Project description:HIV-1 spreads between CD4 T cells most efficiently through virus-induced cell-cell contacts. To test whether this process potentiates viral spread by activating signaling pathways we developed an approach to analyze the phosphoproteome in infected and uninfected mixed population T cells using differential metabolic labeling and mass spectrometry. We discovered HIV-1 induced activation of signaling networks during viral spread encompassing over 200 cellular proteins. Strikingly, pathways downstream of T cell receptor were the most significantly activated, despite the absence of canonical antigen dependent stimulation. The importance of this pathway was demonstrated by depletion of proteins and we show that HIV-1 Env mediated cell-cell contact, T cell receptor and the Src kinase Lck were essential for signaling dependent enhancement of viral dissemination. This study demonstrates that manipulation of signaling at immune cell contacts by HIV-1 is essential for promoting virus replication and defines a new paradigm for antigen independent T cell signaling.
Project description:We focus on the characterization of proteins in the nuclear environment of β-cells after brief, high glucose-stimulation. We compared purified nuclei derived from β-cells stimulated with 17mM glucose for 0, 2, and 5 minutes using quantitative proteomics, a time frame that most likely does not result in translation of new protein in the cell.
Project description:Although the structural and functional effects of exercise on the heart are well established, the metabolic changes that occur in the heart during and after exercise remain unclear. In this study, we used metabolomics to assess time-dependent changes in the murine cardiac metabolome following 1 session of treadmill exercise. After the exercise bout, we also recorded blood lactate, glucose, and ketone body levels and measured cardiac mitochondrial respiration. In both male and female mice, moderate- and high-intensity exercise acutely increased blood lactate levels. In both sexes, low- and moderate-intensity exercise augmented circulating 3-hydroxybutryrate levels immediately after the exercise bout; however, only in female mice did high-intensity exercise increase 3-hydroxybutyrate levels, with significant increases occurring 1 h after the exercise session. Untargeted metabolomics analyses of sedentary female and male hearts suggest considerable sex-dependent differences in basal cardiac metabolite levels, with female hearts characterized by higher levels of pantothenate, pyridoxamine, homoarginine, tryptophan, and several glycerophospholipid and sphingomyelin species and lower levels of numerous metabolites, including acetyl coenzyme A, glucuronate, gulonate, hydroxyproline, prolyl-hydroxyproline, carnosine, anserine, and carnitinylated and glycinated species, as compared with male hearts. Immediately after a bout of treadmill exercise, both male and female hearts had higher levels of corticosterone; however, female mice showed more extensive exercise-induced changes in the cardiac metabolome, characterized by significant, time-dependent changes in amino acids (e.g., serine, alanine, tyrosine, tryptophan, branched-chain amino acids) and the ketone body 3-hydroxybutyrate. Results from experiments using isolated cardiac mitochondria suggest that high-intensity treadmill exercise does not acutely affect respiration or mitochondrial coupling; however, female cardiac mitochondria demonstrate generally higher adenosine diphosphate sensitivity compared with male cardiac mitochondria. Collectively, these findings in mice reveal key sex-dependent differences in cardiac metabolism and suggest that the metabolic network in the female heart is more responsive to physiological stress caused by exercise.
Project description:This SuperSeries is composed of the following subset Series: GSE12278: MYC stimulates EZH2 expression by repression of its negative regulator miR-26a GSE12394: murine MYC-dependent lymphoma cells: Dox vs. NoDox treatment Refer to individual Series
Project description:The classification of histologically similar yet molecularly distinct tumors into specific subtypes remains a clinically challenging task. Classification of such tumors into distinct entities based on their cell surface protein expression profiles has been hindered by the lack of an unbiased global approach. Here we use N-glyco FASP, a recently developed mass spectrometric approach based on lectin-enrichment of N-linked glycoproteins, in conjunction with a super-SILAC based quantitative strategy, on patient derived diffuse large B-cell lymphoma cell lines. We mapped 2383 glycosites on more than 1300 proteins, which were highly enriched for cell membrane proteins. The resulting sub-proteome was highly enriched for cell membrane proteins. This N-glyco sub-proteome alone allowed the segregation of the ABC from the GCB subtypes of diffuse large B-cell lymphoma, which before gene expression studies had been considered one disease entity. Encouragingly, many of the glycopeptides driving the segregation belong to proteins previously characterized as segregators in a deep proteome study of these subtypes (S. J. Deeb et al MCP 2012 PMID 22442255). This conforms to the high correlation that we observed between the expression level of the glycosites and their corresponding proteins. Detailed examination of glycosites and glycoprotein expression levels uncovered, amongst other interesting findings, enrichment of transcription factor binding motifs, including known NF-kappa-B related ones. Thus, enrichment of a class of post-translationally modified peptides can classify cancer types as well as reveal cancer specific mechanistic changes.
Project description:When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. We examine how yeast growth and tRNA charging or aminoacylation is affected during amino acid depletion in the presence and absence of GCN2. tRNA charging is measured using a microarray technique which allows for simultaneous measurement of all cytosolic tRNAs. A fully prototrophic and its isogenic GCN2 deletion strain were used. We measured relative tRNA charging levels in yeast strains with an intact and deleted GCN2.
Project description:HHV-6A is a human herpesvirus that integrates into human sub telomeric regions to acquire latency. This latent virus frequently reactivates causing numerous diseases. The project was aimed to understand changes in host cell prteomics upon virus reactivation, which might helpin understanding the pathophysiology of virus reactivation.
Project description:Metastatic lesions are typically not found until patients self-report symptoms or they become radiologically evident. We have developed an engineered metastatic niche (scaffold) that recruits aggressive tumor cells prior to their colonization in other organs. The engineered niche can be monitored for dynamic gene expression, and changes at this site are analogous to those in a native metastatic site (lung) for triple negative breast cancer (4T1 cells). We were able to develop a 10-gene signature from the scaffold that accurately monitors disease progression and recurrence or resistance to resection therapy. This data set acts to dissect the heterogeneity of the cell populations in the engineered and native metastatic niche and identify the cell types that contribute to the success of the signature.