Determination of Nitric Oxide–Donor Effects on Tissue Gene Expression In Vivo Using Low‐Density Gene Arrays

Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays

BACKGROUND

An accurate gene expression quantification using TaqMan Arrays (TA) could be limited by the low RNA quantity obtained from some clinical samples. The novel cDNA preamplification system, the TaqMan PreAmp Master Mix kit (TPAMMK), enables a multiplex preamplification of cDNA targets and therefore, could provide a sufficient amount of specific amplicons for their posterior analysis on TA.

FINDINGS

A multiplex preamplification of 47 genes was performed in 22 samples prior to their analysis by TA, and relative gene expression levels of non-preamplified (NPA) and preamplified (PA) samples were compared. Overall, the mean cycle threshold (CT) decrement in the PA genes was 3.85 (ranging from 2.07 to 5.01). A high correlation (r) between the gene expression measurements of NPA and PA samples was found (mean r = 0.970, ranging from 0.937 to 0.994; p < 0.001 in all selected cases). High correlation coefficients between NPA and PA samples were also obtained in the analysis of genes from degraded RNA samples and/or low abundance expressed genes.

CONCLUSION

We demonstrate that cDNA preamplification using the TPAMMK before TA analysis is a reliable approach to simultaneously measure gene expression of multiple targets in a single sample. Moreover, this procedure was validated in genes from degraded RNA samples and low abundance expressed genes. This combined methodology could have wide applications in clinical research, where scarce amounts of degraded RNA are usually obtained and several genes need to be quantified in each sample.

Effects of repeated in vivo inhalant nitrite exposure on gene expression in mouse liver and lungs

Exposure to inhalant organic nitrites (drugs of abuse commonly known as "poppers") has been reported to enhance tumor growth in mice, but the mechanism is not fully defined. This study examined the effect of repeated in vivo nitrite exposures on gene expression in the mouse liver and lungs using a gene array panel of 94 cancer- and angiogenesis-related genes. Using 2-fold change as a threshold criterion, repeated nitrite exposure was found to alter the expression of 65 and 23 genes in the liver and lungs, respectively. Six genes were significantly upregulated (p<or=0.05), viz., those encoding VEGF, VEGFD (vascular endothelial growth factor A and D, respectively) in the lungs and FGF1, FGF4 (fibroblast growth factor 1 and 4, respectively), Hsp70 (heat shock 70kDa protein 4), and PF4 (platelet factor 4) in the liver. mRNA encoding HO-1 (heme oxygenase-1) and Smad7 were marginally (p=0.057) stimulated in the liver. Follow-up studies in the liver revealed significant nitrite-induced expression of VEGF protein and mRNA. Immuno-staining of liver slices revealed that the increased hepatic VEGF expression resided mainly in hepatocytes. Stimulation of hepatic VEGF expression by ISBN was not different in endothelial nitric oxide synthase (eNOS) knockout vs. wild-type mice. In conclusion, multiple exposures to inhalant nitrite appeared to cause alteration in the expression of a number of genes relating to cancer and angiogenesis, including VEGF. eNOS presence did not appear to be essential for nitrite-induced VEGF expression. These studies demonstrate that in vivo exposure to inhalant nitrites results in changes in the angiogenesis cascade.