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proteomics pathway

Andrea Schmitt, Daniel Martins-de-Souza, Schahram Akbarian, Juliana S Cassoli, Hannelore Ehrenreich, Andre Fischer, Alfred Fonteh, Wagner F Gattaz, Michael Gawlik, Manfred Gerlach, Edna Grünblatt, Tobias Halene, Alkomiet Hasan, Kenij Hashimoto, Yong-Ku Kim, Sophie-Kathrin Kirchner, Johannes Kornhuber, Theo F J Kraus, Berend Malchow, Juliana M Nascimento, Moritz Rossner, Markus Schwarz, Johann Steiner, Leda Talib, Florence Thibaut, Peter Riederer, Peter Falkai
OBJECTIVES: Despite progress in identifying molecular pathophysiological processes in schizophrenia, valid biomarkers are lacking for both the disease and treatment response. METHODS: This comprehensive review summarises recent efforts to identify molecular mechanisms on the level of protein and gene expression and epigenetics, including DNA methylation, histone modifications and micro RNA expression. Furthermore, it summarises recent findings of alterations in lipid mediators and highlights inflammatory processes...
October 26, 2016: World Journal of Biological Psychiatry
Dorothee Hartmann, Jan Fiedler, Kristina Sonnenschein, Annette Just, Angelika Pfanne, Karina Zimmer, Janet Remke, Ariana Foinquinos, Malte Butzlaff, Katharina Schimmel, Lars Maegdefessel, Denise Hilfiker-Kleiner, Nico Lachmann, Andreas Schober, Natali Froese, Joerg Heineke, Johann Bauersachs, Sandor Batkai, Thomas Thum
BACKGROUND: -The transcription factor GATA2 orchestrates the expression of many endothelial-specific genes illustrating its crucial importance for endothelial cell function. The capacity of this transcription factor in orchestrating endothelial important microRNAs (miRNAs/miR) is unknown. METHODS: -Endothelial GATA2 was functionally analyzed in human endothelial cells in vitro. Endogenous siRNA-mediated knockdown and lentiviral-based overexpression were applied to decipher capacity of GATA2 in regulating cell viability and capillary formation...
October 25, 2016: Circulation
Stephanie M Cossette, Vijesh J Bhute, Xiaoping Bao, Leanne M Harmann, Mark A Horswill, Indranil Sinha, Adam Gastonguay, Shabnam Pooya, Michelle Bordas, Suresh N Kumar, Shama P Mirza, Sean Palecek, Jennifer Strande, Ramani Ramchandran
BACKGROUND: -Cardiac metabolism is critical for the functioning of the heart, and disturbance in this homeostasis is likely to influence cardiac disorders or cardiomyopathy. Our lab has previously shown that sucrose non-fermenting related kinase (SNRK) enzyme, which belongs to the AMP-activated kinase (AMPK) family, was essential for cardiac metabolism in mammals. Snrk global homozygous knockout (KO) mice die at postnatal day 0, and conditional deletion of Snrk in cardiomyocytes (Snrk cmcKO) leads to cardiac failure, and death by 8-10 months...
October 25, 2016: Circulation. Cardiovascular Genetics
Ghazala Mustafa, Setsuko Komatsu
Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. To investigate the possible interactions between NPs and crops under flooding stress, the molecular mechanisms in soybean affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of root including hypocotyl was increased and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway...
October 26, 2016: Journal of Proteome Research
Núria Rovira-Graells, Sara Aguilera-Simón, Elisabet Tintó-Font, Alfred Cortés
The growth phenotype of asexual blood stage malaria parasites can influence their virulence and also their ability to survive and achieve transmission to the next host, but there are few methods available to characterise parasite growth parameters in detail. We developed a new assay to measure growth rates at different starting parasitaemias in a 96-well format and applied it to characterise the growth of Plasmodium falciparum lines 3D7-A and 3D7-B, previously shown to have different invasion rates and to use different invasion pathways...
2016: PloS One
Ursula R Rodgers, Thomas Lanyon-Hogg, Naoko Masumoto, Markus Ritzefeld, Rosemary Burke, Julian Blagg, Anthony I Magee, Edward W Tate
The Sonic Hedgehog (Shh) signaling pathway plays a critical role during embryonic development and cancer progression. N-terminal palmitoylation of Shh by Hedgehog acyltransferase (Hhat) is essential for efficient signaling, raising interest in Hhat as a novel drug target. A recently identified series of dihydrothienopyridines has been proposed to function via this mode of action; however, the lead compound in this series (RUSKI-43) was subsequently shown to possess cytotoxic activity unrelated to canonical Shh signaling...
