Proteomic analysis of human osteoarthritic chondrocytes reveals protein changes in stress and glycolysis

Osteoarthritis (OA) is characterized by cartilage degradation. The chondrocyte is the only cell type present in mature cartilage, and it is important in the control of cartilage integrity. The aim of this study was to analyze, by a proteomic approach, the changes that are characteristic of OA chondrocytes, and to identify new OA-related proteins. Chondrocytes were isolated from the cartilage of ten OA patients undergoing joint replacement and ten donors with no history of joint disease. Whole-cell proteins were resolved by 2-DE and stained with SYPRO Ruby. Protein expression patterns of 2-DE gels from OA and normal chondrocyte proteins were analyzed with PDQuest 7.3.1 software. OA-related proteins were identified by MALDI-TOF or MALDI-TOF/TOF MS. The results were validated for ANXA1, GSTO1, GRP78, and HSP90beta in cells by Western blotting and in tissue cartilage by immunohistochemistry. Results showed an average of 700 protein spots that were present in the 2-DE gels. Compared to normal chondrocytes, 19 protein spots were found to be significantly increased in OA cells (ratio OA:N> or =2.0, p<0.05), whereas nine were decreased in OA chondrocytes (ratio OA:N< or =0.5, p<0.05). Three stress response proteins were increased (HSP90beta, GRP78, and GRP94) and three proteins involved in glycolysis were decreased (enolase, glyceraldehyde 3-phosphate dehydrogenase, and fructose biphosphate aldolase). Functionally, almost all proteins could be classified as proteins involved in cellular metabolism (33%), structure (21%), or protein targeting (21%).     

猪卵母细胞蛋白质组双向电泳体系的建立及初步分析

建立了猪(Sus scrofa)卵母细胞蛋白质双向电泳平台,并对裂解液的组成、样品处理、双向电泳程序等相关技术进行优化,得到清晰的微量卵母细胞蛋白质的电泳图谱.利用上述优化后的体系分别对未成熟和成熟的猪卵母细胞进行双向电泳分析,并用ImageMaser软件对图谱进行比对分析.结果表明,电泳图谱上大约有800个左右的蛋白点,其中差异蛋白35个,包括上调蛋白22个及下调蛋白13个.说明基于双向电泳的蛋白质组学可以用于卵母细胞成熟的蛋白表达差异的研究.     

Proteomic analysis of mouse growth plate cartilage

Cartilage is a highly specialized load-bearing tissue with a small number of cells and a high proportion of extracellular matrix (ECM). The abundance of heavily sulfated proteoglycans and a poorly soluble collagenous ECM presents a major technical challenge to 2-DE. Here we report proteomic analysis of mouse growth plate cartilage using novel methodology for tissue dissection and sample prefractionation. We have successfully resolved cartilage tissue extracts by 2-DE for the first time and identified cartilage ECM proteins by Western blotting and MS/MS.     

Analytical and biological variances associated with proteomic studies of Medicago truncatula by two-dimensional polyacrylamide gel electrophoresis

Two-dimensional polyacrylamide gel electrophoresis (2-DE) and mass spectrometry are being used as proteomic tools in an integrated functional genomics program focused on the model legume Medicago truncatula. Due to the perceived high levels of indeterminate error associated with 2-DE we deemed it necessary to quantify the coefficient of variance (or relative standard deviation) for both analytical and biological sources associated with 2-DE of Medicago truncatula leaf protein extracts. Leaf protein extracts were chosen because of their biological significance and due to the more challenging nature of green tissues. Analytical variance was calculated for fifty proteins from ten replicate 2-DE gels of the same protein extract. Biological variance was calculated for the same fifty proteins from ten independent 2-DE gel analyses of ten independent but similar plants grown under identical conditions. Average analytical and biological variances were calculated for both data sets and represent the average variance of approximately 500 independent measurements of protein concentration. Analytical variance was determined to be 16.2% and biological variance was determined to be 24.2%. These average variances provide a quantified and statistical basis for evaluation of protein expression changes in future comparative proteomic investigations. It is proposed that 2-DE measured protein expression levels should differ by a minimum of 3.92sigma (i.e. /+/-2sigma/ and sigma = standard deviation), or 94.7% based on our measured variances, for the difference to be significant at the 95% confidence level.     

大豆雄性不育系与其保持系不同器官蛋白质比较

采用双向凝胶电泳技术对大豆质核互作雄性不育系NJCMS2A及其保持系NJCMS2B的种子、叶片和花药等不同器官蛋白质进行比较分析.结果显示,不育系NJCMS2A与其保持系NJCMS2B的花药2-DE图谱间存在较多差异表达蛋白点,种子2-DE图谱间仅有少量差异表达蛋白点,而叶片2-DE图谱间基本没有差异表达蛋白点.结果表明,不育基因表达具有时空性和器官特异性,与育性有关的蛋白主要在花药中表达.     

Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius

Background  

Two-dimensional gel electrophoresis (2-DE) is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF), a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).     

Current two-dimensional electrophoresis technology for proteomics

Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the workhorse for proteomics. In spite of promising alternative or complementary technologies (e.g. multidimensional protein identification technology, stable isotope labelling, protein or antibody arrays) that have emerged recently, 2-DE is currently the only technique that can be routinely applied for parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. 2-DE enables the separaration of complex mixtures of proteins according to isoelectric point (pI), molecular mass (M_r), solubility, and relative abundance. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms or post-translational modifications. This is in contrast to liquid chromatography-tandem mass spectrometry based methods, which perform analysis on peptides, where M_r and pI information is lost, and where stable isotope labelling is required for quantitative analysis. Today's 2-DE technology with IPGs (Görg et al., Electrophoresis 2000, 21, 1037–1053), has overcome the former limitations of carrier ampholyte based 2-DE (O'Farrell, J. Biol. Chem. 1975, 250, 4007–4021) with respect to reproducibility, handling, resolution, and separation of very acidic and/or basic proteins. The development of IPGs between pH 2.5–12 has enabled the analysis of very alkaline proteins and the construction of the corresponding databases. Narrow-overlapping IPGs provide increased resolution (δpI = 0.001) and, in combination with prefractionation methods, the detection of low abundance proteins. Depending on the gel size and pH gradient used, 2-DE can resolve more than 5000 proteins simultaneously (˜2000 proteins routinely), and detect and quantify < 1 ng of protein per spot. In this article we describe the current 2-DE/MS workflow including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 2-DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two-dimensional protein databases.     

Comparing SILAC and two-dimensional gel electrophoresis image analysis for profiling urokinase plasminogen activator signaling in ovarian cancer cells

Two-dimensional gel electrophoresis (2-DE) image analysis is conventionally used for comparative proteomics. However, there are a number of technical difficulties associated with 2-DE protein separation that limit the depth of proteome coverage, and the image analysis steps are typically labor-intensive and low-throughput. Recently, mass spectrometry-based quantitation strategies have been described as alternative differential proteome analysis techniques. In this study, we investigated changes in protein expression using an ovarian cancer cell line, OVMZ6, 24 h post-stimulation with the relatively weak agonist, urokinase-type plasminogen activator (uPA). Quantitative protein profiles were obtained by MALDI-TOF/TOF from stable isotope-labeled cells in culture (SILAC), and these results were compared to the quantitative ratios obtained using 2-DE gel image analysis. MALDI-TOF/TOF mass spectrometry showed that differential quantitation using SILAC was highly reproducible (approximately 8% coefficient of variation (CV)), and this variance was considerably lower than that achieved using automated 2-DE image analysis strategies (CV approximately 25%). Both techniques revealed subtle alterations in cellular protein expression following uPA stimulation. However, due to the lower variances associated with the SILAC technique, smaller changes in expression of uPA-inducible proteins could be found with greater certainty.     

Proteomic analysis of cartilage proteins

While the analysis of the cartilage proteome is important for our comprehensive understanding of the development and disease of this important tissue, several unique features of cartilage present some technical obstacles. Firstly, cartilage is difficult to obtain in adequate quantities for many protein analyses, especially from mice which are otherwise powerful experimental models. Furthermore, the cartilage extracellular matrix contains an insoluble network of collagen II-containing fibrils that are integrated within an abundant anionic network of aggrecan and hyaluronan aggregates. These interacting networks provide a structural scaffold for the covalent and non-covalent attachment of other proteins and glycoproteins. Consequently, proteomic analysis of cartilage requires extraction of proteins with chaotropic agents to achieve and significant protein solubilization. Finally, isolated chondrocytes are phenotypically unstable, which requires rapid isolation of cells or the use of specific culture conditions. Despite these problems, recent improvements in the sensitivity and reproducibility of two-dimensional electrophoresis (2-DE) and tandem mass spectrometry (MS/MS) techniques, combined with improved tissue preparation and sample pre-fractionation approaches, have made the proteomic characterization of cartilage tissues possible. Here we review the approaches that have been used and describe in detail protocols for the proteomic analysis of cartilage tissues and cells.     

