A proteomic approach for evaluating the cell response to a novel histone deacetylase inhibitor in colon cancer cells.

Epigenetic inactivation of gene expression is a general phenomenon associated with malignant transformation. Recently, we have found that a novel series of histone deacetylases (HDAC) inhibitors exhibit a broad-spectrum inhibition profile characterized by a marked effect on acetylation of histone and non-histone proteins. RC307, a representative compound of this series, caused a growth-inhibitory effect in colon carcinoma cells HCT116 associated with G2 accumulation and induction of apoptosis. The present study was designed to investigate the effect of RC307 on protein expressions in the HCT116 cells following treatment with cytotoxic drug concentrations. HCT116 cells were cultured in the absence or presence of RC307 and total cell lysates, as well as nuclear proteins, were extracted. The protein samples were then subjected to two-dimensional polyacrylamide gel electrophoresis, and the 2D gel images were compared to discover the protein changes caused by RC307 treatment. A total of 48 and 46 different spots were found to be modulated by RC307 in total lysates and nuclear proteome of HCT116 cell line. The modulated proteins were identified by tandem mass spectrometry. We found that RC307 exposure modulates proteins that are involved in proliferation, cell cycle regulation, apoptosis, gene expression, as well as chromatin and cytoskeleton organization.

Modulation of survival pathways in ovarian carcinoma cell lines resistant to platinum compounds.

Because cytotoxic stress elicits various signaling pathways that may be implicated in cell survival or cell death, their alterations may have relevance in the development of platinum-resistant phenotype. Thus, in the present study, we investigated cell response to the epidermal growth factor receptor (EGFR) inhibitor gefitinib of ovarian carcinoma cell lines, including cells selected for resistance to cisplatin (IGROV-1/Pt1) and oxaliplatin (IGROV-1/OHP). Resistant sublines exhibited a marked decrease in sensitivity to gefitinib and resistance to apoptosis. Gefitinib was capable of inhibiting the phosphorylation of EGFR in all the studied cell lines. The Akt and extracellular signal-regulated kinase 1/2 (ERK1/2) kinases, which act downstream of EGFR, were constitutively active in the three cell lines, but phospho-ERK1/2 levels were increased in the two resistant sublines. This feature was associated with reduced sensitivity to the MEK1/2 inhibitor U0126. Pretreatment of resistant cells with U0126 resulted in restoration of sensitivity to gefitinib. Gefitinib was more effective in inhibiting ERK1/2 and Akt phosphorylation in IGROV-1 cells than in IGROV-1/OHP and IGROV-1/Pt1 cells. Phospho-p38 was up-regulated in the resistant sublines, indicating the concomitant activation of distinct mitogen-activated protein kinases. The up-regulation of phospho-p38 was associated with a peculiar localization of EGFR, which, in resistant sublines, was mainly internalized. In conclusion, our results indicate that the development of resistance to platinum drugs is associated with multiple alterations including deregulation of survival pathways activated by EGFR resulting in a reduced cellular response to gefitinib.

Cooperation between p53 and p73 in cisplatin-induced apoptosis in ovarian carcinoma cells.

The present study was designed to explore the role of p73 in response to cisplatin. In contrast to cisplatin-resistant ovarian carcinoma cells, pharmacological drug concentrations, which caused induction of p53, induced a marginal increase of p73 in sensitive cells. The effect was more marked at high concentrations, with no evidence of p21(WAF1) induction. This behaviour, associated with substantial apoptosis, suggests cell inability to activate DNA damage checkpoint following extensive stress. Although p73 appears to be implicated mainly in response to high stress conditions, the available results support a cooperation between p53 and p73 in cisplatin-induced apoptosis in sensitive cells.

Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study.