October 25, 2016: ACS Chemical Biology
Shohreh Maleki, Sanela Kjellqvist, Valentina Paloschi, Joelle Magné, Rui Miguel Mamede Branca, Lei Du, Kjell Hultenby, Johan Petrini, Jonas Fuxe, Janne Lehtiö, Anders Franco-Cereceda, Per Eriksson, Hanna M Björck
Individuals with a bicuspid aortic valve (BAV) are at significantly higher risk of developing aortic complications than individuals with tricuspid aortic valves (TAV) and defective signaling during the embryonic development and/or life time exposure to abnormal hemodynamic have been proposed as underlying factors. However, an explanation for the molecular mechanisms of aortopathy in BAV has not yet been provided. We combined proteomics, RNA analyses, immunohistochemistry, and electron microscopy to identify molecular differences in samples of non-dilated ascending aortas from BAV (N = 62) and TAV (N = 54) patients...
October 25, 2016: Scientific Reports
Nasrin Dehghan-Nayeri, Mostafa Rezaei-Tavirani, Mir Davood Omrani, Ahmad Gharehbaghian, Kourosh Goudarzi Pour, Peyman Eshghi
Response to dexamethasone (DEXA), as a hallmark drug in the treatment of childhood acute lymphoblastic leukemia (ALL), is one of the pivotal prognostic factors in the prediction of outcome in ALL. Identification of predictive markers of chemoresistance is beneficial to selecting of the best therapeutic protocol with the lowest effect adverse. Hence, we aimed to find drug targets using the 2DE/MS proteomics study of a DEXA-resistant cell line (REH) as a model for poor DEXA responding patients before and after drug treatment...
October 24, 2016: Journal of Cell Communication and Signaling
Dijun Zhang, Weina He, Qianqian Tong, Jun Zhou, Xiurong Su
BACKGROUND: The acquisition of iron is important for the pathogenicity of bacteria and blood. Three different culture environments (Fe stimulation, blood agar plate and normal plate) were used to stimulate Enterobacter cloacae, and their respective pathogenicities were compared at the proteomic, mRNA and metabolomic levels. METHODS: 2D-DIGE combined with MALDI-TOF-MS/MS, RT-PCR and (1)H NMR were used to analyze the differential expression levels of proteins, mRNA and metabolites...
2016: Proteome Science
Erin M M Weisenhorn, Thomas J Van't Erve, Nicholas M Riley, John R Hess, Thomas J Raife, Joshua J Coon
Each year over 90 million units of blood are transfused worldwide. Our dependence on this blood supply mandates optimized blood management and storage. During storage, red blood cells undergo degenerative processes resulting in altered metabolic characteristics which may make blood less viable for transfusion. However, not all stored blood spoils at the same rate, a difference that has been attributed to variable rates of energy usage and metabolism in red blood cells. Specific metabolite abundances are heritable traits; however, the link between heritability of energy metabolism and red blood cell storage profiles is unclear...
October 24, 2016: Molecular & Cellular Proteomics: MCP
Cuixia Gao, Bingxian Yang, Dandan Zhang, Meng Chen, Jingkui Tian
BACKGROUND: Indole alkaloids, which characteristically contain an indole nucleus, have pharmaceutical potential in a diverse range of applications. UV-B can elicit the accumulation of indole alkaloids. The indole alkaloid (6-hydroxyl-1H-indol-3-yl) carboxylic acid methyl ester with cytotoxic activity was found to accumulate in Clematis terniflora DC. leaves after exposure to high level of UV-B irradiation and the dark. However, a more in-depth analysis of the process behind this response has not yet been performed...
October 24, 2016: BMC Plant Biology
Yadong Yu, Tao Li, Na Wu, Lujing Ren, Ling Jiang, Xiao-Jun Ji, He Huang
Arachidonic acid (ARA) is an important polyunsaturated fatty acid, which has various beneficial physiological effects on the human body. The aging of Mortierella alpina (M. alpina) has long been known to significantly improve ARA yield, but the exact mechanism is still elusive. Herein, multiple approaches including large-scale comparative proteomics were employed to systematically investigate the mechanism mentioned above. Upon ultrastructural observation, abnormal mitochondria were found to aggregate around shrunken lipid droplets...
October 25, 2016: Journal of Agricultural and Food Chemistry
Elisabeth Salzer, Deniz Cagdas, Miroslav Hons, Emily M Mace, Wojciech Garncarz, Özlem Yüce Petronczki, René Platzer, Laurène Pfajfer, Ivan Bilic, Sol A Ban, Katharina L Willmann, Malini Mukherjee, Verena Supper, Hsiang Ting Hsu, Pinaki P Banerjee, Papiya Sinha, Fabienne McClanahan, Gerhard J Zlabinger, Winfried F Pickl, John G Gribben, Hannes Stockinger, Keiryn L Bennett, Johannes B Huppa, Loïc Dupré, Özden Sanal, Ulrich Jäger, Michael Sixt, Ilhan Tezcan, Jordan S Orange, Kaan Boztug
RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1...
October 24, 2016: Nature Immunology
Hui Liu, Fan Zhang, Shital Kumar Mishra, Shuigeng Zhou, Jie Zheng
Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data...
