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Proteomics. Clinical Applications

Xiaoping Xiao, Yaoran Liu, Zhengguang Guo, Xiaoyan Liu, Haidan Sun, Qian Li, Wei Sun
Human saliva is an important source for disease biomarker discovery. In this work, we investigate the influence of gender and acid stimulation on the normal human salivary proteome. Un-stimulated and acid-stimulated saliva samples from 5 males and 5 females were labeled with 4-plex iTRAQ and analyzed by 2-DLC MS/MS. A total of 1,770 proteins were identified, and 82 proteins in un-stimulated saliva were found to be gender-specific. These proteins were mainly associated with immune function, metabolism and inflammation...
February 15, 2017: Proteomics. Clinical Applications
Somchai Chutipongtanate, Supawat Chatchen, Jisnuson Svasti
Plasma is a rich source of biomarkers with clinical relevance. However, the wide dynamic range of protein concentration hinders the detection of low abundance proteins. Plasma prefractionation methods serve as indispensable tools to reduce plasma complexity, allowing the opportunity to explore tissue-derived proteins which leak into the circulation. This review summarizes common approaches in plasma prefractionation methods for proteomic analysis and then discusses some considerations in plasma prefractionation for clinical applications, reviewing some examples of its use in clinical situations...
February 14, 2017: Proteomics. Clinical Applications
Nathan Clendenen, Ashley Tollefson, Monika Dzieciatkowska, Alice Cambiaghi, Manuela Ferrario, Miranda Kroehl, Anirban Banerjee, Angelo D'Alessandro, Kirk C Hansen, Nathaen Weitzel
PURPOSE: Despite recent advancements in the use of thrombelastography (TEG) in the surgical setting, adequate technology to accurately predict bleeding phenotypes for patients undergoing cardiopulmonary bypass on the basis of non-mechanical parameters is lacking. While basic science and translational studies have provided key mechanistic insights about the protein components of coagulation cascades and regulatory mediators of hemostasis and fibrinolysis, targeted protein assays are still missing and the association of protein profiles to bleeding phenotypes and TEG readouts have yet to be discovered...
February 8, 2017: Proteomics. Clinical Applications
Quan Xia, Yingli Zhao, Jiali Wang, Wenhao Qiao, Dongling Zhang, Hao Yin, Dujuan Xu, Feihu Chen
PURPOSE: 4-amino-2-trifluoromethyl-phenyl retinate (ATPR) was reported to potentially inhibit proliferation and induce differentiation activity in some tumor cells. In this study, a proteomics approach was used to investigate the possible mechanism by screening the differentially expressed protein profiles of SGC-7901 cells before and after ATPR-treatment in vitro. EXPERIMENTAL DESIGN: Peptides digested from the total cellular proteins were analyzed by reverse phase LC-MS/MS followed by a label-free quantification analysis...
February 6, 2017: Proteomics. Clinical Applications
Subhojit Paul, Kalpana Bhargava, Yasmin Ahmad
PURPOSE: Computational biology has opened a gateway to omics data analysis and shifted the focus from molecules to systemic molecular networks in the domain of hypobaric hypoxia (HH). Yet there are no meta-analytical investigations circum-venting constraints like organism (rat/human), HH exposure conditions (acute/chronic) and the tissues that can be investigated simultaneously in the realm of wet-lab experiments. EXPERIMENTAL DESIGN: We analyzed 154 DE proteins upon HH exposure using IPA tool, without the constraint of using a single organism or tissue type, to determine the most significant pathways and networks that are perturbed across a range of HH conditions RESULTS: : We found Acute phase Response Signaling, FXR/RXR Activation, LXR/RXR Activation, Clathrin-mediated endocytosis signaling, Mitochondrial Dysfunction, Production of Nitric Oxide & ROS in Macrophages and Integrin Signaling to be the most significant universally perturbed pathways...
February 2, 2017: Proteomics. Clinical Applications
Clark M Henderson, James G Bollinger, Jessica O Becker, Jennifer M Wallace, Thomas J Laha, Michael J MacCoss, Andrew N Hoofnagle
PURPOSE: Proteomic analysis of blood proteins in DBS is gaining attention as a possible replacement for measurements in plasma/serum collected by venipuncture. We aimed to develop and provisionally validate a nanoflow LC-PRM-MS method for clinical use. EXPERIMENTAL DESIGN: We used Skyline to develop a nanoflow LC-PRM-MS method to quantify glycated hemoglobin-β, apolipoprotein A-I, and apolipoprotein B in DBS. Precision, linearity, interferences, and stability and were determined and the method was used to analyze samples from 36 human volunteers...
