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proteomics pathway ontology

Nina Zila, Andrea Bileck, Besnik Muqaku, Lukas Janker, Ossia M Eichhoff, Phil F Cheng, Reinhard Dummer, Mitchell P Levesque, Christopher Gerner, Verena Paulitschke
Background: MAP kinase inhibitor (MAPKi) therapy for BRAF mutated melanoma is characterized by high response rates but development of drug resistance within a median progression-free survival (PFS) of 9-12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to specifically gain insight into the pathophysiological process of cerebral metastases. Methods: Cerebral metastases from melanoma patients were initially analyzed by a LC-MS shotgun approach performed on a QExactive HF hybrid quadrupole-orbitrap mass spectrometer...
2018: Clinical Proteomics
Chen Zou, Changjing Han, Minjie Zhao, Jingjing Yu, Lin Bai, Yuan Yao, Shuaixin Gao, Hui Cao, Zhi Zheng
Background: Preoperative treatment of anti-vascular endothelial growth factor (VEGF) agents is extensively used in proliferative diabetic retinopathy (PDR), but the molecular mechanism is not fully understood. The objective of this research is to observe change of protein profile induced by ranibizumab (an anti-VEGF agent) in vitreous humor from PDR patients and reveal the effects of anti-VEGF treatment on PDR. Methods: A proteomic method was used to identify differentially expressed proteins in vitreous humor...
2018: Clinical Proteomics
Jessica M Skeie, Benjamin T Aldrich, Andrew S Goldstein, Gregory A Schmidt, Cynthia R Reed, Mark A Greiner
The objective of this study was to characterize the proteome of the corneal endothelial cell layer and its basement membrane (Descemet membrane) in humans with various severities of type II diabetes mellitus compared to controls, and identify differentially expressed proteins across a range of diabetic disease severities that may influence corneal endothelial cell health. Endothelium-Descemet membrane complex tissues were peeled from transplant suitable donor corneas. Protein fractions were isolated from each sample and subjected to multidimensional liquid chromatography and tandem mass spectrometry...
2018: PloS One
Paul R Evans, Kyle J Gerber, Eric B Dammer, Duc M Duong, Devrishi Goswami, Daniel J Lustberg, Juan Zou, Jenny J Yang, Serena M Dudek, Patrick R Griffin, Nicholas T Seyfried, John R Hepler
Regulator of G Protein Signaling 14 (RGS14) is a complex scaffolding protein that integrates G protein and MAPK signaling pathways. In the adult mouse brain, RGS14 is predominantly expressed in hippocampal CA2 neurons where it naturally inhibits synaptic plasticity and hippocampus-dependent learning and memory. However, the signaling proteins that RGS14 natively engages to regulate plasticity are unknown. Here, we show that RGS14 exists in a high molecular weight protein complex in brain. To identify RGS14 neuronal interacting partners, endogenous RGS14 immunoprecipitated from mouse brain was subjected to mass spectrometry and proteomic analysis...
March 8, 2018: Journal of Proteome Research
Sau Ha Cheung, James Yun Wong Lau
S-sulfhydration is a signalling pathway of hydrogen sulfide (H2S), which is suggested as an anti-atherogenic molecule that may protect against atherosclerosis. The identification of S-sulfhydrated proteins by proteomic approach could be a major step towards understanding the mechanisms of H2S in response to atherosclerosis. The present study studied targeted S-sulfhydrated proteins using the modified biotin switch method followed by matrix-assisted laser desorption/ionisation time of flight tandem mass spectrometry identification...
2018: PloS One
Z Cao, B Meng, R Fan, M Liu, M Gao, Z Xing, X Luan
To explore the key regulatory genes and their translated products involved in Huoyan goose egg laying, we first applied the iTRAQ technology integrated with LC-MS/MS analysis to identify differentially abundant proteins in the ovarian tissue of Huoyan geese between the pre-laying and laying periods. Then, Gene Ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses of the proteins were conducted. As observed, 403 proteins, which included 255 up-regulated and 148 down-regulated proteins, were identified...
