Gene expression profiling of chemically induced rat bladder tumors

Abstract

A variety of genetic alterations and gene expression changes are involved in the pathogenesis of bladder tumors. To explore expression changes in 4-hydroxybutyl(butyl)nitrosamine-induced rat bladder tumors, microarray analysis was performed. Analysis yielded 1,138 known genes and 867 expressed sequence tags that were changed when comparing tumors to normal rat epithelia. Altered genes included cell cycle-related genes, EGFR-Ras signaling genes, apoptosis genes, growth factors, and oncogenes. Using the pathway visualization tool GenMAPP, we found that these genes can be grouped along several pathways that control apoptosis, cell cycle, and integrin-mediated cell adhesion. When comparing current data with previous mouse bladder tumor data, we found that > 280 of the same known genes were differentially expressed in both mouse and rat bladder tumors, including cell cycle-related genes, small G proteins, apoptosis genes, oncogenes, tumor-suppressor genes, and growth factors. These results suggest that multiple pathways are involved in rat bladder tumorigenesis, and a common molecular mechanism was found in both rat and mouse bladder tumors.

Figure 1

Comparison of bladder epithelia and whole bladder tissues as controls to bladder cancers. Among the 1138 known genes found to be differentially expressed in rat bladder tumors compared with epithelia, 770 genes were overexpressed and 368 genes were underexpressed. Green indicates an expression below the mean value for the gene, black indicates an expression near the mean, and red indicates an expression above the mean.

Figure 2

Distribution of 2005 differentially expressed genes and ESTs by microarray analysis and real-time PCR confirmation for selected genes. (A) An overview of the number of genes reveals fold changes different from those in normal bladder epithelia. (B) Comparison of fold change produced by microarray with the relative expression ratio obtained from real-time PCR, with good concordance.

Figure 3

Confirmation of differentially expressed genes for both RNA and protein levels. (A) Comparison of fold change produced by microarray with the relative expression ratio obtained from RT-PCR. (B) 2D protein gel electrophoresis indicates that annexin A1 protein is overexpressed in rat bladder cancers. (C) IHC suggests that both annexin A1 and cyclin D1 are overexpressed in rat bladder cancers.

Figure 4

GenMAPP signaling pathways integrated into rat bladder tumorigenesis with a cutoff fold change of ≥ 1.5 and P < .05. Yellow and blue indicates overexpressed and underexpressed genes in tumor samples, respectively. Grey indicates that selection criteria were not met but the gene was represented in the array. White boxes indicate that the gene was not present in the chip. (A) Apoptosis. (B) Cell cycle. (C) G₁-to-S cell cycle control. (D) Integrin-mediated cell adhesion.

Figure 4

GenMAPP signaling pathways integrated into rat bladder tumorigenesis with a cutoff fold change of ≥ 1.5 and P < .05. Yellow and blue indicates overexpressed and underexpressed genes in tumor samples, respectively. Grey indicates that selection criteria were not met but the gene was represented in the array. White boxes indicate that the gene was not present in the chip. (A) Apoptosis. (B) Cell cycle. (C) G₁-to-S cell cycle control. (D) Integrin-mediated cell adhesion.

Figure 4

GenMAPP signaling pathways integrated into rat bladder tumorigenesis with a cutoff fold change of ≥ 1.5 and P < .05. Yellow and blue indicates overexpressed and underexpressed genes in tumor samples, respectively. Grey indicates that selection criteria were not met but the gene was represented in the array. White boxes indicate that the gene was not present in the chip. (A) Apoptosis. (B) Cell cycle. (C) G₁-to-S cell cycle control. (D) Integrin-mediated cell adhesion.

Figure 4

GenMAPP signaling pathways integrated into rat bladder tumorigenesis with a cutoff fold change of ≥ 1.5 and P < .05. Yellow and blue indicates overexpressed and underexpressed genes in tumor samples, respectively. Grey indicates that selection criteria were not met but the gene was represented in the array. White boxes indicate that the gene was not present in the chip. (A) Apoptosis. (B) Cell cycle. (C) G₁-to-S cell cycle control. (D) Integrin-mediated cell adhesion.