Gene expression profiling of chromophobe renal cell carcinomas and renal oncocytomas by Affymetrix GeneChip using pooled and individual tumours

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.

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Abstract 2654: Differential Local versus Systemic Gene Expression Profiling in Acute Coronary Syndromes

Circulation ◽

10.1161/circ.118.suppl_18.s_761-b ◽

2008 ◽

Vol 118 (suppl_18) ◽

Author(s):

Alexander Akhmedov ◽

Keiko Yonekawa ◽

Christophe Wyss ◽

Roberto Corti ◽

Nils Kucher ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Human Genome ◽

Expression Profiling ◽

Acute Coronary Syndromes ◽

Coronary Occlusion ◽

Plaque Rupture ◽

Affymetrix Genechip ◽

Fluorescent Intensity ◽

Coronary Syndromes

Introduction: Monocytes and leucocytes (WBC) play a key role in acute coronary syndromes (ACS). We hypothesized that gene expression profiling of WBC from the site of coronary occlusion in direct comparison with peripheral WBC from patients with ACS might reveal genetic patterns involved in plaque rupture. Methods: Thrombi (Thr) were aspirated during primary percutaneous coronary intervention (PCI), snap-frozen, and stored at −80°C. Peripheral blood leukocytes (PBL) from the same patients were extracted and treated accordingly. Total RNA was isolated from thrombi and PBL. The quality and quantity of the isolated RNA was determined using bioanalyzer and nanodrop devices. The cDNA was prepared using a primer mix and reverse transcriptase, followed by fragmentation and biotinilation. Biotin-labeled single-stranded cDNA samples were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. An Affymetrix GeneChip Scanner was used to measure the fluorescent intensity emitted by the labelled target. Results: Gene expression profiles of Thr and PBL from 4 patients during PCI were assessed by Affymetrix human genome U133 Plus 2.0 arrays (54′675 probe sets). 653 different genes were locally upregulated in Thr compared to PBL as defined by a more than 8-fold difference in expression and statistical significance (p≤0.01). Genes for proteins of inflammation, thrombosis, endothelial activation, extracellular matrix remodelling, and scavenger receptors were highly upregulated at the site of coronary occlusion (examples see table 1 ). Conclusion: The local gene expression profile in WBC from thrombi differs significantly from the pattern in PBL, reflecting the regulatory and effective role of these cells in plaque rupture and thrombosis. This study identifies the upregulation of genes encoding for a host of established and new pathways involved in inflammation, uptake of oxidized LDL, and coagulation, that might play a crucial role in ACS. Table 1

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Combining differential expression, chromosomal and pathway analyses for the molecular characterization of renal cell carcinoma

Canadian Urological Association Journal ◽

10.5489/cuaj.64 ◽

2012 ◽

Vol 1 (2S) ◽

Cited By ~ 1

Author(s):

Kyle A. Furge ◽

Karl Dykema ◽

David Petillo ◽

Michael Westphal ◽

Zhongfa Zhang ◽

...

Keyword(s):

Gene Expression ◽

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Gene Expression Profiling ◽

Cancer Cells ◽

Expression Profiling ◽

Renal Cell ◽

Molecular Signatures ◽

Genetic Makeup ◽

Papillary Rcc

Using high-throughput gene-expression profiling technology, we can now gaina better understanding of the complex biology that is taking place in cancer cells. This complexity is largely dictated by the abnormal genetic makeup ofthe cancer cells. This abnormal genetic makeup can have profound effectson cellular activities such as cell growth, cell survival and other regulatory processes. Based on the pattern of gene expression, or molecular signatures of the tumours, we can distinguish or subclassify different types of cancers according to their cell of origin, behaviour, and the way they respond to therapeuticagents and radiation. These approaches will lead to better molecularsubclassification of tumours, the basis of personalized medicine. We have, todate, done whole-genome microarray gene-expression profiling on several hundredsof kidney tumours. We adopt a combined bioinformatic approach, based on an integrative analysis of the gene-expression data. These data are used toidentify both cytogenetic abnormalities and molecular pathways that are deregulatedin renal cell carcinoma (RCC). For example, we have identified the deregulationof the VHL-hypoxia pathway in clear-cell RCC, as previously known,and the c-Myc pathway in aggressive papillary RCC. Besides the more commonclear-cell, papillary and chromophobe RCCs, we are currently characterizingthe molecular signatures of rarer forms of renal neoplasia such ascarcinoma of the collecting ducts, mixed epithelial and stromal tumours, chromosomeXp11 translocations associated with papillary RCC, renal medullarycarcinoma, mucinous tubular and spindle-cell carcinoma, and a group of unclassified tumours. Continued development and improvement in the field of molecular profiling will better characterize cancer and provide more accurate diagnosis, prognosis and prediction of drug response.

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