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Omics score: 310

RNA-Seq of oral squamous cell carcinomas and matched normal tissues

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Brian Tuch Rebecca R Laborde David I Smith

PROVIDER: E-GEOD-20116 | ArrayExpress | 2010-02-25

SECONDARY ACCESSION(S): GSE20116SRP002009PRJNA124251

REPOSITORIES: GEO, ArrayExpress, ENA

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Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.

Tuch Brian B BB Laborde Rebecca R RR Xu Xing X Gu Jian J Chung Christina B CB Monighetti Cinna K CK Stanley Sarah J SJ Olsen Kerry D KD Kasperbauer Jan L JL Moore Eric J EJ Broomer Adam J AJ Tan Ruoying R Brzoska Pius M PM Muller Matthew W MW Siddiqui Asim S AS Asmann Yan W YW Sun Yongming Y Kuersten Scott S Barker Melissa A MA De La Vega Francisco M FM Smith David I DI

PloS one 20100219 2

Due to growing throughput and shrinking cost, massively parallel sequencing is rapidly becoming an attractive alternative to microarrays for the genome-wide study of gene expression and copy number alterations in primary tumors. The sequencing of transcripts (RNA-Seq) should offer several advantages over microarray-based methods, including the ability to detect somatic mutations and accurately measure allele-specific expression. To investigate these advantages we have applied a novel, strand-spe ...[more]

PMID: 20174472

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RNA-Seq of oral squamous cell carcinomas and matched normal tissues

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. Overall design: Oral squamous cell carcinomas (OSCC) and matched normal tissue from 3 patients.

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Project description:MicroRNAs (miRNAs) participate in many biological processes and have emerged as key players in carcinogenesis. In order to identify changes in miRNAs specific for betelquid-associated oral squamous cell carcinoma (OSCC), we investigated the expression profiles of 858 miRNAs in a panel of 40 pairs of OSCC specimens and their matched non-tumorous epithelial counterparts. Eighty-four miRNAs were differentially expressed in the OSCC specimens compared to the matched tissue. Among these miRNAs, 19 downregulated miRNAs located in the chromosome 14q32.2 miRNA cluster region were analyzed. This miRNA cluster resides within a parentally imprinted region known to be important in development and growth. The re-expression of miR-329 and miR-410from this cluster significantly reduced OSCC cell proliferation and invasion and downregulated Wnt-7b, an activator of the Wnt/b-catenin pathway. Furthermore, the expression of those 2 miRNAs was restored by 5-aza-2′-deoxycytidine treatment and the expression levels of the 2 miRNAs were inversely correlated with the hypermethylation of the Meg-3 promoter in OSCC cells. Specifically, arecoline, a major betel nut alkaloid, reduces miR-329 and miR-410 expression. Our results thus provide a novel molecular insight into how betel quid may contribute to oral carcinogenesis through the epigenetic silencing of tumor suppressor miRNAs targeting the Wnt/b-catenin signaling pathway. Total RNA was obtained from 40 pairs of OSCC patients with tumor specimens and their adjacent non-tumorous epithelia.

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