2D gel electrophoresis is a tool for measuring protein regulation, involving image analysis by dedicated software (PDQuest, Melanie, etc.). Here, partial least squares discriminant analysis was applied to improve the results obtained by classic image analysis and to identify the significant spots responsible for the differences between two datasets. A human colon cancer HCT116 cell line was analyzed, treated and not treated with a new histone deacetylase inhibitor, RC307. The proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles. Some of the regulated spots were identified by tandem mass spectrometry. The preliminary data are encouraging and the protein modulation reported is consistent with the antitumoral effect of RC307 on the HCT116 cell line. Partial least squares discriminant analysis coupled with backward elimination variable selection allowed the identification of a larger number of spots than classic PDQuest analysis. Moreover, it allows the achievement of the best performances of the model in terms of prediction and provides therefore more robust and reliable results. From this point of view, the multivariate procedure applied can be considered a good alternative to standard differential analysis, also taking into account the interdependencies existing among the variables.

Proteomic approaches for studying chemoresistance in cancer.

The role of various proteins involved in drug resistance in tumor cells is discussed in this review. Two types of studies are covered: those performed in the preproteomics era and those carried out with modern proteomic tools, namely 2D (electrophoretic) maps and 2D chromatography. In the preproteomic studies, one protein had generally been held responsible for a given chemoresistance. However, analysis via proteomic tools may reveal entire sets of proteins that are up- or downregulated (or switched on/off) in chemoresistant tumor cell lines compared with parental tumor lines. Therefore, it appears more realistic to expect that exposure of cells to drugs results in the activation of different mechanisms of resistance. Such investigations have led to the broadly shared opinion that exposure of cells to drugs results in the activation of different mechanisms of resistance, and that a specific drug-resistant phenotype consists of several molecular mechanisms that are simultaneously active. The proteomic papers reviewed clearly support the hypothesis that many metabolic pathways are affected during the resistance process. Although the modulation of expression levels of such proteins is not clear proof of their role in drug resistance per se, at least some of the themes are very likely to be involved in the resistance phenotype, and thus may be potential targets for new drugs. It is hoped that this review will bring new insight in this field and will stimulate novel and deeper searches with proteomic tools (including prefractionation of subcellular organelles, such as nuclei, to bring to the fore low-abundance proteins that might be responsible for the onset of drug resistance).

A proteomic approach to cisplatin resistance in the cervix squamous cell carcinoma cell line A431.

Since drug resistance is a complex and multifactorial event involving activation/repression of multiple biochemical pathways, we used a proteomic approach to study cisplatin resistance and drug response in human tumor cell lines. The cervix squamous cell carcinoma cell line A431 and its cisplatin-resistant subline, A431/Pt, were used as a model system. The experimental set-up involved not just a two-way comparison of the control vs. the drug-resistant cell line, but also an acute cisplatin treatment of both cell lines, leading to a four-way comparison, as follows: 1) A431 vs. A431/Pt cells; 2) A431 vs. A431 cisplatin exposed cells; 3) A431/Pt vs. A431/Pt cisplatin exposed cells; 4) A431 cisplatin exposed cells vs. A431/Pt cisplatin exposed cells. We found modulation of proteins, which could be classified under various categories, such as molecular chaperones (e.g. heat-shock proteins HSP60, HSP90, HSC71, heat-shock cognate 71 kDa protein), Ca2+-binding proteins (e.g. calmodulin, calumenin), proteins involved in drug detoxification (such as peroxiredoxins PRX 2 and PRX 6, and glutathione-S-transferase, GST), anti-apoptotic proteins (such as 14-3-3 switched on in cisplatin-exposed cells) and ion channels (such as VDAC-1, voltage-dependent anion-selective channel). In particular, the basal levels of HSC71 and HSP60 were increased in A431/Pt cells as compared to A431 cells, and cisplatin exposure resulted in up-regulation of HSP60 and HSP90 only in A431 cells. Moreover, cisplatin exposure up-regulated the anti-apoptotic 14-3-3 protein in both cell lines, GST in sensitive cells and PRX6 in A431/Pt cells. These findings are consistent with a constitutive expression of defence factors by resistant cells and with activation by cisplatin of mechanisms acting to protect cells from drug-induced damage. This pattern of response, also observed in parental cells, could reflect an intrinsic resistance of this tumor type.