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proteomics pathway ontology

Huang-Joe Wang, Sung-Fang Chen, Wan-Yu Lo
The angiotensin-converting enzyme 2/angiotensin-(1-7)/Mas axis is a pathway that acts against the detrimental effects of the renin-angiotensin system. However, the effects of angiotensin-(1-7) on endothelial protein expression and the related phenotypes are unclear. We performed a duplicate of iTRAQ quantitative proteomic analysis on human aortic endothelial cells (HAECs) treated with angiotensin-(1-7) for 6 hours. Cofilin-1 was identified as a highly abundant candidate with consistent >30% coverage and >1...
October 17, 2016: Scientific Reports
Jürgen Böhm, Frank Pianka, Nina Stüttgen, Junghyun Rho, Biljana Gigic, Yuzheng Zhang, Nina Habermann, Petra Schrotz-King, Clare Abbenhardt-Martin, Lin Zielske, Paul D Lampe, Alexis Ulrich, Markus K Diener, Cornelia M Ulrich
BACKGROUND: Ventral incisional hernia is the most common long-term complication after an abdominal operation. Among newly diagnosed colorectal cancer patients, we screened the preoperative plasma proteome to explore predictive markers for the development of an incisional hernia. METHODS: We utilized preoperative plasma samples of 72 newly diagnosed colorectal cancer patients who underwent midline incision for tumor resection between 2010 and 2013. A total of 21 patients with incisional hernia occurrence were matched with 51 patients with at least 18 months follow-up without an incisional hernia by sex, age, and body mass index...
October 13, 2016: Surgery
Li Ou, Michael J Przybilla, Chester B Whitley
Mucopolysaccharidosis type I (MPS I) is due to deficiency of α-l-iduronidase (IDUA) and subsequent storage of undegraded glycosaminoglycans (GAG). The severe form of the disease, known as Hurler syndrome, is characterized by mental retardation and neurodegeneration of unknown etiology. To identify potential biomarkers and unveil the neuropathology mechanism of MPS I disease, two-dimensional polyacrylamide gel electrophoresis (PAGE) and nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) were applied to compare proteome profiling of brains from MPS I and control mice (5-month old)...
October 11, 2016: Molecular Genetics and Metabolism
Y Zhang, E J Crofton, X Fan, D Li, F Kong, M Sinha, B A Luxon, H M Spratt, C F Lichti, T A Green
Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs...
October 4, 2016: Neuroscience
Yu Wang, Hua Guan, Da-Fei Xie, Yi Xie, Xiao-Dan Liu, Qi Wang, Li Sui, Man Song, Hong Zhang, Jianhua Zhou, Ping-Kun Zhou
Radiotherapy with heavy ions is considered advantageous compared to irradiation with photons due to the characteristics of the Braggs peak and the high linear energy transfer (LET) value. To understand the mechanisms of cellular responses to different LET values and dosages of heavy ion radiation, we analyzed the proteomic profiles of mouse embryo fibroblast MEF cells exposed to two doses from different LET values of heavy ion 12C. Total proteins were extracted from these cells and examined by Q Exactive with Liquid Chromatography (LC)-Electrospray Ionization (ESI) Tandem MS (MS/MS)...
2016: PloS One
Dilek Colak, Ayodele A Alaiya, Namik Kaya, Nzioka P Muiya, Olfat AlHarazi, Zakia Shinwari, Editha Andres, Nduna Dzimiri
AIMS: The disease pathways leading to idiopathic dilated cardiomyopathy (DCM) are still elusive. The present study investigated integrated global transcriptional and translational changes in human DCM for disease biomarker discovery. METHODS: We used identical myocardial tissues from five DCM hearts compared to five non-failing (NF) donor hearts for both transcriptome profiling using the ABI high-density oligonucleotide microarrays and proteome expression with One-Dimensional Nano Acquity liquid chromatography coupled with tandem mass spectrometry on the Synapt G2 system...
