 overexpression significantly downregulated miR155-5p (P=0.03) and let7b-5p (P<0.0001). Oral cancer cases expressing high level of CCAT1 (P=0.01) presented poor therapeutic outcome. To the best of the authors' knowledge, this is the first study to report the overexpression of the CCAT1 in oral SCCs, and the results suggested that CCAT1 overexpression may sponge miR155-5p and let7b-5p, and may account for poor treatment response.
| S-EPMC5374962 | biostudies-other
Project description:The Atlas human cDNA expression array was used to evaluate gene expression profile changes in the genesis of human lung adenocarcinomas and squamous cell carcinomas. Gene expression changes between adenocarcinomas and squamous cell carcinomas were also analyzed. Of the 588 gene targets, 262 genes were expressed in these tissues and, of these, 45 genes were differentially expressed by at least two-fold in tumor tissues compared to corresponding normal tissues. Semiquantitative reverse-transcriptase polymerase chain reaction was used to confirm gene expression changes. Only those genes that reflected changes in >50% of the analyzed tissues were included in the final analysis. Ultimately, 26 genes were evaluated with 14 genes overexpressed and 12 genes underexpressed compared to matching normal lung tissues. Although similar expression changes were detected in adenocarcinomas and squamous cell carcinomas for most of the genes analyzed, some subtype-specific differences were also found. Genes encoding cell cycle regulators, intracellular signal transducers, cell receptor and adhesion molecules, growth factors, oncogenes, and apoptotic effectors were differentially expressed in this study. These gene expression changes may directly contribute to the initiation or progression of human lung cancer or may be secondary effects of the tumorigenesis process. Regardless, many of these differences may be useful in the diagnosis and/or treatment of this deadly disease.
| S-EPMC1550320 | biostudies-literature
Project description:The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.
| S-EPMC5481414 | biostudies-literature
Project description:Gene functionality is closely connected to its expression specificity across tissues and cell types. RNA-Seq is a powerful quantitative tool to explore genome wide expression. The aim of this study is to provide a comprehensive RNA-Seq dataset across the same 13 tissues for mouse and rat, two of the most relevant species for biomedical research. The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. We also describe our bioinformatics pipeline to process and technically validate the data. Principal component analysis shows that tissue samples from both species cluster similarly. We show by comparative genomics that many genes with high sequence identity with respect to their human orthologues also have a highly correlated tissue distribution profile and are in agreement with manually curated literature data for human. In summary, the present study provides a unique resource for comparative genomics and will facilitate the analysis of tissue specificity and cross-species conservation in higher organisms.
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