iTRAQ‐Based Quantitative Proteomic Analysis of Duck Eggshell During Biomineralization

The avian egg is a valuable model for the calcitic biomineralization process as it is the fastest calcification process occurring in nature and is a clear example of biomineralization. In this study, iTRAQ MS/MS is used to detect and study for the first time: 1) the overall duck eggshell proteome; 2) regional differences in the proteome between the inner and outer portions of the duck eggshell. The new reference protein datasets allow us to identify 179 more eggshell proteins than solely using the current release of Ensembl duck annotations. In total, 484 proteins are identified in the entire duck eggshell proteome. Twenty‐eight novel proteins of unknown function that are involved in eggshell formation are also identified. Among the identified eggshell proteins, 54 proteins show differential abundances between the inner, partially mineralized eggshell (obtained 16 h after ovulation) compared to the overall complete eggshell (normally expulsed eggshell). At least 64 of the abundant matrix proteins are common to eggshell of 4 different domesticated bird species (chicken, duck, quail, turkey) and zebra finch. This study provides a new resource for avian eggshell proteomics, and augments the inventory of eggshell matrix proteins that will lead to a deeper understanding of calcitic biomineralization.     

Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling,Two-dimensional Liquid Chromatography,and Tandem Mass Spectrometry

Formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a potentially valuable resource for protein biomarker investigations. In this study, proteins were extracted by a heat-induced antigen retrieval technique combined with a retrieval solution containing 2% SDS from FFPE tissues of normal nasopharyngeal epithelial tissues (NNET) and three histological types of nasopharyngeal carcinoma (NPC) with diverse differentiation degrees. Then two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling was employed to quantitatively identify the differentially expressed proteins among the types of NPC FFPE tissues. Our study resulted in the identification of 730 unique proteins, the distributions of subcellular localizations and molecular functions of which were similar to those of the proteomic database of human NPC and NNET that we had set up based on the frozen tissues. Additionally, the relative expression levels of cathepsin D, keratin8, SFN, and stathmin1 identified and quantified in this report were consistent with the immunohistochemistry results acquired in our previous study. In conclusion, we have developed an effective approach to identifying protein changes in FFPE NPC tissues utilizing iTRAQ technology in conjunction with an economical and easily accessible sample preparation method. (J Histochem Cytochem 58:517–527, 2010)     

Comparative iTRAQ‐Based Quantitative Proteomic Analysis of Pelteobagrus vachelli Liver under Acute Hypoxia: Implications in Metabolic Responses

More and more frequently these days, aquatic ecosystems are being stressed by nutrient enrichment, pollutants, and global warming, leading to a serious depletion in oxygen concentrations. Although a sudden, significant lack of oxygen will result in mortality, fishes can have an acute behavior (e.g., an increase in breathing rate, reduction in swimming frequency) and physiology responses (e.g., increase in oxygen delivery, and reduction in oxygen consumption) to hypoxia, which allows them to maintain normal physical activity. Therefore, in order to shed further light on the molecular mechanisms of hypoxia adaptation in fishes, the authors conduct comparative quantitative proteomics on Pelteobagrus vachelli livers using iTRAQ. The research identifies 511 acute hypoxia‐responsive proteins in P. vachelli. Furthermore, comparison of several of the diverse key pathways studied (e.g., peroxisome pathway, PPAR signaling pathway, lipid metabolism, glycolysis/gluco‐neogenesis, and amino acid metabolism) help to articulate the different mechanisms involved in the hypoxia response of P. vachelli. Data from proteome analysis shows that P. vachelli can have an acute reaction to hypoxia, including detoxification of metabolic by‐products and oxidative stress in light of continued metabolic activity (e.g., peroxisomes), an activation in the capacity of catabolism to get more energy (e.g., lipolysis and amino acid catabolism), a depression in the capacity of biosynthesis to reduce energy consumption (e.g., biosynthesis of amino acids and lipids), and a shift in the aerobic and anaerobic contributions to total metabolism. The observed hypoxia‐related changes in the liver proteome of the fish can help to understand or can be related to the hypoxia‐related response that takes place in similar conditions in the liver or other proteomes of mammals.     