2016: PloS One
Yang Wang, Zhi-Hao Huang, Yang-Jia Li, Gui-Wei He, Ru-Yuan Yu, Jie Yang, Wan-Ting Liu, Bin Li, Qing-Yu He
Emerging evidence suggested that necroptosis has essential functions in many human inflammatory diseases, but the molecular mechanisms of necroptosis remain unclear. Here, we employed SILAC quantitatively dynamic proteomics to compare the protein changes during TNF-α-induced necroptosis at different time points in murine fibrosarcoma L929 cells with caspase-8 deficiency, and then performed the systematical analysis on the signaling networks involved in the progress using bioinformatics methods. Our results showed that a total of 329, 421 and 378 differentially expressed proteins were detected at three stages of necroptosis, respectively...
October 4, 2016: Apoptosis: An International Journal on Programmed Cell Death
Xiaoshan Yue, Jessica K Lukowski, Eric M Weaver, Susan B Skube, Amanda B Hummon
Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined and notable differences in both the proteome and the phosphoproteome were determined by nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) to assess how growth configuration affects molecular expression...
October 3, 2016: Journal of Proteome Research
Oh Kwang Kwon, Sun Joo Kim, Sangkyu Lee
Lysine acetylation is an important post-translational modification. Since the development of mass spectrometry (MS)-based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and biologic studies. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D...
October 2, 2016: Electrophoresis
Jun-Wei Wang, Xin Zhou, Qian Zhou, Zhi-Yong Liu, Lei Sheng, Long Wang, Shun-Chang Cheng, Shu-Juan Ji
BACKGROUND: Postharvest ripening of the 'Nanguo' pear (Pyrus ussuriensis Maxim) can be impeded by low temperature storage. However, pears after long-term refrigeration are prone to peel browning (PB) when returned to room temperature conditions. This study investigated the browning mechanism of 'Nanguo' pear stored at a low temperature by analyzing the differentially expressed proteins between healthy and PB fruit. RESULTS: The results showed that 181 proteins underwent statistically significant changes...
October 3, 2016: Journal of the Science of Food and Agriculture
Prudence Mutowo, A Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax, John P Overington
BACKGROUND: The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification of novel 'targets', usually proteins that can be modulated by small molecule drugs to cure or minimise the effects of a disease. Of the 20,000 proteins currently reported as comprising the human proteome, just under a quarter of these can potentially be modulated by known small molecules Storing information in curated, actively maintained drug discovery databases can help researchers access current drug discovery information quickly...
September 27, 2016: Journal of Biomedical Semantics
Xia Yang, Zichang Zhang, Tao Gu, Mingchao Dong, Qiong Peng, Lianyang Bai, Yongfeng Li
: Barnyardgrass (Echinochloa crus-galli) is one of the top 15 herbicide-resistant weeds around the world that interferes with rice growth, resulting in major losses of rice yield. Thus, multi-herbicide resistance in barnyardgrass presents a major threat, with the underlying mechanisms that contribute to resistance requiring elucidation. In an attempt to characterize this multi-herbicide resistance at the proteomic level, comparative analysis of resistant and susceptible barnyardgrasses was performed using iTRAQ, both with and without quinclorac, bispyribac-sodium and penoxsulam herbicidal treatment...
September 23, 2016: Journal of Proteomics
Zhiwei Qiao, Xiaoqing Pan, Cuneyd Parlayan, Hidenori Ojima, Tadashi Kondo
Vascular invasion is a pathological hallmark of hepatocellular carcinoma (HCC), associated with poor prognosis; it is strongly related to the early recurrence and poor survival after curative resection. In order to determine the proteomic backgrounds of HCC carcinogenesis and vascular invasion, we employed a novel modified aptamer-based array (SOMAscan) platform. SOMAscan is based on the Slow Off-rate Modified Aptamers (SOMAmers), which rely on the natural 3D folding of single-stranded DNA-based protein affinity reagents...
September 20, 2016: Biochimica et Biophysica Acta
Yanbin Zhang, Yue Liu, Yingjiang Ye, Danhua Shen, Hui Zhang, Hongyan Huang, Sha Li, Shan Wang, Jun Ren
PURPOSE: To evaluate a new strategy for profiling proteomic changes in colorectal cancer (CRC). METHODES: We used laser capture microdissection (LCM) to obtain cells from 20 CRC and paired normal mucosal tissues. The differential proteins between the microdissected tumor cells and normal mucosa epithelia were analyzed by acetylation stable isotopic labeling coupled with L linear ion trap Fourier transform ion cyclotron resonance mass spectrometry (LTQ-FT MS). Western blotting was used to assess the differential expression of proteins...
