International journal of proteomics最新文献

{"title":"Adsorption of urinary proteins on the conventionally used urine collection tubes: possible effects on urinary proteome analysis and prevention of the adsorption by polymer coating.","authors":"Iwao Kiyokawa,&nbsp;Kazuyuki Sogawa,&nbsp;Keiko Ise,&nbsp;Fumie Iida,&nbsp;Mamoru Satoh,&nbsp;Toshihide Miura,&nbsp;Ryo Kojima,&nbsp;Katsuhiro Katayama,&nbsp;Fumio Nomura","doi":"10.1155/2011/502845","DOIUrl":"https://doi.org/10.1155/2011/502845","url":null,"abstract":"<p><p>One possible factor determining recovery of trace amount of protein biomarker candidates during proteome analyses could be adsorption on urine tubes. This issue, however, has not been well addressed so far. Recently, a new technical device of surface coating by poly(2-methacryloyloxyethyl phosphorylcholine (MPC)-co-n-butyl methacrylate (BMA)) (poly(MPC-co-BMA)) has been developed mainly to prevent the adsorption of plasma proteins. We assessed whether conventionally used urine tubes adsorb trace amount of urinary proteins and, if any, whether the surface coating by poly(MPC-co-BMA) can minimize the adsorption. Proteinuric urine samples were kept in poly(MPC-co-BMA)-coated and noncoated urine tubes for 15 min and possibly adsorbed proteins and/or peptides onto urine tubes were analyzed by SDS-PAGE, 2-DE, and the MALDI-TOF MS. It was found that a number of proteins and/or peptides adsorb on the conventionally used urine tubes and that surface coating by poly(MPC-co-BMA) can minimize the adsorption without any significant effects on routine urinalysis test results. Although it remains to be clarified to what extent the protein adsorption can modify the results of urinary proteome analyses, one has to consider this possible adsorption of urinary proteins when searching for trace amounts of protein biomarkers in urine.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3200127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30373668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat shock proteins in association with heat tolerance in grasses.","authors":"Yan Xu,&nbsp;Chenyang Zhan,&nbsp;Bingru Huang","doi":"10.1155/2011/529648","DOIUrl":"https://doi.org/10.1155/2011/529648","url":null,"abstract":"<p><p>The grass family Poaceae includes annual species cultivated as major grain crops and perennial species cultivated as forage or turf grasses. Heat stress is a primary factor limiting growth and productivity of cool-season grass species and is becoming a more significant problem in the context of global warming. Plants have developed various mechanisms in heat-stress adaptation, including changes in protein metabolism such as the induction of heat shock proteins (HSPs). This paper summarizes the structure and function of major HSPs, recent research progress on the association of HSPs with grass tolerance to heat stress, and incorporation of HSPs in heat-tolerant grass breeding.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/529648","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30255714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics-based disease biomarkers.","authors":"David E Misek,&nbsp;Tadashi Kondo,&nbsp;Mark W Duncan","doi":"10.1155/2011/894618","DOIUrl":"https://doi.org/10.1155/2011/894618","url":null,"abstract":"Sequencing of the human genome has greatly impacted the proteomics-based analysis of disease by providing a framework for understanding the proteome of diseased cells, tissues, and biological fluids. Consequently, there is a growing interest in applying proteomics technologies to define protein pathways involved in various diseases, to identify new biomarkers that correlate with diseases, ideally in their early stages, and to accelerate the development of new therapeutic targets. However, disease-related proteomics applications require that we improve our ability to separate and characterize the components of complex protein mixtures in such a way as to boost both throughput and sensitivity. In response to these demands, the proteomics technologies have been improved markedly over recent years. Today, proteomics, in all its various forms, is proving to be invaluable to our understanding of the biochemistry of health and disease and will likely play a central role in the evolution of personalized medicine. In this special issue, we include reports of novel research findings together with several reviews that highlight advances in key areas. \u0000 \u0000The first two papers of this special issue focus on lung cancer. The first paper, by H. C. Gong et al., addresses the profiling of receptor tyrosine kinase pathway activation and the role of key genetic mutations in human lung tumor cell lines and human lung tumors. The authors defined molecular pathways which may assist in development of targeted lung tumor therapies. Within the second paper, Q. Zhang et al. used proteomic profiling to delineate expression and subcellular localization of multiple forms of aldehyde dehydrogenase in lung adenocarcinoma cell lines. The next two papers focus on pancreatic cancer. The third paper, by R. S. Kwon and D. M. Simeone, reviews the use of protein-based biomarkers for the diagnosis of cystic tumors of the pancreas. The fourth paper, by M. Abulaizi et al., utilizes a three-step proteomic protocol (immunodepletion of abundant serum proteins, followed by fractionation by RP-HPLC and further separation by 2D-PAGE) to discover candidate early detection biomarkers of pancreatic cancer. \u0000 \u0000The next