Impacts of Dietary Pleurotus eryngii Polysaccharide on Nutrient Digestion,Metabolism, and Immune Response of the Small Intestine and Colon—An iTRAQ‐Based Proteomic Analysis

Pleurotus eryngii polysaccharides have been shown to exert significant biological activities to the host. However, few studies have been conducted on its effects on gastrointestinal tract (GIT) health alteration. In the present study, small intestinal and colonic proteome alterations generated by dietary supplementation with a novel homogeneous P. eryngii polysaccharide (PEP) in C57BL/6 mice, based on the isobaric tag for relative and absolute quantification (iTRAQ) proteomics, are investigated. Compared to the control group, PEP supplementation result in a total of 113 and 194 significant differential proteins (DPs) in the small intestine and colon, respectively. Interestingly, DPs in small intestine are mainly related to the transport and biosynthetic process, along with the digestion and absorption pathway of nutrients, whereas the colonic DPs are significantly found participating in numerous metabolic processes. Moreover, the alterations of some DPs in small intestine and colon are speculated to correlate with the colonic microbiota structure and are involved in the regulation of host immune response. Subsequently, some critical DPs of small intestine and colon are selected and validated by Western blotting. The current research facilitated the generation of potential insights into the health benefit activities and functional mechanisms of polysaccharides from P. eryngii.     

Proteomic investigation of 5-fluorouracil resistance in a human hepatocellular carcinoma cell line

Multi-drug resistance (MDR) is a major obstacle towards a successful treatment of hepatocellular carcinoma (HCC). The mechanisms of MDR are intricate and have not been fully understood. Therefore, we employed a cell-line model consisting of the 5-fluorouracil (5-FU) resistant BEL7402/5-FU cell line and its parental BEL7402 cell line. Using relative and absolute quantification (iTRAQ)-coupled 2D LC-MS/MS, a successfully exploited high-throughput proteomic technology, in total, 660 unique proteins were identified and 52 proteins showed to be differentially expressed in BEL7402/5-FU compared with BEL7402. Several differentially expressed proteins were further validated by Western blot and real-time quantitative RT-PCR analysis. Furthermore, the association of MDR with ANXA3, one of the highly expressed proteins in BEL7402/5-FU, was verified. Our study represents the first successful application of iTRAQ technology for MDR mechanisms analysis in HCC. Many of the differentially expressed proteins identified had not been linked to MDR in HCC before, which provide valuable information for further understanding of MDR.     

An automated in‐gel digestion/iTRAQ‐labeling workflow for robust quantification of gel‐separated proteins

Simple protein separation by 1DE is a widely used method to reduce sample complexity and to prepare proteins for mass spectrometric identification via in‐gel digestion. While several automated solutions are available for in‐gel digestion particularly of small cylindric gel plugs derived from 2D gels, the processing of larger 1D gel‐derived gel bands with liquid handling work stations is less well established in the field. Here, we introduce a digestion device tailored to this purpose and validate its performance in comparison to manual in‐gel digestion. For relative quantification purposes, we extend the in‐gel digestion procedure by iTRAQ labeling of the tryptic peptides and show that automation of the entire workflow results in robust quantification of proteins from samples of different complexity and dynamic range. We conclude that automation improves accuracy and reproducibility of our iTRAQ workflow as it minimizes the variability in both, digestion and labeling efficiency, the two major causes of irreproducible results in chemical labeling approaches.     

Differential Proteomic Analysis of Dimethylnitrosamine (DMN)‐Induced Liver Fibrosis

Liver fibrosis is a common pathological feature of many chronic liver diseases. To characterize the entire panorama of proteome changes in dimethylnitrosamine (DMN)‐induced liver fibrosis, isobaric tags for relative and absolute quantitation (iTRAQ)‐based differential proteomic analysis is performed with DMN‐induced liver fibrosis rats. A total of 4155 confidently identified proteins are found, with 365 proteins showing significant changes (fold changes of >1.5 or < 0.67, p < 0.05). In metabolic activation, proteins assigned to drug metabolism enzymes (e.g., CYP2D1) change, suggesting that the liver protection mechanism is activated to relieve DMN toxicity. In addition, the altered proteins of immune response and oxidative stress may activate hepatic stellate cells. Glucose metabolism disorder in DMN model rats is demonstrated by a decrease in key enzymes (e.g., ACSL1) in fatty acid metabolism, a tricabolic acid cycle‐related enzyme (SDH), glycogenolysis enzyme, and gluconeogenesis enzymes (PC, PCKGC) and by an increase in glycolysis enzymes (e.g., HXK1). Meanwhile, alterations in iron and calcium ion homeostasis proteins are observed. Our results also show that mitochondrial dysfunction may be involved in DMN hepatotoxicity. In conclusion, these altered liver proteins in the DMN model and control rats provide data for understanding the functional mechanism of liver fibrosis.     