January 23, 2017: Proteomics. Clinical Applications
Dandan Linghu, Lili Guo, Yinghua Zhao, Zhiming Liu, Mingwei Zhao, Lvzhen Huang, Xiaoxin Li
PURPOSE: To analysis proteins in the tissue of pterygia, and to investigate their potential roles in pterygia, using the comparative proteomic technique of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) coupled with offline 2DLC-MS/MS, Western-bolt. METHOD: The tissues of pterygia and healthy conjunctiva were collected from 10 pterygia patients (6 females, 4 males; average age was 52 years old; average course of disease was 6 years) in our hospital from September, 2015 to March, 2016...
January 13, 2017: Proteomics. Clinical Applications
Deborah Chen, Peter Schubert, Dana V Devine
PURPOSE: Post-collection manipulations (PCMs) aim to increase blood product safety. However, PCMs improve safety at a cost to quality, causing elevated hemolysis. As hemolysis is linked to red blood cell (RBC) membrane integrity, a quantitative proteomics approach was employed to assess membrane proteome alterations induced by PCMs. EXPERIMENTAL DESIGN: Three ABO-matched whole blood (WB) units were pooled-and-split into three identical units. One WB unit was treated with riboflavin/ultraviolet illumination prior to red cell concentrate (RCC) production (RCC(WB*) )...
January 13, 2017: Proteomics. Clinical Applications
Xia Wang, Qiang Hao, Yuanli Zhao, Yi Guo, Wei Ge
PURPOSE: Detailed and exact mechanisms underlying brain arteriovenous malformations (bAVM) are still clinically confusing. Understanding the quantitative changes in proteins and signaling pathways would provide useful information for clinicians to understand the formation and development of bAVM, guiding individualized treatment strategies. This study was performed to establish a large human bAVM proteome database using tandem mass tag (TMT)-labeling and to detect changes of protein expression and pathways in human bAVM...
January 13, 2017: Proteomics. Clinical Applications
Fabio Pastorino, Mirco Ponzoni, Giuseppina Simone
Galectin decorates the cell membrane and forms an extracellular molecular association with galactoside units. Here, galactoside probes have been used to study galectin expression in neuroblastoma cells. The hypothesis behind this investigation has been that the molecular mechanisms by which glycans modulate neural metastatic cells involve a protein-carbohydrate association, galectin-galactose. Preliminary screening to validate the hypothesis has been performed with galactose moieties anchored to beads. The molecular association has been studied by FACS...
January 9, 2017: Proteomics. Clinical Applications
Claudia Corbo, Armando Cevenini, Francesco Salvatore
About one million people/year develop colorectal cancer (CRC) and approximately half of them die. The extent of the disease (i.e. local invasion at the time of diagnosis) is a key prognostic factor. The 5-year survival rate is almost 90% in the case of delimited CRC and 10% in the case of metastasized CRC. Hence, one of the great challenges in the battle against CRC is to improve early diagnosis strategies. Large-scale proteomic approaches are widely used in cancer research to search for novel biomarkers. Such biomarkers can help in improving the accuracy of the diagnosis and in the optimization of personalized therapy...
December 26, 2016: Proteomics. Clinical Applications
Esther Nkuipou-Kenfack, Petra Zürbig, Harald Mischak
Clinical proteomics aims at the development and the implementation of novel biomarkers that demonstrate a clear clinical benefit in the management of diseases. However, though the attention in the field is increasing and multiple articles on biomarker research are published, clinical implementation of these biomarkers is scarce. In this manuscript, we aim towards identifying the hurdles on the path towards implementation, and present one successful approach, based on capillary electrophoresis coupled to mass spectrometry...
December 26, 2016: Proteomics. Clinical Applications
AnneMarie C Brescia, Megan M Simonds, Kathleen E Sullivan, Carlos D Rose
OBJECTIVE: The goal was to investigate the specific contribution of fibroblast-like synoviocytes (FLS) to the inflammatory milieu of the synovium in juvenile idiopathic arthritis (JIA) through detection of secreted proteins. METHODS: Expression of 89 cytokines and chemokines was determined on unprocessed synovial fluid from controls and JIA patients using antibody arrays. Supernatants from pure cell cultures of FLS grown from synovial fluids or tissues from JIA and controls were also examined for protein expression...
December 23, 2016: Proteomics. Clinical Applications
Qi Shi, Li-Na Chen, Yan Lv, Bao-Yun Zhang, Kang Xiao, Wei Zhou, Cao Chen, Jing Sun, Xiao-Dong Yang, Xiao-Ping Dong
PURPOSE: To analyze the proteomics patterns in the cortex regions of scrapie strains 139A- and ME7-infected mice collected in the middle and terminal stages. EXPERIMENTAL DESIGN: Western Blot and immunohistochemistry methods are used to analyze the pathological changes in mice collected in the middle and terminal stages. The technique of iTRAQ and multidimensional LC and MS are used to analyze the proteomics patterns of mice in different stages. RESULTS: In total, 2891 with 95% confidence interval are identified...