September 22, 2016: Journal of Cancer Research and Clinical Oncology
Jingjing Wang, Xiao Song, Chengli Guo, Ying Wang, Yanhui Yin
MAGEC2, a cancer/testis antigen, is expressed in a wide variety of cancer types but not in normal somatic cells. MAGEC2 has long been recognized as a tumor-specific target, however, its functions remain largely unknown. In this study, we established MAGEC2-knockout A375 melanoma cell lines using the CRISPR/Cas9 system. Seven clonal cell lines were generated by using four single guide RNAs targeting the coding region of the MAGEC2 gene, which produced indels that abolished MAGEC2 protein expression. To identify the differentially expressed protein profiles associated with MAGEC2 loss, iTRAQ based comparative proteomics experiments were carried out on the MAGEC2-knockcout and control A375 cells...
September 16, 2016: Cancer Science
Jiafeng Li, Jinsheng Zhao, Yue Li
Overexpression of the nucleoporin NUP88 has been observed in a large number of tumors and has been experimentally proven to promote tumorigenesis. However, the mechanism underlying the tumor-promoting activity of overexpressed NUP88 is not clear. To investigate the potential pathways that drive tumorigenesis under NUP88 overexpressed condition, we applied a proteomic approach to identify NUP88-associated proteins at a subcellular compartment level. Gene ontology analysis revealed significant associations between NUP88 interactome and biological processes that are related to nuclear transport, RNA processing, cell cycle progression, metabolic regulation, and viral infection...
September 16, 2016: Genes, Chromosomes & Cancer
Patrick Georgoff, Ihab Halaweish, Vahagn Nikolian, Gerald Higgins, Tess Bonham, Celia Tafatia, Henriette Remmer, Rajasree Menon, Baoling Liu, Yongqing Li, Hasan B Alam
BACKGROUND: High doses of the histone deacetylase inhibitor Valproic Acid (VPA, 150-400 mg/kg) improve outcomes in animal models of lethal insults. We are conducting an FDA approved phase 1, double blind, placebo-controlled trial to evaluate the safety and tolerability of ascending doses of VPA in human volunteers. We hypothesized that VPA would induce significant changes in the proteome of healthy humans when given at doses lower than those used in prior animal studies. METHODS: Peripheral blood mononuclear cells were obtained from three healthy subjects randomized to receive VPA (120 mg/kg over one hour) at baseline, 4, and 8 hours following infusion...
September 3, 2016: Journal of Trauma and Acute Care Surgery
Evangelos I Kanonidis, Marcia M Roy, Ruth F Deighton, Thierry Le Bihan
Although correlation network studies from co-expression analysis are increasingly popular, they are rarely applied to proteomics datasets. Protein co-expression analysis provides a complementary view of underlying trends, which can be overlooked by conventional data analysis. The core of the present study is based on Weighted Gene Co-expression Network Analysis applied to a glioblastoma multiforme proteomic dataset. Using this method, we have identified three main modules which are associated with three different membrane associated groups; mitochondrial, endoplasmic reticulum, and a vesicle fraction...
2016: PloS One
Xiang Li, Ting Wan, Sijie Zhang, Dongliang Li, Xiaofeng Han
Two human bone marrow stromal cell lines, HS5 and HS27a, co-cultured with myeloid cells, have been frequently used in studies of crosstalk between cells in the bone marrow microenvironment and hematopoietic cells. Altered expression of proteins is typically associated with cell-cell signal transduction and regulation of cellular functions. Many studies have focused on key proteins that contribute to functional differences in cell co-culture models, but global quantitative proteome analysis of HS5 and HS27a has not been performed...
August 15, 2016: Experimental Hematology
Fekadu Yadetie, Silje Bjørneklett, Hilde Kristin Garberg, Eystein Oveland, Frode Berven, Anders Goksøyr, Odd André Karlsen
BACKGROUND: Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of MeHg-mediated toxicity, we have used label-free quantitative mass spectrometry to analyze the liver proteome of Atlantic cod (Gadus morhua) exposed in vivo to MeHg (0, 0.5, 2 mg/kg body weight) for 2 weeks. RESULTS: Out of a toltal of 1143 proteins quantified, 125 proteins were differentially regulated between MeHg-treated samples and controls...
2016: BMC Genomics
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