Comparative Proteomics Analysis Reveals Trans Fatty Acid Isomers Activates Different Pathways in Human Umbilical Vein Endothelial Cell

Trans fatty acid (TFA), a group of unsaturated fats with at least one double bond in the trans configuration, plays a role in lipid metabolism, the structure of the cell membrane phospholipids, and apoptosis. Previous studies demonstrated that TFA was associated with coronary heart disease, obesity, and insulin resistance. Herein, a quantitative proteomics approach estimated the relative abundance of proteins in human umbilical vein endothelial cells treated with TFA (two different TFA structural isomers: 9t‐18:1 and 9t,12t‐18:2). The results revealed that 174 identified proteins were significantly altered with respect to expression. Furthermore, based on the cutoff values, 35 proteins were differentially expressed in the 9t‐18:1 group as compared to the control group, 69 proteins were differentially expressed in 9t,12t‐18:2 group as compared to the control group, and 120 proteins were differentially expressed in the 9t,12t‐18:2 group as compared to the 9t‐18:1 group. Based on the bioinformatics analysis, we found that TFA could alter the structural constitution of the cytoskeleton through protein interactions, localization into the cell membrane, and incorporation into the phospholipid of the cell. In addition, 17 differential apoptosis‐related proteins, including cell division cycle 42, superoxide dismutase 1, glyoxalase I, and macrophage migration inhibitory factor were also identified. Together, these results might emphasize the need for studying TFA‐induced biological processes.     

Proteome‐base biomarkers in diabetes mellitus: Progress on biofluids' protein profiling using mass spectrometry

The worldwide number of individuals suffering from diabetes mellitus (DM) has been projected to rise from 171 million in 2000 to 366 million in 2030. Identification of specific biomarkers for prediction and monitoring of DM is needed not only for the adequate screening diagnosis but also to assist the design of interventions to prevent or delay progression of this pathology and its attendant complications. Proteomic methods based on MS hold special promise for the identification of novel biomarkers that might form the foundation for new clinical tests, but to date, their contribution has been somehow unfruitful. Indeed, from more than 300 proteins found differently modulated in body fluids from diabetic patients, approximately 50 were validated with other approaches like ELISA or Western blotting and the clinical trials are being initiated to employ biofluids’ proteomics (specifically urinary proteomics) in clinical decision. This review provides an overview of MS‐based applications in the identification of potential biomarkers for DM, emphasizing the methodological challenges involved.     

Integrative proteomics for the future US HUPO Fifth Annual Conference from genes to function 22-25 February 2009, San Diego, CA, USA

This report reviews the 5th US HUPO annual conference which was held in San Diego, California, from 22th to 25th February, 2009. The major goal of this year's meeting was to discuss future prospects within the field of proteomics and to push it towards integration with other synergizing technologies. Each day's sessions were guided by three broad themes: The Interface of Proteomics and Genomics, Systems Medicine, and Protein Structure and Modifications. As a summary this meeting has shown, that integration of multiple disciplines and high performance proteomics is needed to meet the demands of future proteomics.     

Anatomic site‐specific proteomic signatures of gastrointestinal stromal tumors

The gastrointestinal stromal tumor (GIST) is the most common mesenchymal malignancy of the gastrointestinal tract. Its clinical course ranges widely from a curable disorder to a highly malignant disease. Although its clinical and molecular characteristics depend on the anatomic site of origin, the molecular background of GIST arising in different anatomical site has not been studied yet. To investigate the proteomic background of GIST, we examined the proteomic features corresponding to the anatomic site of tumor origin. Comparison of the proteomic profile of gastric (23 cases) and small intestinal (9 cases) GIST by 2‐DE revealed 105 protein spots with significantly different intensity (p <0.01) between the two groups. Mass spectrometric study identified 68 distinct proteins for these 105 protein spots, including cancer‐associated ones such as prohibitin, pigment epithelium‐derived factor, and alpha‐actinin 4. The intensity of 37/105 (35.2%) protein spots was significantly concordant with the corresponding mRNA levels (p <0.01). Although both 2‐D DIGE and microarray experiments showed significant up‐regulation of vimentin expression in small intestinal GIST, Western blotting did not show a significant difference between the two groups. In conclusion, our study demonstrates the proteins specially expressed in GIST depending on their site of origin, as well as the unique advantage offered by use of proteomics to acquire such data. The identified proteins may provide clues to understanding the different characteristics of GIST depending on their site of origin.     