two papers focus on breast cancer, with the fifth paper, by D. E. Misek and E. H. Kim, reviewing the development of protein biomarkers for the early detection of breast cancer. The sixth paper, by J. He et al., addresses LC-MS/MS identification of protein biosignatures in breast tumors, as protein-based markers that correctly classify tumor subtypes and predict therapeutic response would be of great clinical utility in guiding patient treatment. The next two papers are both by M. S. Sabel et al., and focus on melanoma. The seventh paper reviews the use of proteomics for the discovery of new prognostic and predictive biomarkers. The eighth paper explores the clinical utility of serum autoantibodies that were detected in melanoma patients. The investigators profiled serum antibodies a","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/894618","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30277028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of Proteomics in the Diagnosis and Treatment of Women's Cancers: Current Trends in Technology and Future Opportunities.","authors":"Eun-Kyoung Yim Breuer,&nbsp;Mandi M Murph","doi":"10.1155/2011/373584","DOIUrl":"https://doi.org/10.1155/2011/373584","url":null,"abstract":"<p><p>Technological and scientific innovations over the last decade have greatly contributed to improved diagnostics, predictive models, and prognosis among cancers affecting women. In fact, an explosion of information in these areas has almost assured future generations that outcomes in cancer will continue to improve. Herein we discuss the current status of breast, cervical, and ovarian cancers as it relates to screening, disease diagnosis, and treatment options. Among the differences in these cancers, it is striking that breast cancer has multiple predictive tests based upon tumor biomarkers and sophisticated, individualized options for prescription therapeutics while ovarian cancer lacks these tools. In addition, cervical cancer leads the way in innovative, cancer-preventative vaccines and multiple screening options to prevent disease progression. For each of these malignancies, emerging proteomic technologies based upon mass spectrometry, stable isotope labeling with amino acids, high-throughput ELISA, tissue or protein microarray techniques, and click chemistry in the pursuit of activity-based profiling can pioneer the next generation of discovery. We will discuss six of the latest techniques to understand proteomics in cancer and highlight research utilizing these techniques with the goal of improvement in the management of women's cancers.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/373584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30115496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Urine glycoprotein profile reveals novel markers for chronic kidney disease.","authors":"Anuradha Vivekanandan-Giri, Jessica L Slocum, Carolyn L Buller, Venkatesha Basrur, Wenjun Ju, Rodica Pop-Busui, David M Lubman, Matthias Kretzler, Subramaniam Pennathur","doi":"10.1155/2011/214715","DOIUrl":"10.1155/2011/214715","url":null,"abstract":"<p><p>Chronic kidney disease (CKD) is a significant public health problem, and progression to end-stage renal disease leads to dramatic increases in morbidity and mortality. The mechanisms underlying progression of disease are poorly defined, and current noninvasive markers incompletely correlate with disease progression. Therefore, there is a great need for discovering novel markers for CKD. We utilized a glycoproteomic profiling approach to test the hypothesis that the urinary glycoproteome profile from subjects with CKD would be distinct from healthy controls. N-linked glycoproteins were isolated and enriched from the urine of healthy controls and subjects with CKD. This strategy identified several differentially expressed proteins in CKD, including a diverse array of proteins with endopeptidase inhibitor activity, protein binding functions, and acute-phase/immune-stress response activity supporting the proposal that inflammation may play a central role in CKD. Additionally, several of these proteins have been previously linked to kidney disease implicating a mechanistic role in disease pathogenesis. Collectively, our observations suggest that the human urinary glycoproteome may serve as a discovery source for novel mechanism-based biomarkers of CKD.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9554383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein biomarkers for the early detection of breast cancer.","authors":"David E Misek,&nbsp;Evelyn H Kim","doi":"10.1155/2011/343582","DOIUrl":"https://doi.org/10.1155/2011/343582","url":null,"abstract":"<p><p>Advances in breast cancer control will be greatly aided by early detection so as to diagnose and treat breast cancer in its preinvasive state prior to metastasis. For breast cancer, the second leading cause of cancer-related death among women in the United States, early detection does allow for increased treatment options, including surgical resection, with a corresponding better patient response. Unfortunately, however, many patients' tumors are diagnosed following metastasis, thus making it more difficult to successfully treat the malignancy. There are, at present, no existing validated plasma/serum biomarkers for breast cancer. Only a few biomarkers (such as HER-2/neu, estrogen receptor, and progesterone receptor) have utility for diagnosis and prognosis. Thus, there is a great need for new biomarkers for breast cancer. This paper will focus on the identification of new serum protein biomarkers with utility for the early detection of breast cancer.