Blue Native/SDS‐PAGE and iTRAQ‐Based Chloroplasts Proteomics Analysis of Nicotiana tabacum Leaves Infected with M Strain of Cucumber Mosaic Virus Reveals Several Proteins Involved in Chlorosis Symptoms

Virus infection in plants involves necrosis, chlorosis, and mosaic. The M strain of cucumber mosaic virus (M‐CMV) has six distinct symptoms: vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery, and secondary mosaic. Chlorosis indicates the loss of chlorophyll which is highly abundant in plant leaves and plays essential roles in photosynthesis. Blue native/SDS‐PAGE combined with mass spectrum was performed to detect the location of virus, and proteomic analysis of chloroplast isolated from virus‐infected plants was performed to quantify the changes of individual proteins in order to gain a global view of the total chloroplast protein dynamics during the virus infection. Among the 438 proteins quantified, 33 showed a more than twofold change in abundance, of which 22 are involved in the light‐dependent reactions and five in the Calvin cycle. The dynamic change of these proteins indicates that light‐dependent reactions are down‐accumulated, and the Calvin cycle was up‐accumulated during virus infection. In addition to the proteins involved in photosynthesis, tubulin was up‐accumulated in virus‐infected plant, which might contribute to the autophagic process during plant infection. In conclusion, this extensive proteomic investigation on intact chloroplasts of virus‐infected tobacco leaves provided some important novel information on chlorosis mechanisms induced by virus infection.     

Study of monocyte membrane proteome perturbation during lipopolysaccharide‐induced tolerance using iTRAQ‐based quantitative proteomic approach

Human monocytes' exposure to low‐level lipopolysaccharide (LPS) induces temporary monocytic insensitivity to subsequent LPS challenge. The underlying mechanism of this phenomenon could have important clinical utilities in preventing and/or treating severe infections. In this study, we used an iTRAQ‐based quantitative proteomic approach to comprehensively characterize the membrane proteomes of monocytes before and after LPS exposure. We identified a total of 1651 proteins, of which 53.6% were membrane proteins. Ninety‐four percent of the proteins were quantified and 255 proteins were shown to be tightly regulated by LPS. Subcellular location analysis revealed organelle‐specific response to LPS exposure: more than 90% of identified mitochondrial membrane proteins were significant downregulated, whereas the majority of proteins from other organelles such as ER, Golgi and ribosome were upregulated. Moreover, we found that the expression of most receptors potentially involved in LPS signal pathway (CD14, toll‐like receptor 4, CD11/CD18 complex) were substantially decreased, while the expression of molecules involved in LPS neutralization were enhanced after LPS challenge. Together, these findings could be of significance in understanding the mechanism of LPS tolerance and provide values for designing new approaches for regulating monocytic responses in sepsis patients.     

烟草叶片衰老期过程中的蛋白质组学分析

大田烟叶生产过程中因打顶打叉的处理,改变了烟叶正常的衰老模式。为研究这一特殊的衰老机制,我们自旺长期开始,对‘云烟87’不同发育阶段烟株的中部叶片,进行形态观测、生理生化分析及蛋白质组学检测。结果显示：随着烟叶的逐渐成熟和衰老,烟草的叶色逐渐变黄,叶片逐渐变短、变窄,厚度减少;解剖结构清晰看到栅栏组织和海绵组织从最初的整齐排列到逐渐排列紊乱,组织细胞间轮廓不明显,细胞间隙明显增大;亚显微观测表明,淀粉粒在叶绿体中逐渐积累,类囊体片层结构被挤散,叶绿体膜被撑破。生理与生化分析表明衰老过程伴随着光合作用速率下降,光合色素降解加速,呼吸代谢的增加,这可能与衰老叶片中叶绿体逐渐崩塌和细胞膜透性增加相一致。iTRAQ标记方法共检测到不同发育阶段432个差异表达蛋白质,其中注释到308个与多种生命过程相关。蛋白差异富集分析表明,烟草叶片衰老过程中与光合作用等合成代谢相关蛋白多下调表达,而逆境反应及呼吸作用等分解代谢相关蛋白多上调表达。     

