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Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [miRNA-Seq]

ABSTRACT: The purpose of this study was to systematically profile the expression of both mRNAs and miRNAs in OSCC and its premalignant disease to identify some novel potential biomarkers for the detection of malignant transformation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70664 | GEO | 2017/02/10

SECONDARY ACCESSION(S): PRJNA289314

REPOSITORIES: GEO

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Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [mRNA-Seq]

Project description:The purpose of this study was to systematically profile the expression of both mRNAs and miRNAs in OSCC and its premalignant disease to identify some novel potential biomarkers for the detection of malignant transformation.

2017-02-10 | GSE70665 | GEO

Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation

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Expression of m6A methylation-modified circRNA in malignant transformation of oral leukoplakia tissue

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Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.

Project description:Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.

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Genotyping of human premalignant oral keratinocyte line SVpgC2a loss of heterozygosity (LOH) during FOXM1B-induced malignant transformation

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2009-06-23 | E-GEOD-11782 | biostudies-arrayexpress

Real-time quantitative PCR analysis of 232 microRNAs in human oral tissues

Project description:Oral squamous cell carcinoma (OSCC) is the sixth most common cause of cancer mortality worldwide, and the five-year survival rate remains low in patients with advanced OSCC. Many studies indicate that microRNAs (miRNAs) may paly critical roles in OSCC carcinogenesis, but the dynamic composition and functions of miRNAs-mRNAs regulatory networks in OSCC pathogenesis remain largely unknown. Thus, detailed investigations of OSCC-associated miRNAs and their regulated networks may provide insights into mechanistic understanding of OSCC progression and development of new strategies of OSCC management. To this end, we first sought to compile from a systems perspective the miRNA-mRNA networks underlying OSCC pathogenesis. Our targeted, qRT-PCR-based expression profiling of 232 miRNAs in 49 human oral tissue samples (including 19 normal and 30 OSCC specimens) identified 49 differentially expressed miRNAs (p-value < 0.01 and fold change > 2) in OSCC tissues.

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Integrated analysis of long non-coding RNAs and mRNAs associated with malignant transformation of gastrointestinal stromal tumors.

Project description:Malignant transformation of gastrointestinal stromal tumors (GISTs) is correlated with poor prognosis; however, the underlying biological mechanism is not well understood. In the present study, low-risk (LR) GISTs, GISTs categorized as high-risk based on tumor size (HBS), and on mitotic rate (HBM) were collected for RNA sequencing. Candidate hub lncRNAs were selected by Oncomine analysis. Expression of a selected hub lncRNA, DNM3OS, and its correlation with patients' prognosis were analyzed using FISH staining, followed with the determination of function and underlying mechanism. Our results revealed a series of key pathways and hub lncRNAs involved in the malignant transformation of GISTs. Oncomine analysis revealed a tight association between clinical signatures and DNM3OS and suggested that DNM3OS is a hub lncRNA that is involved in the Hippo signaling pathway. In addition, DNM3OS was upregulated in HBS, HBM, and HBS/M GIST and correlated with worse prognosis in patients with GISTs. In addition, DNM3OS promoted GIST cell proliferation and mitosis by regulating the expression of GLUT4 and CD36. Collectively, these results improve our understanding of the malignant transformation of GISTs and unveil a series of hub lncRNAs in GISTs.

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Project description:Our study was designed to elucidate whether there were miRNA and mRNA aberrantly expression profiles and potential role in malignant transformation of 16HBE induced by Cd.mRNA and miRNA expression profiles were determined in 35th Cd-induced 16HBE and untreated 16HBE by microarray. A series of bioinformatics analyses such as predicting targets, GO, KEGG were performed to find DEGs, coexpressing networks between miRNAs and mRNAs and its functions.498 DEGs were found. 8 Cd-responsive novel miRNAs predicted previously were identified, and 5 of them were downregulated. 214 target genes were predicted for the Cd-responsive miRNAs, many of which appeared to regulate gene networks. Target gene CCM2 was showed reciprocal effect by miRNAs. According to the combination analysis, hsa-miR-27b-3p regulated most of the mRNAs, especially upregulated expression genes. The differentially expressed miRNAs are involved in the biological processes and channels, and these GO and KEGG enrichment analyses result were significantly enriched in the Cd-responsive.These results provided a tight link for the miRNA-mRNA integrated network and implied the role of novel miRNAs in malignant transformation of 16HBE induced by Cadmium. It is better to understand the novel molecular mechanism of cadmium-induced tumorigenesis.

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