Bad-dependent rafts alteration is a consequence of an early intracellular signal triggered by interleukin-4 deprivation

Many molecules are inducibly localized in lipid rafts, and their alteration inhibits early activation events, supporting a critical role for these domains in signaling. Using confocal microscopy and cellular fractionation, we have shown that the pool of Bad, attached to lipid rafts in proliferating cells, is released when cells undergo apoptosis. Kinetic studies indicate that rafts alteration is a consequence of an intracellular signal triggered by interleukin-4 deprivation. Growth factor deprivation in turn induces PP1alpha phosphatase activation, responsible for cytoplasmic Bad dephosphorylation as well as caspase-9 and caspase-3 activation. Caspases translocate to rafts and induce their modification followed by translocation of Bad from rafts to mitochondria, which correlates with apoptosis. Taken together, our results suggest that alteration of lipid rafts is an early event in the apoptotic cascade indirectly induced by interleukin-4 deprivation via PP1alpha activation, dephosphorylation of cytoplasmic Bad, and caspase activation.     

Quantitative profiling of LNCaP prostate cancer cells using isotope-coded affinity tags and mass spectrometry

Androgens are involved in the pathogenesis of diseases including adenocarcinoma of the prostate. These hormones are important for growth, maintenance, and integrity of structure and function of the prostate. Androgen-deprivation is currently the only effective systemic therapy for prostate cancer but the effects of androgens on the proteome are still poorly described. Here we quantitatively profile changes in the proteome of LNCaP human prostate cancer cells in response to androgen using the newly developed isotope-coded affinity tag (ICAT) labeling and two-dimensional liquid chromatography-tandem mass spectroscopy (2-D LC-MS/MS). ICAT enables the concurrent identification and comparative quantitative analysis of proteins present in various biological samples including human cell and tissue extracts. Quantification and identification of 139 proteins in complex protein mixtures obtained from androgen-stimulated and unstimulated LNCaP cells were achieved. Changes in levels of 77 proteins in response to androgens were detected. Some of these proteins have been previously reported to be regulated by androgens and include spermine synthase, fatty acid synthase and calreticulin precursor. A large number of proteins that have not been previously reported to be expressed in prostate cells were also quantitatively identified. Examples of these include members of the dual specificity protein phosphatase subfamily, "similar" to hypothetical protein DKFZp434B0328.1, "similar" to 14-3-3 protein zeta and "similar" to hypothetical protein 458, components of the actin cytoskeleton and a range of unknown/uncharacterized proteins. This catalogue of proteins provides an overview of the proteome of prostate cancer cells and the global changes that occur in response to androgens.     

In vitro and in silico processes to identify differentially expressed proteins

We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications.     

Frequencies of ex vivo-activated human immunodeficiency virus type 1-specific gamma-interferon-producing CD8+ T cells in infected children correlate positively with plasma viral load

HIV-specific CD8+ T cells are critical in controlling human immunodeficiency virus (HIV) replication. We present the evaluation of a gamma-interferon (IFN-gamma)-based enzyme linked immunospot (ELISPOT) assay for the quantification of HIV-specific CD8+ T cells from HIV-infected children. We studied 20 HLA-A*0201-positive HIV-infected children. The IFN-gamma production in response to stimulation with two HLA-A*0201-restricted immunodominant CD8 epitopes (SLYNTVATL [SL9] in Gag and ILKEPVHGV [IV9] in Pol) was tested using the ELISPOT assay. The results were compared to labeling with the corresponding tetramers. Among the 20 children, 18 had detectable responses against the SL9 and/or the IV9 epitope using the ELISPOT assay (medians, 351 and 134 spot-forming cells/10(6) peripheral blood mononuclear cells, respectively). Comparison of results from the tetramer and ELISPOT assays suggests that only a fraction of HIV-specific CD8+ T cells were able to produce IFN-gamma. Most importantly, we found that the frequencies of IFN-gamma-producing CD8+ T cells were positively correlated with the viral load whereas the frequencies of tetramer-binding CD8+ T cells were not. The high sensitivity of the ELISPOT assay and the fact that this functional assay provided information different from that of tetramer labeling support its use for measurement of HIV-specific CD8+ T cells. In conclusion, our results show that the ex vivo-activated IFN-gamma-producing HIV-specific CD8+ T-cell subset is dependent upon continuous antigenic stimulation.     

Endogenous expression of nNOS protein in several neuronal cell lines

Several neuronal cell lines were screened for endogenous expression of neuronal nitric oxide synthase (nNOS) protein using Western blot analysis. Detectable levels of the nNOS protein were evident in the SK-N-SH, SH-SY5Y, and N1E-115 neuroblastoma cell lines, as well as the NG108-15 neuroblastoma x glioma hybrid. Only trace amounts were visible in Neuro2A human neuroblastoma cells. The presence of endogenously expressed nNOS in these cells may allow for the study of the interaction between nNOS and the endogenous receptor systems expressed in the same cells.     

