MeRIP-Seq reveals the genome-wide maps of m6A modification on mRNA and lncRNA in OSCC
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE197457 | GEO | 2022/07/19
REPOSITORIES: GEO
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Project description:Oral bacterial species Streptococcus mitis, Neisseria flavescens, and Haemophilus parainfluenzae, and Porphyromonas gingivalis were each co-cultured with the OSCC cell lines CAL27, SCC4 and SCC25 individually. Total RNA was extracted from the cell lines, followed by gene expression profiling with microarray analysis.
2021-09-11 | GSE183911 | GEO
Project description:Oral squamous cell carcinoma (OSCC) is a main reason of oral cancer mortality and morbidity. Cancer of oral cavity in central south Asia, ranks among third most common kinds of cancer. The discovery of candidate markers to differentiate normal from malignant cells in clinical diagnosis of OSCC would be of critical importance because this malignancy has poor prognosis. To improve the clinical outcome in OSCC patients, the present study was aimed at identifying robust candidate biomarkers for early OSCC diagnosis and to enhance understanding of the mechanisms of disease progression and pathogenesis. Of particular interest are proteins that can be found in tissue lysates of OSCC tumor vs normal adjacent mucosa samples and secreted in cell line Secretomes of HNSCC for non-invasive detection. We analysed 17 paired human malignant OSCC tissues and normal adjacent tissue in addition to secretomes of 9 HNSCC cell lines. The proteome dataset of OSCC and normal tissues consisted of 5,123 protein groups, including 299 proteins with strong differential expression (p-value <0.01, fold change barrier to ˃+2 and <-2, 205 upregulated and 94 down regulated) and 134 common proteins were also found out of total dataset of 4473 identified proteins of HNSCC cell line secretomes. Functional data analysis revealed that these differential proteins were significantly associated with multiple biological processes. Myogenesis, Fatty Acid Metabolism and KRAS Signaling DN were associated with the proteins downregulated in cancer tissues, while Protein Secretion, Unfolded Protein Response, Spliceosomal complex assembly, Protein localization to endosome and Interferon Gamma Response were enriched in the set of upregulated proteins and these regulated proteins may be classically or non-classically secreted. Furthermore, we found differential enrichment of Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP transcription factors potentially regulating these major pathways.
2022-04-04 | PXD025701 | Pride
Project description:In order to identify genes with differential gene expression or alternative splicing between the groups Normal and late stage OSCC (Stage III and IV), we study 16 hybridizations (6 normal; 10 late stage OSCC) on the HumanGene10ST array using mixed model analysis of variance. 1323 genes with significant gene expression differences between the groups and 357 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 129 genes with both gene and possible splicing differences (p<0.01). Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes (p<0.01). Algorithm ANOVA study of 16 HumanGene10ST files. Factorial arrangment NORMALvs late stage OSCC samples
2014-09-30 | E-GEOD-56532 | biostudies-arrayexpress
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: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.
2011-07-22 | GSE30784 | GEO
Project description:Carcinogenesis is a genetic process in which molecular changes occur earlier than histomorphological changes. The key to early detection of oral squamous cell carcinoma (OSCC) is to identify genetic alterations. However, aberrant lncRNA expression profiles in OSCC plasma is still largely unknown. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC plasma compared with paired healthy volunteer plasma. Our data revealed 7473 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 3972 lncRNAs were significantly up-regulated and 3501 lncRNAs were down-regulated in OSCC compared with paired healthy volunteer plasma.
2021-01-22 | GSE97251 | GEO
Project description:Purpose No blood biomarkers to detect early OSCC without clinical signs exist - diagnosis is solely based on histology of a visible tumor. Most OSCC patients are diagnosed at advanced stage, which leads to significant morbidity and poor survival. If high-risk patients were identified with blood-based biomarkers before clear clinical manifestations, tumors could be detected and treated at earlier stage. Patients and Methods Serum samples were collected from patients with OSCC at the Department of Otorhinolaryngology – Head and Neck Surgery, Helsinki University Hospital (Finland). Age and gender matched healthy individuals served as controls. Quantitative proteomic analysis with mass spectrometry was performed. Results We quantified 388 proteins in the serum samples. A complete separation between cases and controls was seen based on the protein expression profiles. With statistical analyses, we identified a set of eight proteins that most reliably separated OSCC patients from healthy individuals. Although the tumor stages varied from I to IVa, this set of proteins was able to identify all OSCCs and thus is sensitive for detecting even early tumors. Conclusion We are the first to suggest a set of serum biomarkers to be evaluated further as a diagnostic panel to detect preclinical OSCC in risk patients.
2018-04-25 | PXD005263 | Pride
Project description:Hypoxic microenvironment plays important roles in the progression of solid tumors including oral squamous cell carcinoma (OSCC). Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. However, it is not clear whether lncRNAs could regulate hypoxia-adaptation of OSCC, and which lncRNAs participate in this process. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa as well as in hypoxic OSCC cells compared with normoxic OSCC cells. Our data revealed 2053 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 934 lncRNAs were significantly up-regulated and 1119 lncRNAs were down-regulated in OSCC compared with paired normal mucosa. Six OSCC tissues and paired normal oral mucosa were obtained from 6 patients with OSCC. LncRNA expression profiles were evaluated by an Agilent Human LncRNA Array v3.0 (8 x 60K, Arraystar).
2016-07-26 | E-GEOD-84805 | biostudies-arrayexpress
Project description:According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the epigenome, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate aberrent methylation patterns are prevalent in OSCC patients with ABC risk factors. Genomic DNA was collected from tumor and non-tumor pair-wise samples. These biopsies were obtained from 40 male OSCC patients who regularly drink alcohol, chew areca nut and smoking.
2015-04-01 | E-GEOD-38532 | biostudies-arrayexpress
Project description:Differentially expressed genes between T4 and T1 stage human oral squamous cell carcinoma (OSCC) 36 OSCC samples separated by tumor size T stage, in dual color microarray, using a pool of human cell lines as control. Screening for differentially expressed genes was performed in a cohort of 36 patients randomly selected. Transcriptional profiles were performed using Agilent one color hybridizations in a G4851A platform.
2015-06-23 | E-GEOD-59069 | biostudies-arrayexpress