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Proteomics. Clinical Applications

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https://www.readbyqxmd.com/read/29159954/unraveling-the-mechanistic-complexity-of-the-glomerulocystic-phenotype-in-dicer-conditional-ko-mice-by-2d-gel-electrophoresis-coupled-mass-spectrometry
#1
Claudia Vincenza Fiumara, Domenica Scumaci, Anna Iervolino, Angela Mena Perri, Antonio Concolino, Laura Tammè, Federica Petrillo, Giovambattista Capasso, Giovanni Cuda
PURPOSE: Dicer, an RNase III type endonuclease, is a key enzyme involved in miRNA biogenesis. It has been shown that this enzyme is essential for several aspects of postnatal kidney functions and homeostasis. In this study, we have examined conditional knockout (cKO) mice for Dicer in Pax8 (Paired-box gene 8) expressing cells to investigate the kidney protein profile. This specific model develops a glomerulocystic phenotype coupled with urinary concentration impairment, proteinuria and severe renal failure...
November 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148239/metabolic-signature-of-microvescicles-from-umbilical-cord-mesenchimal-stem-cells-of-preterm-and-term-infants
#2
Maurizio Bruschi, Laura Santucci, Silvia Ravera, Martina Bartolucci, Andrea Petretto, Daniela Calzia, Gianmarco Ghiggeri, Luca A Ramenghi, Giovanni Candiano, Isabella Panfoli
PURPOSE: Microvesicles, 200-1000 nm bodies budding from the cell plasma membrane, are a promising source of biomarkers. This study aimed at comparing the proteome of Microvesicles collected by ultracentrifugation from cultured Mesenchymal Stem Cells from Human Umbilical Cord of Preterm newborns(<34-weeks gestational age) in comparison to infants at Term(≥37 weeks). This discovery study was designed to establish the signature of prematurity. EXPERIMENTAL DESIGN: Orbitrap mass spectrometry, statistical, bioinformatics and biochemical analyses were employed...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148229/proteomics-of-diabetes-obesity-and-related-disorders
#3
EDITORIAL
Robert Moulder, Domitille Schvartz, David R Goodlett, Loïc Dayon
No abstract text is available yet for this article.
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148176/differential-proteomic-analysis-reveals-protein-networks-and-pathways-that-may-contribute-to-helicobacter-pylori-fkbp-type-ppiase-associated-gastric-diseases
#4
Yanmei Zhu, Yuehua Gong, Aodi Li, Moye Chen, Dan Kang, Jun Liu, Yuan Yuan
PURPOSE: Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN: We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein (GFP) using two-dimensional (2-D) gel electrophoresis and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS)...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29105359/glp-1-analogue-exendin-4-modulates-mapks-activity-but-not-the-heat-shock-response-in-human-hepg2-cells
#5
Dhanya Madhu, Maha Hammad, Sina Kavalakatt, Abdelkrim Khadir, Ali Tiss
PURPOSE: Glucagon-like peptide-1 (GLP-1) analogues reduce ER stress and inflammation in key metabolic organs, including the liver. However, their effects on heat shock response (HSR) and mitogen-activated protein kinases (MAPKs) have not yet been elucidated. In the present study, we investigated whether the GLP-1 analogue, exendin-4, triggers the expression of HSR and increases MAPK activity under metabolic stress. EXPERIMENTAL DESIGN: The effects of exendin-4 in the presence or absence of palmitic acid (PA; 400 μM) or glucose (30 mM) in the HepG2 liver cell line were assessed using Western blots, quantitative real-time PCR and label-free proteomics...