December 19, 2016: Proteomics. Clinical Applications
Chengjian Tu, Wilfrido Mojica, Robert M Straubinger, Jun Li, Shichen Shen, Miao Qu, Lei Nie, Rick Roberts, Bo An, Jun Qu
PURPOSE: The heterogeneous structure in tumor tissues from colorectal cancer (CRC) patients excludes an informative comparison between tumors and adjacent normal tissues. Here, we develop and apply a strategy to compare paired cancerous (CEC) vs. normal (NEC) epithelial cells enriched from patients and discover potential biomarkers and therapeutic targets for CRC. EXPERIMENTAL DESIGN: CEC and NEC cells were respectively isolated from five different tumor and normal locations in the resected colon tissue from each patient (N = 12 patients) using an optimized epithelial cell adhesion molecule (EpCAM)-based enrichment approach...
December 12, 2016: Proteomics. Clinical Applications
Lei Ye, Yuan Hu, Fei-Hong Xu, Cheng-Yun Cai, Da-Wei Song, Zhen-Shan Xu, Wei-Dong Du
PURPOSE: Plasma leptin is secreted from adipose tissues and plays pivotal roles in human physiological and pathological processes. Here, we aimed at conducting a protein biochip-based sandwich-like approach for detection of plasma leptin among healthy individuals, obesity, and diabetes patients. EXPERIMENTAL DESIGN: Totally, 96 plasma samples, including 45 healthy individuals with standard body mass index (BMI), 28 obesity and 23 diabetes patients, were recruited in the study...
December 6, 2016: Proteomics. Clinical Applications
Yvan Caspar, Cécile Garnaud, Mariya Raykova, Sébastien Bailly, Marie Bidart, Danièle Maubon
PURPOSE: Fast species diagnosis has an important health care impact, as rapid and specific antibacterial therapy is of clear benefit for patient's outcome. Here, a new protocol for species identification directly from positive blood cultures is proposed. EXPERIMENTAL DESIGN: Four in-house protocols for bacterial identification by MS directly from clinical positive blood cultures evaluating two lytic agents, SDS and saponin, and two protein extraction schemes, fast (FP) and long (LP) are compared...
December 6, 2016: Proteomics. Clinical Applications
Tao Xu, Bojin Su, Peiyu Huang, Weihong Wei, Yanming Deng, Vasudha Sehgal, Donghui Wang, Jun Jiang, Guoyi Zhang, Anfei Li, Huiling Yang, Francois X Claret
PURPOSE: In patients with Epstein-Barr virus (EBV) associated nasopharyngeal carcinoma (NPC), intertumor heterogeneity causes interpatient heterogeneity in the risk of distant metastasis. We aimed to identify novel biomarkers of metastasis risk using reverse phase protein array (RPPA) profiling of NPC patients at risk for metastasis and considering plasma EBV DNA load. EXPERIMENTAL DESIGN: A total of 98 patients with NPC with and without metastasis after treatment, matched with respect to clinical parameters, are enrolled...
November 24, 2016: Proteomics. Clinical Applications
Saravanan Ramanujam, Bharathselvi Muthuvel, Babu Aravind C, Jyothirmay Biswas, N Sulochana Konerirajapuram
PURPOSE: Eales' disease (ED), an enigmatic inflammatory disease, affects peripheral retinal veins and thereby vision in males. This study was aimed at identifying and deciphering the role of a novel 88-kDa protein reported in the serum and vitreous of patients with ED. EXPERIMENTAL DESIGN: The purified 88-kDa protein was identified by UPLC coupled ESI-QTOF-MS. The identified proteins were quantified in the serum from 20 ED patients and controls (age and sex matched), respectively by ELISA...
January 2017: Proteomics. Clinical Applications
Eva Brauers, Andreas Roos, Laxmikanth Kollipara, René P Zahedi, Alf Beckmann, Nilane Mohanadas, Hartmut Bauer, Martin Häusler, Stéphanie Thoma, Wolfram Kress, Jan Senderek, Joachim Weis
PURPOSE: In the era of next-generation sequencing, we are increasingly confronted with sequence variants of unknown significance. This phenomenon is also known for variations in Caveolin-3 and can complicate the molecular diagnosis of the disease. Here, we aimed to study the ambiguous character of the G56S Caveolin-3 variant. EXPERIMENTAL DESIGN: A comprehensive approach combining genetic and morphological studies of muscle derived from carriers of the G56S Caveolin-3 variant were carried out and linked to biochemical assays (including phosphoblot studies and proteome profiling) and morphological investigations of cultured myoblasts...
January 2017: Proteomics. Clinical Applications
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