October 24, 2016: Scientific Reports
Diane Lefaudeux, Bertrand De Meulder, Matthew J Loza, Nancy Peffer, Anthony Rowe, Frédéric Baribaud, Aruna T Bansal, Rene Lutter, Ana R Sousa, Julie Corfield, Ioannis Pandis, Per S Bakke, Massimo Caruso, Pascal Chanez, Sven-Erik Dahlén, Louise J Fleming, Stephen J Fowler, Ildiko Horvath, Norbert Krug, Paolo Montuschi, Marek Sanak, Thomas Sandstrom, Dominic E Shaw, Florian Singer, Peter J Sterk, Graham Roberts, Ian M Adcock, Ratko Djukanovic, Charles Auffray, Kian F Chung
BACKGROUND: Asthma is a heterogeneous disease in which there is a differential response to asthma treatments. This heterogeneity needs to be evaluated so that a personalised management approach can be provided. OBJECTIVES: We stratified patients with moderate-to-severe asthma based on clinico-physiological parameters and performed an -omics analysis of sputum. METHODS: Partition-around-medoid clustering was applied to a training set of 266 asthma participants from the European U-BIOPRED adult cohort using 8 pre-specified clinic-physiological variables...
October 20, 2016: Journal of Allergy and Clinical Immunology
Johanna Korvala, Kowan Jee, Emmi Porkola, Alhadi Almangush, Neda Mosakhani, Carolina Bitu, Nilva K Cervigne, Flávia S Zandonadi, Gabriela V Meirelles, Adriana Franco Paes Leme, Ricardo D Coletta, Ilmo Leivo, Tuula Salo
Complex molecular pathways regulate cancer invasion. This study overviewed proteins and microRNAs (miRNAs) involved in oral tongue squamous cell carcinoma (OTSCC) invasion. The human highly aggressive OTSCC cell line HSC-3 was examined in a 3D organotypic human leiomyoma model. Non-invasive and invasive cells were laser-captured and protein expression was analyzed using mass spectrometry-based proteomics and miRNA expression by microarray. In functional studies the 3D invasion assay was replicated after silencing candidate miRNAs, miR-498 and miR-940, in invasive OTSCC cell lines (HSC-3 and SCC-15)...
October 20, 2016: Experimental Cell Research
Sophie Sabherwal, Jane A English, Melanie Föcking, Gerard Cagney, David R Cotter
Recent evidence supports an association between systemic abnormalities and the pathology of psychotic disorders which has led to the search for peripheral blood-based biomarkers. Areas covered: Here, we summarize blood biomarker findings in schizophrenia from the literature identified by two methods currently driving biomarker discovery in the human proteome; mass spectrometry and multiplex immunoassay. From a total of 14 studies in the serum or plasma of drug-free schizophrenia patients; 47 proteins were found to be significantly altered twice or more, in the same direction...
October 22, 2016: Expert Review of Proteomics
Feixiong Cheng, Junfei Zhao, Ariella B Hanker, Monica Red Brewer, Carlos L Arteaga, Zhongming Zhao
PURPOSE: Phosphatidylinositol 3-kinase (PI3K)/AKT pathway aberrations are common in human breast cancer. Furthermore, PIK3CA mutations are commonly associated with resistance to anti-epidermal growth factor receptor 2 (HER2) or anti-estrogen receptor (ER) agents in HER2 or ER positive (HER2(+)/ER(+)) breast cancer. Hence, deciphering the underlying mechanisms of PIK3CA mutations in HER2(+)/ER(+) breast cancer would provide novel insights into elucidating resistance to anti-HER2/ER therapies...
October 22, 2016: Breast Cancer Research and Treatment
Johnson Lin
Quantification of gene expression of Acinetobacter strain Y under 1000 mg/l of phenol was investigated using qPCR and proteomic analyses. The results show that Acinetobacter strain Y utilized 100 % of phenol within 18 h of exposure. The results of qPCR and proteomic analyses demonstrate a sequential expression of phenol-degrading genes of Acinetobacter strain Y via the ortho-pathway followed by the β-ketoadipate pathway. Many stress-responsive proteins such as chaperones, chaperonins, porins and the enzymes involved in the signal transduction pathway were upregulated especially in the early stage...
October 22, 2016: Archives of Microbiology
Jianhe Peng, Jing Cao, Fui Mee Ng, Jeffrey Hill
: Pseudomonas aeruginosa infection is difficult to treat because of its drug resistance, but how it develops drug resistance remains largely unknown. In this study we investigated Ciprofloxacin resistance development in P. aeruginosa. Different Ciprofloxacin concentrations selected different low level resistant mutants, and high level resistant mutants emerged from low level resistant mutants if stressed further by Ciprofloxacin. A deep quantitative proteomic study of the Ciprofloxacin resistant mutants uncovered the cellular pathways that supported such resistances...
October 19, 2016: Journal of Proteomics
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