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The Use of Reverse Phase Protein Arrays (RPPA) to Explore Protein Expression Variation within Individual Renal Cell Cancers
Published on: January 22, 2013
Microarray gene expression profiling and analysis in renal cell carcinoma
Louis S Liou1, Ting Shi, Zhong-Hui Duan
1Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, USA. lioul@ccf.org
Background:
Renal cell carcinoma (RCC) is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays.
Methods:
Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC.
Results:
Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR). Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved.
Conclusions:
This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most notably, genes involved in cell adhesion were dominantly up-regulated whereas genes involved in transport were dominantly down-regulated. This study reveals significant gene expression alterations in key biological pathways and provides potential insights into understanding the molecular mechanism of renal cell carcinogenesis.
Insights
This study analyzed gene expression in renal cell carcinoma (RCC), finding cell adhesion genes were upregulated and transport genes downregulated. These findings offer insights into RCC molecular mechanisms and carcinogenesis.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Renal cell carcinoma (RCC) is the most common kidney cancer in adults.
- Current diagnosis, prognosis, and treatment are limited by poor molecular understanding.
- Gene expression profiling of RCC aims to elucidate its underlying genetics and biology.
Purpose of the Study:
- To profile the expression of 7,129 genes in clear cell RCC tissue and cell lines.
- To understand the genetics and biology of RCC at a molecular level.
- To identify differentially expressed genes and pathways in RCC.
Main Methods:
- Oligonucleotide arrays (Affymetrix HuFL) were used to profile gene expression.
- Total RNAs from RCC tumors, adjacent normal tissue, and cell lines were analyzed.
- Gene expression data were analyzed using functional ontology, clustering, and singular value decomposition; RT-PCR validated findings.
Main Results:
- Seventy-four commonly differentially expressed genes with >5-fold changes in RCC tissues were identified.
- Gene expression patterns showed significant differences between RCC tissue and cell lines, though key patterns were preserved.
- Genes involved in cell adhesion were predominantly upregulated, while transport genes were predominantly downregulated.
Conclusions:
- This study provides functional ontology analysis of a large gene set in RCC.
- Identified gene expression alterations in key biological pathways offer insights into RCC molecular mechanisms.
- Upregulation of cell adhesion genes and downregulation of transport genes are notable findings in renal cell carcinogenesis.