Proteomic analysis of the ventromedial nucleus of the hypothalamus (pars lateralis) in the female rat

The use of proteomics to study changes in the expression of CNS proteins, which may underlie the regulation of physiological and/or behavioral responses, represents an emerging application of this technology. In the current study, the Palkovits' microdissection method was evaluated as a means of obtaining proteomic data from discrete brain nuclei. The pars lateralis of the ventromedial nucleus of the hypothalamus (VMN) was chosen for the initial studies because of its established role in the expression of gonadal hormone dependent female sexual behavior. The VMN from ovariectomized rats was microdissected from 300 microm frozen brain sections using a 500 microm punch. Total proteins were separated using 2-DE. A group consensus of 432 protein spots, visualized by SYPRO Ruby stain, was obtained from gels from four independent VMN samples. A low mean CV and high gel-to-gel correlation coefficients indicate that reproducible 2-DE gels can be generated from microdissected tissue samples. Proteins from the mediobasal hypothalamus (MBH) were also separated on 2-DE gels. Evaluation of the 2-DE maps from the VMN and the MBH revealed different protein profiles, and indicates that microdissection improves the detection of low-abundance proteins, and reduces the relative occurrence of abundant proteins on 2-DE maps.     

Peroxisomal proteomics, a new tool for risk assessment of peroxisome proliferating pollutants in the marine environment

In an attempt to improve the detection of peroxisome proliferation as a biomarker in environmental pollution assessment, we have applied a novel approach based on peroxisomal proteomics. Peroxisomal proteins from digestive glands of mussels Mytilus galloprovincialis were analyzed using 2-DE and MS. We have generated a reference 2-DE map from samples obtained in a well-studied reference area and compared this with peroxisomal proteomes from other sequenced genomes. In addition, by comparing 2-DE maps from control samples with samples obtained in a polluted area, we have characterized the peroxisome proliferation expression pattern associated with exposure to a polluted environment. Over 100 spots were reproducibly resolved per 2-DE map; 55 differentially expressed spots were quantitatively detected and analyzed, and 14 of these showed an increase in protein expression of more than fourfold. Epoxide hydrolase, peroxisomal antioxidant enzyme, and sarcosine oxidase (SOX) have been identified by ESI MS/MS, and acyl-CoA oxidase, multifunctional protein, and Cu,Zn-superoxide dismutase were immunolocalized by Western blotting. Our results indicate that a peroxisomal protein pattern associated to marine pollutant exposure can be generated, and this approach may have a greater potential as biomarker than traditional, single-protein markers.     

Comparative proteomics analysis of serum proteins in ulcerative colitis patients

In the present study, we investigated the differentially expressed proteins associated with ulcerative colitis (UC) using proteomic methods. Two-dimensional electrophoresis (2-DE) technology was performed to separate the total proteins of ulcerative tissues from those of the normal tissues of UC patients. PDQuest software was applied to analyze the obtained 2-DE images. Candidate protein spots between the two groups were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and bioinformatics analysis. The well resolution and reproducible 2-DE patterns of UC and normal tissues were established. Of the 12 differentially expressed proteins, 9 were successfully identified, of which 6 proteins were up-regulated including apolipoprotein C-III, haptoglobin, receptor tyrosine kinase, aldehyde reductase, pericentriolar material 1, and heat shock factor protein 2, and 3 were down-regulated including keratin, filamin A-interacting protein 1, and tropomyosin 3. These identified proteins were related to hormonal modulation, immune response, oxidative stress, and signal conduction. The 2-DE protein expression profile of the UC tissues displays an obvious difference from that of the normal controls. Various proteins may be involved in the occurrence of UC.     

一个新的前列腺癌细胞系分泌蛋白磷酸甘油酸酯激酶的鉴定与分析

目的：建立前列腺癌细胞系C4-2B分泌蛋白双向电泳图谱,并对感兴趣的蛋白进行质谱鉴定,对其表达调控进行初步分析。方法：收集前列腺癌细胞系C4-2B的分泌蛋白,利用双向电泳结合质谱的方法对感兴趣的蛋白进行鉴定,而后利用Western blot等方法对结果进行验证和分析。结果：得到较为稳定的前列腺癌细胞系分泌蛋白C4-2B双向电泳图谱,鉴定了一个新的前列腺癌细胞系分泌蛋白磷酸甘油酸酯激酶,并发现1nmol/L人工合成雄激素R1881可上调其表达。结论：建立了简便的前列腺癌细胞系分泌蛋白双向电泳及质谱分析的研究方法,初步证明磷酸甘油酸酯激酶是前列腺癌细胞系C4-2B新的分泌蛋白,且人工合成雄激素R1881可诱导其表达上调。     

Evaluation of 2-DE protein patterns from pre- and postnatal stages of the mouse brain