蛋白质组学研究进展及其在植物学研究中的应用

蛋白质组是后基因组时代出现的一个新兴研究领域。蛋白质组的研究主要是先通过双向凝胶电泳等方法分离蛋白质,然后用质谱等技术进行鉴定。它是后基因组重要的研究方向之一,具有巨大的商业应用前景,将会推动整个生命科学的发展。蛋白质组研究取得了很大进展,已经成为生物技术中的一个重要领域。     

Differentially expressed proteins during fat accumulation in bovine skeletal muscle

The objective of this study was to identify the proteins involved in bovine intramuscular fat (IMF) development. Global proteins were monitored in bovine skeletal muscle at muscle-developing versus IMF-increasing stages and with higher versus lower IMF scores, respectively. We identified two differentially expressed (two-fold or more) proteins at the IMF-increasing stage, up-regulated heat shock protein beta 1 (HSPB1) and down-regulated ATP synthase D chain (ATP5H), and two down-regulated proteins with higher IMF scores, carbonic anhydrase 2 (CA2) and myosin light chain 3 (MYL3). In vitro, after adipogenic differentiation, the mRNA expression of HSPB1 and ATP5H did not be changed, but that of CA2 and MYL3 decreased significantly (P < 0.05). After myogenic differentiation, the mRNA expression of HSPB1 increased significantly (P < 0.05), but expression of other genes did not vary. We suggested that CA2 and MYL3, which expressed down during adipogenic differentiation, could be indicative markers for negative regulation of IMF development.     

Identification of melanoma‐specific serological markers using proteomic analyses

The discovery of novel melanoma markers for not only early detection but also monitoring disease status is promising to improve the clinical outcome of patients. In the present study, we performed proteomic comparative analysis of plasma proteins between healthy volunteers and melanoma patients using NanoLC and MALDI‐TOF‐MS. As a result, we were successful in identifying nine proteins that were specifically expressed in melanoma plasma compared with healthy plasma, most of which had not previously been identified as plasma markers of melanoma. The mRNA expression levels of four proteins [pro‐platelet basic protein precursor (PPBP), serum amyloid A2 (SAA2), complement factor H‐related protein 1 precursor (FHR1), inter‐alpha‐trypsin inhibitor heavy chain H4 precursor (IAIH4)] were prominently up‐regulated in several melanoma cell lines compared with melanocytes. Moreover, two proteins (PPBP, SAA) were shown to be expressed in tumor specimens from melanoma patients. In the survival time analysis regarding melanoma patients, the semi‐quantified plasma PPBP levels were statistically negatively correlated with the survival time. Most interestingly, the significant survival benefit was seen in low PBPP level group (< index 20) versus high level (≥ index 20) group. The results suggest that PPBP might be a novel promising serological marker and a prognostic factor specific to melanomas.     

Challenges and advances in systems biology analysis of Bacillus spore physiology; molecular differences between an extreme heat resistant spore forming Bacillus subtilis food isolate and a laboratory strain

Bacterial spore formers are prime organisms of concern in the food industry. Spores from the genus Bacillus are extremely stress resistant, most notably exemplified by high thermotolerance. This sometimes allows surviving spores to germinate and grow out to vegetative cells causing food spoilage and possible intoxication. Similar issues though more pending toward spore toxigenicity are observed for the anaerobic Clostridia.The paper indicates the nature of stress resistance and highlights contemporary molecular approaches to analyze the mechanistic basis of it in Bacilli. A molecular comparison between a laboratory strain and a food borne isolate, very similar at the genomic level to the laboratory strain but generating extremely heat resistant spores, is discussed. The approaches cover genome-wide genotyping, proteomics and genome-wide expression analyses studies. The analyses aim at gathering sufficient molecular information to be able to put together an initial framework for dynamic modelling of spore germination and outgrowth behaviour. Such emerging models should be developed both at the population and at the single spore level. Tools and challenges in achieving the latter are succinctly discussed.     

人前列腺癌PC-3细胞膜蛋白组学的分析

目的分析人前列腺癌PC-3细胞中的所有膜蛋白,全面展示PC-3细胞中的蛋白质表达谱。方法采用一维SDS-PAGE,结合高效液相色谱-串联质谱的方法,分离并鉴定PC-3细胞中的膜蛋白。结果在严格的过滤参数条件下,PC-3细胞中鉴定出2172种蛋白,其中1499种经过基因本体评注(GOA)显示为已知细胞组分,其余为未知细胞组分。在已知细胞组分中,564种(37.6%)蛋白为质膜蛋白,其中138种为跨膜蛋白。跨膜蛋白中,21.17%被预测至少有1个跨膜区,57.66%有1～3个跨膜区,30.66%有4～9个跨膜区,11.66%有不少于10个跨膜区。许多新的蛋白也被鉴定,其中包括假设蛋白和一些cD-NA序列。结论这些被鉴定蛋白的生物学功能和理化性质将有助于进一步理解前列腺癌侵袭和转移的分子机制,为寻找与前列腺癌转移相关的分子提供新的实验证据。