March 1, 2018: Poultry Science
Sara Faccidomo, Katarina S Swaim, Briana L Saunders, Taruni S Santanam, Seth M Taylor, Michelle Kim, Grant T Reid, Vallari R Eastman, Clyde W Hodge
RATIONALE: There is a clear need for discovery of effective medications to treat behavioral pathologies associated with alcohol addiction, such as chronic drinking. OBJECTIVE: The goal of this preclinical study was to assess effects of chronic alcohol drinking on the nucleus accumbens (NAcb) proteome to identify and validate novel targets for medications development. MATERIALS AND METHODS: Two-dimensional difference in-gel electrophoresis (2D-DIGE) with matrix-assisted laser desorption ionization tandem time-of-flight (MALDI-TOF/TOF) was used to assess effects of chronic voluntary home-cage (24-h access) alcohol drinking on the NAcb proteome of C57BL/6J mice...
March 3, 2018: Psychopharmacology
Chunyu Hou, Yuan Li, Huiqin Liu, Mengjiao Dang, Guoxuan Qin, Ning Zhang, Ruibing Chen
Background: Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are still not fully understood. In this study, proteomics and bioinformatics analyses were performed to establish a protein-protein interaction (PPI) network associated with PKCζ, laying a stepping stone to further understand the diverse biological roles of PKCζ. Methods: Protein complexes associated with PKCζ were purified by co-immunoprecipitation from breast cancer cell MDA-MB-231 and identified by LC-MS/MS...
2018: Proteome Science
Hongtao Liu, Li Jia, Wenfei Guo, Yingying Sun, Rining Zhu, Shuguang Li, Guanggang Qu, Hexiang Jiang, Junjie Wang, Jingmin Gu, Changjiang Sun, Xin Feng, Wenyu Han, Liancheng Lei
Streptococcus suis serotype 2 (SS2) is a zoonotic pathogen that can cause meningitis both in pigs and in human beings. However, the pathogenesis of central nervous system (CNS) infection caused by SS2 have not yet been elucidated. To find the key molecules in cerebrospinal fluid (CSF) needed for the pathogenesis, a SS2 meningoencephalitic pig model and a SS2 non-meningoencephalitic pig model were established in this study. CSF was collected from infected piglets, and protein profiling was performed with label-free proteomics technology...
2018: Frontiers in Cellular and Infection Microbiology
Blake Miller, Nathalie Selevsek, Jonas Grossman, Tanya Kilminster, Tim Scanlon, Matthew Daniels, Paolo Nanni, John Milton, Chris Oldham, Johan Greef, Aspinas Chapwanya, Don Bergfelt, André M de Almeida
The effect of feed restriction on the liver protein profiles of two different breeds of sheep was studied. We compared Merino with the Damara, breeds with respectively low and high tolerance to nutritional stress. Each breed was grouped into two nutritional treatments: restricted (12-14% loss of live weight) and control (maintenance). The trial lasted 42 days. Animals were sacrificed and liver samples subjected to label free shotgun proteomics. The resultant proteins had both their fold change and statistical significance in an unpaired t-test calculated to identify differential protein abundance...
February 18, 2018: Journal of Proteomics
Gabriel Velez, Daniel A Machlab, Peter H Tang, Yang Sun, Stephen H Tsang, Alexander G Bassuk, Vinit B Mahajan
Differences in regional protein expression within the human retina may explain molecular predisposition of specific regions to ophthalmic diseases like age-related macular degeneration, cystoid macular edema, retinitis pigmentosa, and diabetic retinopathy. To quantify protein levels in the human retina and identify patterns of differentially-expressed proteins, we collected foveomacular, juxta-macular, and peripheral retina punch biopsies from healthy donor eyes and analyzed protein content by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2018: PloS One
Jing Xia, Ling Kong, Li-Juan Zhou, Shui-Zhen Wu, Li-Jie Yao, Cheng He, Cynthia Y He, Hong-Juan Peng
Toxoplasma gondii rhoptry protein ROP18 ( Tg ROP18) is a key virulence factor secreted into the host cell during invasion, where it modulates the host cell response by interacting with its host targets. However, only a few Tg ROP18 targets have been identified. In this study, we applied a high-throughput protein-protein interaction (PPI) screening in human cells using bimolecular fluorescence complementation (BiFC) to identify the targets of Type I strain ROP18 (ROP18I ) and Type II strain ROP18 (ROP18II )...
