Proteomic analysis as related to transcriptome data in the lung of chromium(VI)-treated rats

Assessing the parallelism between transcriptome data and proteome data represents one of the major challenges of post-genomic research. We evaluated the levels of 380 proteins in lung S12 fractions from Sprague-Dawley rats by antibody microarrays. Approximately half of these proteins were detectable under physiological conditions. There was a poor parallelism between mRNA and protein levels for a subset of 84 coinciding or related activities, whose gene expression had previously been investigated by cDNA array. The proportion of detectable proteins was almost twice as high as the proportion of transcriptionally active genes, which reflects the longer half-life of proteins compared to mRNA. Following the local stimulus provided by a short-term and high-dose exposure to sodium dichromate by the intra-tracheal route, 64 additional proteins were detectable in lung S12 fractions, and the correlation between gene expression and protein levels became significant. Sixteen proteins were increased more than twice following chromium(VI) administration. They included ten activities involved in the positive regulation of the cell cycle, three proteins involved in stress response and protein repair, two pro-apoptotic activities, and one protein involved in lipoprotein catabolism. An increase of P53 protein was detected by Western blot in lung nuclear fractions. Post-genomic analyses, highlighting the stimulation of defence mechanisms triggered by DNA damage, contribute to explain the previously reported discrepancy between the ability of chromium(VI) to induce oxidative stress and genotoxic damage in the lung and its failure to induce lung tumors under comparable experimental conditions. The proteome analysis showed a prominent role of apoptosis, counter-balanced by a positive regulation of the cell cycle aimed at replacing lost cells. In conclusion, our results suggest that, under basal conditions, mRNA undergoes a selective inactivation and post-transcriptional regulation resulting in de-coupling of transcriptome data and proteome data. However, this parallelism is re-established when the cell undergoes genotoxic damage.