Proteome Analysis with Classical 2D-PAGE

2021 ◽  
pp. 53-62
Author(s):  
Caroline May ◽  
Frederic Brosseron ◽  
Kathy Pfeiffer ◽  
Kristin Fuchs ◽  
Helmut E. Meyer ◽  
...  
Keyword(s):  
2012 ◽  
Vol 33 (16) ◽  
pp. 2537-2545 ◽  
Author(s):  
Katja Walpurgis ◽  
Maxie Kohler ◽  
Andreas Thomas ◽  
Folker Wenzel ◽  
Hans Geyer ◽  
...  

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Magnus Centlow ◽  
Stefan R. Hansson ◽  
Charlotte Welinder

The human placenta is a difficult tissue to work with using proteomic technology since it contains large amounts of lipids and glycogen. Both lipids and glycogen are known to interfere with the first step in the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the isoelectric focusing. In order to gain the best possible protein separation on 2D-PAGE, an optimized sample preparation protocol for placental proteins was developed. Two different buffers, urea/CHAPS and Hepes, were used for solubilization in combination with six different precipitation methods. The removal of glycogen from the samples by centrifugation was crucial for the final proteome maps. Solubilization with urea/CHAPS in combination with dichloromethane/methanol or acidified acetone proved to be the best precipitation procedures. When applied to clinical placenta samples apolipoprotein A1 was found to be accumulated in the preeclamptic placenta, where it may either have a nutritional effect or act as a modifier of signal transduction.


2005 ◽  
Vol 2005 (Fall) ◽  
Author(s):  
Stephanie Pütz ◽  
Lars Hofmann ◽  
Thorsten Stiewe ◽  
Albert Sickmann

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1915-1915
Author(s):  
Marc Weinkauf ◽  
Grit Hutter ◽  
Yvonne Zimmermann ◽  
Elena Hartmann ◽  
Andreas Rosenwald ◽  
...  

Abstract Abstract 1915 Poster Board I-938 Introduction: Protein kinase C beta (PKCbeta), a pivotal enzyme in B-cell signaling and survival, is over-expressed in most cases of mantle cell lymphoma (MCL) and results in activation of PI3K/AKT pathway. Enzastaurin, an oral serine/threonine kinase inhibitor, suppresses signaling through PKCbeta/PI3K/AKT pathways, induces apoptosis, reduces proliferation, and suppresses tumor-induced angiogenesis. Aim: To optimize the treatment options with this promising inhibitor the goal of this study was to elucidate the molecular pathways altered by Enzastaurin treatment in MCL. Methods: Four documented MCL cell lines (Granta 519, HBL-2, Jeko-1, Rec-1) were harvested after 2-8h Enzastaurin exposure at a previously defined dose of 10μM and analyzed by RNA-array and proteome analysis as previously described (2D-polyacrylamide-gel-electrophoresis (2D-PAGE); Weinkauf 2009). Regulated molecules were mapped in a functional interaction network and candidates representing different pathways were verified by Western blotting. Results: Enzastaurin exposure led to significant reduction of cell viability in all cell lines (15-20%). This was also reflected in distinct alterations of the observed protein patterns in 2D-PAGE after enzastaurin exposure. Of a total of 977 concurrent protein spots 115 (12%) spots exhibited significantly (>3fold) altered protein levels after 4h of enzastaurin exposure. Mass spectrometry of 62 protein spots (39 increase; 23 decreased) identified 108 different candidate proteins, which were used to create a protein interaction network identifying the affected functional pathways. The results of the 2D-PAGE analysis were verified by Western blot in selected candidate proteins of apoptosis (VIM, PLEC1), DNA-repair (RAD50, PCNA, RFC1) and gene expression (EEF1D, SMC1A) pathways. In parallel, RNA-expression array analysis identified 180 different genes regulated early after enzastaurin treatment. Again these genes were mapped to an interaction network, highlighting enzastaurin involvement in e.g. NFkB-, apoptosis and B-cell- and death receptor signaling pathways. Interestingly, the involved genes complemented the regulated proteins in the functional pathways. Network analysis of both screenings (2D-PAGE-based proteomics and RNA-expression array) classified the candidate molecules in functional groups, including DNA repair and replication (e.g. RAD50, PCNA), apoptosis (e.g.PSMC4, VIM), signal transduction (e.g. GRB2, EF1D) and gene expression/mRNA processing (e.g.EEF1D, SFRS7). Thus, combined analysis of both screening methods resulted in a more comprehensive network than each respective analysis. Conclusion: Enzastaurin-treatment affects three main cellular control mechanisms as highlighted by two independent screening approaches (proteomics and expression array analysis). Interestingly, these two layers of molecular response (protein and RNA respectively) resulted in minimal overlap of identified molecules at this early (4h) time, but indicated common pathways nonetheless. Ongoing experiments now incorporate this knowledge to select optimal combination partners of enzastaurin. Disclosures: Dreyling: Lilly Deutschland GmbH: Research Funding.


BMC Genomics ◽  
2004 ◽  
Vol 5 (1) ◽  
Author(s):  
Mary Kathryn Doud ◽  
Michael W Schmidt ◽  
David Hines ◽  
Claudia Naumann ◽  
Andreas Kocourek ◽  
...  

2000 ◽  
Vol 10 (6) ◽  
pp. 0705-0711 ◽  
Author(s):  
Jong-Soon Choi ◽  
Dae-Sup Kim ◽  
Jinsuk Lee ◽  
Soo-Jung Kim ◽  
Seung-Il Kim ◽  
...  

2005 ◽  
Vol 94 (3) ◽  
pp. 302-314 ◽  
Author(s):  
Dagmar Fuchs ◽  
Isabel Winkelmann ◽  
Ian T. Johnson ◽  
Edwin Mariman ◽  
Uwe Wenzel ◽  
...  

The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.


2000 ◽  
Vol 10 (6) ◽  
pp. 705-711 ◽  
Author(s):  
Jong-Soon Choi ◽  
Dae-Sup Kim ◽  
Jinsuk Lee ◽  
Soo-Jung Kim ◽  
Seung-Il Kim ◽  
...  

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Sanja Kiprijanovska ◽  
Sotir Stavridis ◽  
Oliver Stankov ◽  
Selim Komina ◽  
Gordana Petrusevska ◽  
...  

Proteome analysis of the urine has shown that urine contains disease-specific information for a variety of urogenital system disorders, including prostate cancer (PCa). The aim of this study was to determine the protein components of urine from PCa patients. Urine from 8 patients with clinically and histologically confirmed PCa was analyzed by conventional 2D PAGE. The MS identification of the most prominent 125 spots from the urine map revealed 45 distinct proteins. According to Gene Ontology, the identified proteins are involved in a variety of biological processes, majority of them are secreted (71%), and half of them are enzymes or transporters. Comparison with the normal urine proteome revealed 11 proteins distinctive for PCa. Using Ingenuity Pathways Analysis, we have found 3 proteins (E3 ubiquitin-protein ligase rififylin, tumor protein D52, and thymidine phosphorylase) associated with cellular growth and proliferation (p=8.35×10-4-3.41×10-2). The top network of functional associations between 11 proteins was Cell Death and Survival, Cell-To-Cell Signaling and Interaction, and System Development and Function (p=10-30). In summary, we have created an initial proteomic map of PCa patient’s urine. The results from this study provide some leads to understand the molecular bases of prostate cancer.


Author(s):  
Caroline May ◽  
Frederic Brosseron ◽  
Kathy Pfeiffer ◽  
Helmut E. Meyer ◽  
Katrin Marcus
Keyword(s):  

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