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Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma

ABSTRACT: Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52793 | GEO | 2014/11/25

SECONDARY ACCESSION(S): PRJNA230059

REPOSITORIES: GEO

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Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma

Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples. Bisulphite lsconverted DNA from the 82 oral rinse samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip

2014-11-25 | E-GEOD-52793 | biostudies-arrayexpress

CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma

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Project description:Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO We measured methylation of 42 OSCC tumors, 2 normal oral epithelial tissues, and 2 normal blood samples with Illumina HumanMethylation450 arrays

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2013-10-22 | E-GEOD-51265 | biostudies-arrayexpress

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Project description:Array Comparative Genomic Hybridization (CGH) profiling of Oral Leukoplakia (OPL) and early stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with disease progression and clinico-pathological parameters. The array CGH hybridizations were performed for 24 OPL and 38 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.

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Project description:Gene Expression Profiling of Oral Leukoplakia (OPL) and Early Stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate gene/s clusters with potential to distinguish normal, OPL and tumor tissue from Gingivobuccal complex. All tissue samples were collected after obtaining written informed consent. The RNA profile of 15 OPL and 34 OSCC samples was compared with 1 independent controls Gingivobuccal complex tissue from healthy donors.

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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. DNA copy number aberrations were determined using high resolution arrays on 151 samples (2x105K, n=82 samples, and 4x180K, n=69 samples) (Agilent Technologies, Palo Alto, CA, USA). Labeling, hybridization, scanning and feature extraction were performed as previously described using the cross hybridization method previously described [Castagnola P, Malacarne D, Scaruffi P, Maffei M, Donadini A, et al. (2011) Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue. BMC Cancer 11: 445.].

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Project description:This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization). Oral NFs and CAFs were obtained from tissues derived from 12 healthy people undergoing plastic surgery and 12 OSCC patiens undergoing surgical resection. RNA samples from NFs and CAFs were pooled respectively before hybridization.

2012-01-26 | E-GEOD-35356 | biostudies-arrayexpress

Gene expression profiling of oral squamous cell carcinoma (OSCC)

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