Hepatocyte polarity and the peroxisomal compartment: a comparative study

In search of factors that regulate the phenotype of the peroxisomal compartment in wild-type liver parenchymal cells, we compared hepatocyte polarity to peroxisome differentiation, using adult liver as the standard. Differentiation parameters were evaluated in a three-dimensional culture model (spheroid), in 'sandwich' and monolayer primary hepatocyte cultures, and in 15.5 and 18.5-day-old foetal rat liver.Peroxisomes, studied by immunohistochemistry, enzyme histochemistry, and catalase specific activity, were better differentiated depending on foetal age (day 18.5 > day 15.5) and culture type (spheroid > sandwich > monolayer). The hepatocyte polarity markers ATP-, ADP-, and AMP-hydrolysing activities were, in all models, mislocalized at the lateral plasma membrane, whereas in contrast the multidrug resistance-associated protein 2 (mrp2) antigen was always correctly immunolocalized at the apical membrane domain. In cultures, the correct secretion of fluorescein (mrp2-mediated) into bile canaliculi was observed. Bile canaliculi (branching, ultrastructure and immunolocalization of the tight-junction associated protein ZO-1), were better differentiated in 18.5 than in 15.5-day-old foetal liver and in spheroid > sandwich > monolayer cultures.Our results show a parallelism between changes of the peroxisomal compartment and bile canalicular structure together with mrp2-mediated secretory function. Distinct polarization characteristics do not necessarily change simultaneously, suggesting different regulatory mechanisms.     

Synergy between extracellular modules of vascular endothelial cadherin promotes homotypic hexameric interactions

Vascular endothelial (VE) cadherin is an endothelial specific cadherin that plays a major role in remodeling and maturation of vascular vessels. Recently, we presented evidence that the extracellular part of VE cadherin, which consists of five homologous modules, associates as a Ca(2+)-dependent hexamer in solution (Legrand, P., Bibert, S., Jaquinod, M., Ebel, C., Hewat, E., Vincent, F., Vanbelle, C., Concord, E., Vernet, T., and Gulino, D. (2001) J. Biol. Chem. 276, 3581-3588). In an effort to identify which extracellular modules are involved in the elaboration and stability of this hexameric structure, we expressed various VE cadherin-derived fragments overlapping individual or multiple successive modules as soluble proteins, purified each to homogeneity, and tested their propensity to self-associate. Altogether, the results demonstrate that, as their length increases, VE cadherin recombinant fragments generate increasingly complex self-associating structures; although single module fragments do not oligomerize, some two or three module-containing fragments self-assemble as dimers, and four module-containing fragments associate as hexamers. Our results also suggest that, before elaborating a hexameric structure, molecules of VE cadherin self-assemble as intermediate dimers. A synergy between the extracellular modules of VE cadherin is thus required to build homotypic interactions. Placed in a cellular context, this particular self-association mode may reflect the distinctive biological requirements imposed on VE cadherin at adherens junctions in the vascular endothelium.     

Alkyl-lysophospholipid accumulates in lipid rafts and induces apoptosis via raft-dependent endocytosis and inhibition of phosphatidylcholine synthesis

The synthetic alkyl-lysophospholipid (ALP), 1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine, is an antitumor agent that acts on cell membranes and can induce apoptosis. We investigated how ALP is taken up by cells, how it affects de novo biosynthesis of phosphatidylcholine (PC), and how critical this is to initiate apoptosis. We compared an ALP-sensitive mouse lymphoma cell line, S49, with an ALP-resistant variant, S49(AR). ALP inhibited PC synthesis at the CTP:phosphocholine cytidylyltransferase (CT) step in S49 cells, but not in S49(AR) cells. Exogenous lysophosphatidylcholine, providing cells with an alternative way (acylation) to generate PC, rescued cells from ALP-induced apoptosis, indicating that continuous rapid PC turnover is essential for cell survival. Apoptosis induced by other stimuli that do not target PC synthesis remained unaffected by lysophosphatidylcholine. Using monensin, low temperature and albumin back-extraction, we demonstrated that ALP is internalized by endocytosis, a process defective in S49(AR) cells. This defect neither involved clathrin-coated pit- nor fluid-phase endocytosis, but depended on lipid rafts, because disruption of these microdomains with methyl-beta-cyclodextrin or filipin (sequestering cholesterol) or bacterial sphingomyelinase reduced uptake of ALP. Furthermore, ALP was found accumulated in isolated rafts and disruption of rafts also prevented the inhibition of PC synthesis and apoptosis induction in S49 cells. In summary, ALP is internalized by raft-dependent endocytosis to inhibit PC synthesis, which triggers apoptosis.