November 3, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29090858/proteomic-analysis-of-ipec-j2-cells-in-response-to-coinfection-by-porcine-transmissible-gastroenteritis-virus-and-enterotoxigenic-escherichia-coli-k88
#6
Lu Xia, Lei Dai, Liqi Zhu, Weiwei Hu, Qian Yang
Piglet diarrhea causes large economic losses to the swine industry. Epidemiological investigations show that piglet diarrhea is often caused by mixed infections, but the mechanisms by which multiple microorganisms cause disease are unclear. Because transmissible gastroenteritis virus (TGEV) and enterotoxigenic Escherichia coli K88 (ETEC K88) are important contributors to piglet diarrhea, coinfection experiments were conducted using porcine intestinal columnar epithelial cells (IPEC-J2) as a model system. LC-MS/MS coupled to iTRAQ was used to profile expressed proteins in IPEC-J2 cells infected by TGEV alone, ETEC K88 alone, and by both agents together...
November 1, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29068532/alteration-of-liver-peroxisomal-and-mitochondrial-functionality-in-the-nzo-mouse-model-of-metabolic-syndrome
#7
Birgit Knebel, Simon Göddeke, Sonja Hartwig, Tina Hörbelt, Pia Fahlbusch, Hadi Al-Hasani, Sylvia Jacob, Cornelia Koellmer, Ulrike Nitzgen, Martina Schiller, Stefan Lehr, Jorg Kotzka
PURPOSE: MetS consist of five risk factors: elevated blood pressure and fasting glucose, visceral obesity, dyslipidemia and hypercholesterinemia. The physiological impact of lipid metabolism indicated as visceral obesity and hepatic lipid accumulation on MetS is still under debate. One major cause of disturbed lipid metabolism might be dysfunction of cellular organelles controlling energy homeostasis, i.e. mitochondria and peroxisomes. EXPERIMENTAL DESIGN: The New Zealand Obese (NZO) mouse model exhibits a polygenic syndrome of obesity, insulin resistance, triglyceridemia and hypercholesterolemia that resembles human metabolic syndrome...
October 25, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29064629/proteomics-and-protein-adsorption-on-hemodialysis-membranes
#8
Mario Bonomini
Adsorption of plasma proteins onto the membrane surface during the hemodialysis session represents a key feature of membranes used for chronic dialysis therapy. In this issue of Proteomics - Clinical Applications, Han et al. [Proteomics - Clinical Applications 2017, XX] originally describe how, by using proteomic technologies, the adsorptive properties of two membranes made from the same biomaterial (Polyamix) may have different flux characteristics (low-flux and high-flux, the former having smaller pore size)...
October 24, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29059504/intersection-of-proteomics-and-genomics-to-solve-the-unsolved-in-rare-disorders-such-as-neurodegenerative-and-neuromuscular-diseases
#9
Andreas Roos, Rachel Thompson, Rita Horvath, Hanns Lochmüller, Albert Sickmann
Despite recent rapid advances in sequencing technologies, a significant proportion of patients with rare genetic disorders do not receive a genetic diagnosis after exhaustive testing, and even fewer have a potential therapeutic target identified. Taking rare neuromuscular and neurodegenerative disorders as a paradigm that can be extended to other rare Mendelian disorders, this viewpoint explores the opportunities that are brought about by the integration of genomics and proteomics, as well as the limitations and remaining challenges of this newly emerging field of proteogenomics...
October 23, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29028163/early-detection-of-urinary-proteome-biomarkers-for-effective-early-treatment-of-pulmonary-fibrosis-in-a-rat-model
#10
Jianqiang Wu, Xundou Li, Mindi Zhao, He Huang, Wei Sun, Youhe Gao
PURPOSE: Pulmonary fibrosis (PF) is a progressive and devastating lung disease. With limited effective treatments available in the late stage, PF has a very poor prognosis. Molecular biomarkers are highly desired for PF, especially for its early phase. MATERIAL AND METHODS: Urine is a good biomarker source, and accumulates systemic changes in the body especially in the early-stage of diseases. In this study, a bleomycin (BLM)-induced rat model was used to mimic PF...