Brains of the mouse from three developmental stages, embryo day 16 (Ed16), postnatal stage one week (1W) and eight weeks (8W), were distributed to different laboratories for a collaborative proteome analysis (The Human Brain Proteome Project). As one of the laboratories involved in this project, we separated total protein extracts of the brains by large gel 2-DE. From the 2-DE protein patterns a section was evaluated for each of the three stages according to resolution, reproducibility and quantitative changes using an image analysis software. The evaluated pattern section was selected to allow comparisons of 2-DE patterns between different laboratories on the basis of optimum separation. Changes in protein expression were analysed within two phases of development: Stage Ed16 versus stage 1W and stage 1W versus stage 8W. Out of the 200 protein spots evaluated 5-6% showed quantitative changes in the range of > or = 30% between two stages. The relationship in the frequency of up- and down-regulated protein spots differed between the two investigated phases. Most of the protein spots which showed altered expression between two stages were identified by MS. High quality in protein separation and evaluation is demonstrated.     

Proteomic Analysis of Osteoblasts Exposed to Fluoride In Vitro

Proteomical analysis is defined as the characterization of the entire set of protein encoded a genome. Two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) are main techniques used in proteomic analysis to achieve information about protein expression profiles. Knowledge about the mechanism of skeletal fluorosis can be gained by recognizing changes in protein expression. To better understand the skeletal fluorosis process, osteoblasts isolated from calvarial of neonatal mouse were cultured and treated with 2 ppm fluoride for 72 h, and proteins of the osteoblast were profiled by 2-DE. With the analysis of Image-Master 2D analysis software, we detected a total number of 493 matching spots on 2-DE images. Among them, 28 protein spots showed twofold significant alteration (P < 0.05) in fluoride-exposed groups. Moreover, 12 proteins were identified by MALDI-TOF MS. These identified proteins in fluoride-exposed group were associated with cell proliferation, metabolism, and oxidative folding. Thus, our study provides useful information on fluoride-related changes of proteome and shows that proteomical analysis is a powerful methodology for the better understanding of skeletal fluorosis.     

Proteomic analysis of differential protein expression in platelets of septic patients

Sepsis is one of the major health problems all over the world. Early diagnostic of sepsis is an attractive strategy to decrease the mortality of septic patients. However, an effective biomarker that fulfills all the necessary requirements for the accurate characterization of sepsis is still unavailable until now. In this study, the 2-DE technique followed by mass spectrometry and a database search was used for searching and identifying the differential expressed proteins in platelets between septic patients and paired healthy controls. Platelet 2-DE profiles of septic patients and paired healthy controls with high resolution and reproducibility were obtained. Differential platelet 2-DE profiles between septic patients and paired healthy controls were established. Differential protein spots between normal healthy volunteers and septic patients from platelet 2-DE profiles were identified by 2-DE followed with mass spectrometry and a database search. Five proteins with increased expression were identified between septic patients and healthy controls from platelet samples. These up-expressed proteins were EF-hand calcium-binding domain-containing protein 7, actin, interleukin-1β, glycoprotein IX, and glycoprotein IIB. Sepsis induces a complex regulation of platelet protein changes. Our study highlights the important role of these differential expressed proteins in sepsis, which deserve further research as potential candidates for therapeutic strategies. Furthermore, our research is beneficial for the future developments of sepsis diagnosis and therapy.     

Proteome analysis of rat pancreas induced by pancreatectomy

The previous study demonstrated that the streptozotocin (STZ)-induced diabetic mice can be cured by injecting the regenerating pancreatic extract (RPE) of the partially pancreatectomized Wistar-Kyoto rats. In this study, to characterize the complex pattern of protein expression in RPE, the proteins of altered expression level after the pancreatectomy were identified by 2-dimensional electrophoresis (2-DE) and mass spectrometry. Of 76 significantly up- or down-regulated protein spots, 61 were identified by MALDI-TOF/MS. Moreover, the whole RPE was fractionated into 4 groups using an anion-exchange chromatography and each fraction's cell proliferating activity was measured by MTT assay. Compared to the normal pancreatic extract, fraction 3 and 4 of RPE showed the maximal cell proliferating activity. On 2-DE of 3 and 4 fractions, a total of 10 spots, which are differentially expressed after the pancreatectomy, were identified by MS/MS. Of these identified proteins, Reg III which might be functionally associated with well known regenerating factor (Reg I) was found. Taken together, our results demonstrated that the differential protein expression associated with pancreas regeneration could be sought by 2-DE and mass spectroscopy and suggested that the pre-fractionation method combined with in vitro cell proliferation assay is effectively used to pinpoint the active components for pancreas regeneration.