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/343582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30109823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive proteomic profiling of aldehyde dehydrogenases in lung adenocarcinoma cell lines.","authors":"Qing Zhang,&nbsp;Ayumu Taguchi,&nbsp;Mark Schliekelman,&nbsp;Chee-Hong Wong,&nbsp;Alice Chin,&nbsp;Rork Kuick,&nbsp;David E Misek,&nbsp;Samir Hanash","doi":"10.1155/2011/145010","DOIUrl":"https://doi.org/10.1155/2011/145010","url":null,"abstract":"<p><p>We have explored the potential of proteomic profiling to contribute to the delineation of the range of expression and subcellular localization of aldehyde dehydrogenases (ALDHs) in lung adenocarcinoma. In-depth quantitative proteomics was applied to 40 lung adenocarcinoma cell lines resulting in the identification of the known members of the ALDH family. Substantial heterogeneity in the level and occurrence of ALDHs in total lysates and on the cell surface and in their release into the culture media was observed based on mass spectrometry counts. A distinct pattern of expression of ALDHs was observed in cells exhibiting epithelial features relative to cells exhibiting mesenchymal features. Strikingly elevated levels of ALDH1A1 were observed in two cell lines. We also report on the occurrence of an immune response to ALDH1A1 in lung cancer.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/145010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30277025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Signatures of drug sensitivity in nonsmall cell lung cancer.","authors":"Hua C Gong,&nbsp;Sean Wang,&nbsp;Gary Mayer,&nbsp;Guoan Chen,&nbsp;Glen Leesman,&nbsp;Sharat Singh,&nbsp;David G Beer","doi":"10.1155/2011/215496","DOIUrl":"https://doi.org/10.1155/2011/215496","url":null,"abstract":"<p><p>We profiled receptor tyrosine kinase pathway activation and key gene mutations in eight human lung tumor cell lines and 50 human lung tumor tissue samples to define molecular pathways. A panel of eight kinase inhibitors was used to determine whether blocking pathway activation affected the tumor cell growth. The HER1 pathway in HER1 mutant cell lines HCC827 and H1975 were found to be highly activated and sensitive to HER1 inhibition. H1993 is a c-MET amplified cell line showing c-MET and HER1 pathway activation and responsiveness to c-MET inhibitor treatment. IGF-1R pathway activated H358 and A549 cells are sensitive to IGF-1R inhibition. The downstream PI3K inhibitor, BEZ-235, effectively inhibited tumor cell growth in most of the cell lines tested, except the H1993 and H1650 cells, while the MEK inhibitor PD-325901 was effective in blocking the growth of KRAS mutated cell line H1734 but not H358, A549 and H460. Hierarchical clustering of primary tumor samples with the corresponding tumor cell lines based on their pathway signatures revealed similar profiles for HER1, c-MET and IGF-1R pathway activation and predict potential treatment options for the primary tumors based on the tumor cell lines response to the panel of kinase inhibitors.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/215496","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30259366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The application of a three-step proteome analysis for identification of new biomarkers of pancreatic cancer.","authors":"Mayinuer Abulaizi,&nbsp;Takeshi Tomonaga,&nbsp;Mamoru Satoh,&nbsp;Kazuyuki Sogawa,&nbsp;Kazuyuki Matsushita,&nbsp;Yoshio Kodera,&nbsp;Jurat Obul,&nbsp;Shigetsugu Takano,&nbsp;Hideyuki Yoshitomi,&nbsp;Masaru Miyazaki,&nbsp;Fumio Nomura","doi":"10.1155/2011/628787","DOIUrl":"https://doi.org/10.1155/2011/628787","url":null,"abstract":"<p><p>We searched for novel tumor markers of pancreatic cancer by three-step serum proteome analysis. Twelve serum abundant proteins were depleted using immunoaffinity columns followed by fractionation by reverse-phase high-performance liquid chromatography. Proteins in each fraction were separated by two-dimensional gel electrophoresis. Then the gel was stained by Coomassie Brilliant Blue. Protein spots in which the expression levels were significantly different between cancer and normal control were identified by LC-MS/MS. One hundred and two spots were upregulated, and 84 spots were downregulated in serum samples obtained from patients with pancreatic cancers, and 58 proteins were identified by mass spectrometry. These candidate proteins were validated using western blot analysis and enzyme-linked immunosorbent assay (ELISA). As a result of these validation process, we could confirm that the serum levels of apolipoprotein A-IV, vitamin D-binding protein, plasma retinol-binding protein 4, and tetranectin were significantly decreased in patients with pancreatic cancer.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/628787","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30259367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics in pancreatic cancer research.","authors":"Ruihui Geng,&nbsp;Zhaoshen Li,&nbsp;Shude Li,&nbsp;Jun Gao","doi":"10.1155/2011/365350","DOIUrl":"https://doi.org/10.1155/2011/365350","url":null,"abstract":"<p><p>Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/365350","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30109822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}