October 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29028155/a-parallel-reaction-monitoring-mass-spectrometric-method-for-analysis-of-potential-csf-biomarkers-for-alzheimer-s-disease
#11
Gunnar Brinkmalm, Simon Sjödin, Anja Hviid Simonsen, Steen Gregers Hasselbalch, Henrik Zetterberg, Ann Brinkmalm, Kaj Blennow
PURPOSE: The aim of this study was to develop and evaluate a parallel reaction monitoring mass spectrometry (PRM-MS) assay consisting of a panel of potential protein biomarkers in cerebrospinal fluid (CSF). EXPERIMENTAL DESIGN: Thirteen proteins were selected based on their association with neurodegenerative diseases and involvement in synaptic function, secretory vesicle function, or innate immune system. CSF samples were digested and 2-3 peptides per protein were quantified using stable isotope-labeled peptide standards...
October 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28981210/proteome-and-structural-organization-of-the-knob-complex-on-the-surface-of-the-plasmodium-infected-red-blood-cell
#12
ShubaVarshini Alampalli, Manish Grover, Syama Chandran, Utpal Tatu, Pragyan Achary
PURPOSE: The cell membrane of the erythrocytes infected with the malaria parasite Plasmodium falciparum undergoes several changes during the course of parasite life cycle and forms protrusions known as 'knobs' on its surface during the mature trophozoite and schizont stages. The structural organization of knob components especially PfEMP1 on the iRBC surface is the main determinant for the cytoadhesive and rosetting capacity of the iRBC by binding to various host receptors as well as for the variable antigenicity, which is crucial for immunoevasion...
October 5, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28980455/clinical-proteomics-for-precision-medicine-the-bladder-cancer-case
#13
REVIEW
Agnieszka Latosinska, Maria Frantzi, Antonia Vlahou, Axel S Merseburger, Harald Mischak
Precision medicine can improve patient management by guiding therapeutic decision based on molecular characteristics. The concept has been extensively addressed through the application of -omics based approaches. Proteomics attract high interest, as proteins reflect a "real-time" dynamic molecular phenotype. Focusing on proteomics applications for personalized medicine, a literature search was conducted to cover: a) disease prevention, b) monitoring/ prediction of treatment response, c) stratification to guide intervention and d) identification of drug targets...
October 5, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28975715/data-independent-acquisition-based-quantitative-proteomic-analysis-reveals-potential-biomarkers-of-kidney-cancer
#14
Yimeng Song, Lijun Zhong, Juntuo Zhou, Min Lu, Tianying Xing, Lulin Ma, Jing Shen
PURPOSE: Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. EXPERIMENTAL DESIGN: Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition...
October 4, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28975709/ubiquitin-conjugating-enzyme-e2-l3-is-downregulated-by-the-chikungunya-virus-nsp2-protease
#15
Suwipa Ramphan, Sarawut Khongwichit, Chonticha Saisawang, Duangnapa Kovanich, Albert J Ketterman, Sukathida Ubol, Prasert Auewarakul, Sittiruk Roytrakul, Duncan R Smith, Atichat Kuadkitkan
PURPOSE: Chikungunya virus (CHIKV) is a mosquito transmitted alphavirus that causes chikungunya fever in humans. The CHIKV nonstructural protein 2 (nsP2) is a multifunctional protein that additionally modulates the host cell to dampen the innate immune response and inhibit other cellular processes. EXPERIMENTAL DESIGN: To further investigate the interactions of nsP2 with host cells, the protease domain of CHIKV nsP2 (nsP2-pro) was transfected into Hela cells, and differential protein expression was detected by 2-dimension (2D) polyacrylamide gel electrophoresis...
October 4, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28975736/comparison-of-targeted-mass-spectrometry-techniques-with-an-immunoassay-a-case-study-for-hsp90%C3%AE
#16
Coşkun Güzel, Natalia I Govorukhina, Christoph Stingl, Lennard J M Dekker, Alexander Boichenko, Ate G J van der Zee, Rainer Bischoff, Theo M Luidert
PURPOSE: The objective of this study was to better understand factors governing the variability and sensitivity in SRM and PRM, compared to immunoassay. EXPERIMENTAL DESIGN: A 2D-LC-MS/MS-based SRM and PRM assay was developed for quantitative measurements of HSP90α in serum. Forty-three control sera were compared by SRM, PRM and ELISA following the manufacturer's instructions. Serum samples were trypsin-digested and fractionated by SCX chromatography prior to SRM and PRM measurements...
