Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profiling of oral squamous cell carcinoma

ABSTRACT: Oral squamous cell carcinoma (OSCC) is a solid neoplasm exhibiting aggressive tumor phenotypes with unpredictable biological behavior and usually a very unfavorable prognosis. The comprehension of the molecular basis of the variability within this cancer disease should lead to the development of satisfactory targeted therapies as well as to improvements in diagnosis specificity and sensitivity. Due to the lack of definite molecular concepts in OSCC, this study aimed to detail molecular characteristics possibly reflecting differences in tumor progression mechanisms through genome-wide gene expression profiles. Keywords: disease-state analysis Nine tumor samples differing in their TNM classification and their respective surgical margins were used in this study. They were obtained from individual patients during tongue and floor of the mouth tumor resection surgery. Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). This platform utilizes bioarrays consisting of 30-base, single pre-validated oligonucleotide probe per gene target. CodeLink Whole-Genome bioarrays, containing 55,000 human transcripts, were used for all experiments. Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A total of 11 arrays were hybridized in this study. Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).

ORGANISM(S): Homo sapiens

SUBMITTER: Patricia Severino

PROVIDER: E-GEOD-9792 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites.

Severino Patricia P Alvares Adriana M AM Michaluart Pedro P Okamoto Oswaldo K OK Nunes Fabio D FD Moreira-Filho Carlos A CA Tajara Eloiza H EH

BMC research notes 20081113

<h4>Background</h4>Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis.<h4>Results</h4>Samples of primary OSCCs and their corresponding surgical margins were obtained from male patients during surgery and their ...[more]

PMID: 19014556

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Project description:The inadequate function of the antigen presenting cells, such as dendritic cells (DCs) in cancer is one of the major factors leading to compromised anti-tumor immune response. Cell-to-cell interactions and cell migration are essential features of the immunological response in cancer. Vascular endothelial growth factor (VEGF) has been shown to affect DCs differentiation and maturation processes, thus leading to impaired DCs function. This study aimed to compare the expression of adherence and cytoskeleton-related genes between mature monocyte-derived dendritic cells (mDCs) and mDCs previously exposed to VEGF (mDCVs). VEGF is known to stimulate cell migration and actin rearrangement, but its association with adhesion molecules has not been largely explored in the context of DCs. Our results show that immature human DCs exposed to VEGF up-regulated CD80 and CD86, typical cell surface markers of DC maturation. However, unlike mDCs, mDCVs showed alterations in cell morphology, with broad changes in the characteristic cytoplasmic processes. DNA microarray analysis revealed that mDCVs up-regulated a significant subset of genes related to cell migration, including cell adhesion molecules and related signaling pathways as well as cytoskeleton-related genes. Our results suggest that VEGF, known to be involved in the inhibition of DC maturation, interferes in cell mechanisms leading to cytoskeleton reorganization and the expression of cell adhesion molecules. Cell morphology is associated with DC maturation and migration, both impaired in pathological conditions such as cancer. Keywords: Gene expression profiling Gene expression profiling was carried out in freshly isolated CD14+ cells prior to cultivation (“D0” samples) and in DCs after 6 days (“D6” samples) and 7 days in culture, with or without VEGF treatment (“D7V” and “D7” samples, respectively). Blood samples were collected on the same day and processed concomitantly. Cell culture, RNA extraction, and microarray hybridization were also carried out simultaneously in an attempt to minimize technical inconsistencies. A total of 14 independent microarray hybridizations were carried out with oligonucleotide microarrays, covering approximately 55,000 human transcripts (Whole Genome CodeLink™ Bioarrays, GE Healthcare). Target preparation and hybridization procedures strictly followed protocols provided by the manufacturer.Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.1 software (Axon Instruments).

Dataset Information

Gene expression profiling of oral squamous cell carcinoma

Publications

Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites.

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