Discovery and identification of serum potential biomarkers for pulmonary tuberculosis using iTRAQ‐coupled two‐dimensional LC‐MS/MS

Pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis is a chronic disease. Currently, there are no sufficiently validated biomarkers for early diagnosis of TB infection. In this study, a panel of potential serum biomarkers was identified between patients with pulmonary TB and healthy controls by using iTRAQ‐coupled 2D LC‐MS/MS technique. Among 100 differentially expressed proteins screened, 45 proteins were upregulated (>1.25‐fold at p < 0.05) and 55 proteins were downregulated (<0.8‐fold at p < 0.05) in the TB serum. Bioinformatics analysis revealed that the differentially expressed proteins were related to the response to stimulus, the metabolic and immune system processes. The significantly differential expression of apolipoprotein CII (APOCII), CD5 antigen‐like (CD5L), hyaluronan‐binding protein 2 (HABP2), and retinol‐binding protein 4 (RBP4) was further confirmed using immunoblotting and ELISA analysis. By forward stepwise multivariate regression analysis, a panel of serum biomarkers including APOCII, CD5L, and RBP4 was obtained to form the disease diagnostic model. The receiver operation characteristic curve of the diagnostic model was 0.98 (sensitivity = 93.42%, specificity = 92.86%). In conclusion, APOCII, CD5L, HABP2, and RBP4 may be potential protein biomarkers of pulmonary TB. Our research provides useful data for early diagnosis of TB.     

Possible target‐related proteins and signal network of bufalin in A549 cells suggested by both iTRAQ‐based and label‐free proteomic analysis

Bufalin (BF) exhibited antiproliferation and antimigration effects on human A549 lung cancer cells. To search its target‐related proteins, protein expression profiles of BF‐treated and control cells were compared using two quantitative proteomic methods, iTRAQ‐based and label‐free proteomic analysis. A total of 5428 proteins were identified in iTRAQ‐based analysis while 6632 proteins were identified in label‐free analysis. The number of common identified proteins of both methods was 4799 proteins. By application of 1.20‐fold for upregulated and 0.83‐fold for downregulated cutoff values, 273 and 802 differentially expressed proteins were found in iTRAQ‐based and label‐free analysis, respectively. The number of common differentially expressed proteins of both methods was 45 proteins. Results of bioinformational analysis using Metacore^TM showed that the two proteomic methods were complementary and both suggested the involvement of oxidative stress and regulation of gene expression in the effects of BF, and fibronectin‐related pathway was suggested to be an important pathway affected by BF. Western blotting assay results confirmed BF‐induced change in levels of fibronectin and other related proteins. Overexpression of fibronectin by plasmid transfection ameliorated antimigration effects of BF. Results of the present study provided information about possible target‐related proteins and signal network of BF.     

LCM纯化的鼻咽癌间质和正常鼻咽间质的定量蛋白质组学研究

间质在肿瘤发生发展中的作用越来越受到重视．为寻找与鼻咽癌( nasopharyngeal carcinoma,NPC )发生发展相关的特异性间质蛋白,采用激光捕获显微切割技术( laser capture microdissection,LCM )纯化鼻咽癌间质和正常鼻咽黏膜间质,荧光差异双向凝胶电泳( fluorescent two-dimensional difference gel electrophoresis 2-D,DIGE )结合质谱技术分离鉴定间质相关蛋白．Western blot及免疫组织化学技术验证了其中3个差异蛋白(CapG、L-plastin和S100A9),证实了2D-DIGE结果的可靠性．建立了LCM 纯化的鼻咽癌间质和正常鼻咽间质的荧光差异蛋白表达图谱,高通量筛选与肿瘤发生相关的间质蛋白,共得到34个有统计学意义的蛋白质点,质谱鉴定得到20个差异蛋白．研究结果提示：这些差异表达的蛋白质将有助于阐明鼻咽癌细胞和周围间质的关系．对间质蛋白功能的进一步研究,将有助于解析间质在肿瘤发生中的作用机制,并为从间质途径寻找肿瘤治疗靶标提供新思路．