October 3, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28975713/pepsweetener-a-web-based-tool-to-support-manual-annotation-of-intact-glycopeptide-ms-spectra
#17
Marcin Jakub Domagalski, Davide Alocci, Andreia Almeida, Daniel Kolarich, Frédérique Lisacek
PURPOSE: PepSweetener is a web-based visualization tool designed to facilitate the manual annotation of intact glycopeptides from mass spectrometry (MS) data regardless of the instrument that produced this data. EXPERIMENTAL DESIGN: This exploratory tool uses a theoretical glycopeptide dataset to visualize all peptide-glycan combinations that fall within the error range of the query precursor ion. PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass...
October 3, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28972305/mass-spectrometric-analysis-of-cerebrospinal-fluid-ubiquitin-in-alzheimer-s-disease-and-parkinsonian-disorders
#18
Simon Sjödin, Oskar Hansson, Annika Öhrfelt, Gunnar Brinkmalm, Henrik Zetterberg, Ann Brinkmalm, Kaj Blennow
PURPOSE: Dysfunctional proteostasis, with decreased protein degradation and an accumulation of ubiquitin into aggregated protein inclusions, is a feature of neurodegenerative diseases. Identifying new potential biomarkers in cerebrospinal fluid (CSF) reflecting this process could contribute important information on pathophysiology. EXPERIMENTAL DESIGN: A method combining SPE and PRM-MS and monitored the concentration of ubiquitin in CSF from subjects with Alzheimer's disease (AD), Parkinson's disease (PD), and progressive supranuclear palsy (PSP) is developed...
October 3, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28967185/itraq-based-proteomics-suggests-ephb6-as-a-potential-regulator-of-the-erk-pathway-in-the-prefrontal-cortex-of-chronic-social-defeat-stress-model-mice
#19
Hua Guo, Zhi-Lin Huang, Wei Wang, Shu-Xiao Zhang, Juan Li, Ke Cheng, Ke Xu, Yong He, Si-Wen Gui, Peng-Fei Li, Hai-Yang Wang, Zhi-Fang Dong, Peng Xie
PURPOSE: Major depressive disorder (MDD) is a worldwide concern and devastating psychiatric disease. The World Health Organization claims that MDD leads to at least 11.9% of the global burden of disease. However, the underlying pathophysiology mechanisms of MDD remain largely unknown. EXPERIMENTAL DESIGN: Herein, we proteomic-based strategy is used to compare the prefrontal cortex (PFC) in chronic social defeat stress (CSDS) model mice with a control group. Based on pooled samples, differential proteins are identified in the PFC proteome using iTRAQ coupled with LC-MS/MS...
October 1, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28960920/a-proteo-genomic-analysis-of-haptoglobin-in-malaria
#20
Gauri Awasthi, Suchi Tyagi, Vipin Kumar, Sandip Kumar Patel, Dharmendar Rojh, Vijeth Sakrappanavar, Sanjay Kumar Kochar, Arunansu Talukdar, Biaus Samanta, Aparup Das, Sanjeeva Srivastava, Swati Patankar
Haptoglobin (Hp), an acute phase inflammatory protein has been associated with malaria pathogenesis in several proteomics studies. The gene has two co-dominant alleles: Hp1 and Hp2 that produce three genotypes: Hp1/Hp1, Hp1/Hp2 and Hp2/Hp2. In this study, we perform validation of the proteomics data with Multiple Reaction Monitoring Mass Spectroscopy (MRM-MS). We further analyze the association of the Hp gene variants with severe, non-severe malaria and community (healthy) controls using genotyping PCRs and DNA sequencing...
September 27, 2017: Proteomics. Clinical Applications
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