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Expression Profiling of Oral Squamous Cell Carcinoma and Mucosa of healthy non-tumor patients

ABSTRACT: In an attempt to further elucidate the pathomechanisms in oral squamous cell carcinoma (OSCC), gene expression profiling to a set of 35 primary OSCCs compared to 6 oral mucosa from healthy non-tumor patients was performed. Keywords: expression profiling

ORGANISM(S): Homo sapiens

PROVIDER: GSE10121 | GEO | 2008/01/12

SECONDARY ACCESSION(S): PRJNA108239

REPOSITORIES: GEO

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Expression Profiling of Oral Squamous Cell Carcinoma and Mucosa of healthy non-tumor patients

Project description:In an attempt to further elucidate the pathomechanisms in oral squamous cell carcinoma (OSCC), gene expression profiling to a set of 35 primary OSCCs compared to 6 oral mucosa from healthy non-tumor patients was performed. Keywords: expression profiling Gene expression profiling using a whole-transcriptome chip that contains 35,035 gene-specific 70mere oligonucleotides (Human Oligoset 4.0; Operon) to a set of 35 primary OSCCs and 6 mucosa of healthy non-tumor patients.

2008-01-12 | E-GEOD-10121 | biostudies-arrayexpress

Expression data from oral squamous cell carcinoma (OSCC)-derived cell lines and normal oral keratinocytes

Project description:Oral squamous cell carcinoma (OSCC) is a lethal disease and early death usually occurs as a result of local invasion and regional lymph node metastases. We used microarrays to identify down or upregulated genes in OSCCs compared with non-malignant controls. To identify genes whose transcription is deregulated in OSCC, the gene expression profiles of eight OSCC cell lines (H-series and M9) and three primary cultures of normal oral keratinocytes (NKs) were examined using Affymetrix HG-U133A and HG-U133 Plus 2.0 arrays.

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Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa

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Expression data from oral squamous cell carcinoma (OSCC)-derived cell lines and normal oral keratinocytes

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Affymetrix SNP array data for oral squamous cell carcinoma samples

Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. To identify genes responsible for OSCC development, we performed high-density single-nucleotide polymorphism array analysis and genome-wide gene expression profiling on OSCC tumors. These analyses identified "absent in melanoma (AIM2)" and "interferon-inducible gene 16 (IFI16)," mapped to the hematopoietic IFN-inducible nuclear proteins with 200-amino acid repeat (HIN-200) gene cluster in the amplified region of chromosome 1q23, with overexpression in OSCCs. AIM2 and IFI16 are cytoplasmic double-stranded DNA sensors for innate immunity and act as tumor suppressors in several human cancers. Knockdown of AIM2 or IFI16 in OSCC cells resulted in the suppression of cell growth and the induction of apoptosis, accompanied by the downregulation of NF-κB activation. Because all of the OSCC cell lines had impairment of p53 activity, wild-type p53 was introduced in p53-deficient OSCC cells, and as a result, the expression of wild-type p53 suppressed cell growth and induced apoptosis via suppression of NF-κB activity. Finally, the coexpression of AIM2 and IFI16 significantly enhanced cell growth in p53-deficient cells; in contrast, the expression of AIM2 and/or IFI16 in cells bearing wild-type p53 suppressed cell growth. Moreover, AIM2 and IFI16 synergistically enhanced NF-κB signaling in p53-deficient cells. Thus, expression of AIM2 and IFI16 may have oncogenic functions in OSCC cells inactivating p53 system. Copy number analysis of Affymetrix 250K SNP arrays was performed for 5 oral leukoplakia samples, 20 oral squamous cell carcinoma samples, and 8 oral squamous cell carcinoma cell lines.

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Comparative gene expression profiling of tobacco-associated HPV-positive versus negative oral squamous carcinoma cell lines

Project description:HPV-positive oral squamous cell carcinomas (OSCCs) are specific biological and clinical entities, characterized by a more favorable prognosis compared to HPV-negative OSCCs and occurring generally in non-smoking and non-drinking younger individuals. However, poor information is available on the molecular and the clinical behavior of HPV-positive oral cancers occurring in smoking/drinking subjects. Thus, this study was designed to compare, at molecular level, two OSCC cell lines, both derived from drinking and smoking individuals and differing for presence/absence of HPV infection.

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MiRNA SIGNATURE FOR ORAL SQUAMOUS CELL CARCINOMA

Project description:The present study is aimed at profiling the miRNA expression pattern in oral squamous cell carcinoma (OSCC) and adjacent oral mucosa to develop a new miRNA signature for oral cancer. Agilent Human miRNA Microarray v2.0 (G4470B, Agilent Technologies) was used to identify miRNAs differentially expressed in OSCC. MicroRNA processing was carried out according to the manufacturer’s instructions. Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings. Data pre-processing and differential expression analysis were done in R Studio using the Bioconductor AgiMicroRna package.12 The Total Gene Signal provided by the AFE image analysis software was used for data analysis. Data were normalized between arrays using the quantile method. Microarray profiling identified a set of 105 miRNAs to be differentially expressed in OSCC, out of which a subset of 19 most dysregulated miRNAs were considered to formulate the miRNA signature for oral cancer.

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Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa

2016-07-26 | GSE84805 | GEO

Affymetrix SNP array data for oral squamous cell carcinoma

Project description:In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from normal oral tissues and OSCC specimens. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 112 OSCC specimens and 10 non-cancerous samples.

2011-08-31 | E-GEOD-25103 | biostudies-arrayexpress

Genomic DNA damage in oral potentially malignant disorders (OPMDs) and oral squamous cell carcinomas (OSCCs). Early detection of DNA aneuploidy and chromosomal aberrations in non dysplastic OPMDs.

Project description:Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention. DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs. Samples from OPMDs and OSCCs were processed for high resolution DNA flow cytometry (hr DNA-FCM) to determine the relative DNA content expressed with the DNA index (DI). Additionally, on a subset of these samples, array-Comparative Genomic Hybridization (aCGH) analysis was performed on DNA obtained from diploid nuclei suspension or from aneuploid-enriched nuclei suspensions.

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