Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of oral squamous cell cancer (OSCC) surgical margins defined by narrow band imaging.

ABSTRACT: The purpose of this study was to provide molecular evidence that surgical margin definition using narrow band imaging (NBI) resulted in more complete OSCC excision that conventional while light (WL) imaging. Samples were taken prospectively from 18 patients undergoing surgical resection for intraoral SCC (excluding lip, pharynx and hypopharynx). Biopsies were taken from the tumour and from 5mm beyond each of the abnormal tissue margins defined by WL and NBI. Transcriptional profiling was performed by microarray.

ORGANISM(S): Homo sapiens

SUBMITTER: Camile Farah

PROVIDER: E-MTAB-5933 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Improved surgical margin definition by narrow band imaging for resection of oral squamous cell carcinoma: A prospective gene expression profiling study.

Farah Camile S CS Dalley Andrew J AJ Nguyen Phan P Batstone Martin M Kordbacheh Farzaneh F Perry-Keene Joanna J Fielding David D

Head & neck 20150626 6

<h4>Background</h4>Incomplete primary tumor excision contributes to localized postsurgical recurrence of oral squamous cell carcinoma (OSCC). The purpose of this study was to provide molecular evidence that surgical margin definition using narrow band imaging (NBI) resulted in more complete OSCC excision than conventional white light (WL) panendoscopy.<h4>Methods</h4>Molecular divergence among tumor, WL, and NBI-defined surgical margins was compared in 18 patients through microarray analysis (Ge ...[more]

PMID: 25545703

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Project description:LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology and defective hormonal and stimulus responses. HY5 thus acts as an integrater that links various gene networks to coordinate plant development. Here we report an effort to experimentally map the HY5-mediated gene networks in Arabidopsis by integrating genomic loci occupied by HY5 and HY5-dependent gene expression profiles. Our results indicate HY5 binds to over 9,000 genes, which detectably impact the expression of over 1,100 genes, either positively or negatively. Further, HY5 indirectly regulates many other genes through sub-networks mediated by other regulators. In particular, we show that HY5 regulates eight microRNA (miRNA) genes, which in turn control transcript abundance of specific target genes. Over-expressing the HY5-targeted miR408 resulted in phenotypes that are opposite to hy5 mutants. Together our results revealed both the transcriptional and post-transcriptional components of the HY5-mediated gene networks responsible for the phenotypic complexity in plants. Chromatin isolation was performed with 4-day-old whole seedlings grown under wild type light (WL) or 8hr darkness treatment according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4M-BM-0C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 500 bp. Chromatin was immunoprecipitated, washed, reverse cross-linked, amplified, and hybridized according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. A polyclonal HY5 antibody purified from anti-HY5 rabbit IgG using Sepharose 4B beads coupled with purified recombinant HY5 protein was used. M-bM-^@M-^XFlow-throughM-bM-^@M-^Y IgG devoid of the HY5 antibody was used as a negative control. An aliquot of untreated sonicated chromatin was reverse cross-linked and used as a total input DNA control for ChIP-PCR experiments. Four biological replicates for each experimental condition and two biological replicates for each control condition were hybridized to tiling arrays, resulting in a total of 12 chips.

Dataset Information

Transcription profiling by array of oral squamous cell cancer (OSCC) surgical margins defined by narrow band imaging.

Publications

Improved surgical margin definition by narrow band imaging for resection of oral squamous cell carcinoma: A prospective gene expression profiling study.

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