2018: Frontiers in Immunology
Shunhua Wu, Jing Li, Xiang Jin
Long-term consumption of sodium arsenite contaminated water can cause endemic arsenic disease. The proteome profile changes of liver fibrosis after exposure to arsenite containing water remain unclear. In this study, Sprague-Dawley (SD) male rats were treated with sodium arsenite (iAs3+), using a daily dose of 1.36 mg/kg body weight (medium dose group, M), 2.73 mg/kg body weight (high dose group, H) or deionized water (control group, C). Isobaric tags for relative and absolute quantitation (iTRAQ) were used to identify the different abundant proteins (DAPs) after arsenic-induced liver fibrosis...
February 19, 2018: Scientific Reports
Fangqiong Li, Dongxiao Zhao, Suwen Yang, Juan Wang, Qin Liu, Xin Jin, Wei Wang
BACKGROUND/AIMS: Triptolide (TP) is a diterpenoid triepoxide extracted from the traditional Chinese medical herb Tripterygium wilfordii that exerts prominent broad-spectrum anticancer activity to repress proliferation and induce cancer cell apoptosis through various molecular pathways. We previously observed that TP inhibits the progression of A549 cells and pancreatic cancer cells (PNCA-1) in vitro. However, the complex molecular mechanism underlying the anticancer activity of TP is not well understood...
February 2, 2018: Cellular Physiology and Biochemistry
Heng-Dao Lin, Li-Sung Hsu, Chih-Ching Chien, Ssu-Ching Chen
Ametrym (AMT) is the most widely used herbicide and frequently detected in the aquatic environment. AMT also represent a potential health risk to aquatic organisms and animals, including humans. However, little data are available on their toxicity to zebrafish (Danio rerio). The aim of the present study was to evaluate the toxicological effects of AMT exposure on zebrafish embryos. In the acute toxicity test, 6 hpf embryos were exposed to various concentrations of AMT for 24 or 48 h. The results indicated that AMT induced malformation in larvae...
February 10, 2018: Environmental Toxicology
Jian-Qin Wang, Miao Yu, Ying Zhou, Bang-Ce Ye
Biological science discovery often involves comparing conditions to a normal state, but little is known about "normal." Therefore, we used proteomic strategy to compare data from replicate samples of Bacillus subtilis 168 which were grown under identical condition. The results show that 294 differentially expressed proteins were annotated in 88 Gene Ontology functional groups and enriched in 13 KEGG pathways. We assume that normal expression differences are associated with adaptation to diverse environments...
February 9, 2018: Current Microbiology
R Singh, G S Sengar, U Singh, R Deb, V Junghare, S Hazra, S Kumar, S Tyagi, A K Das, T V Raja, A Kumar
Male infertility is one of the prime concerns of dairy cattle production. The study was designed to find out differentially expressed proteins in categorized crossbred (Holstein Friesian × Sahiwal) bull semen to serve as potential biomarkers for male infertility. Frozen crossbred bull semen with satisfactory phenotypic records were defined as "good" and "poor" based on their fertility rates. A total of 1,547 proteins were detected in bull spermatozoa using liquid chromatography-mass spectrometer (LC-MS/MS) analysis...
February 7, 2018: Reproduction in Domestic Animals, Zuchthygiene
Yoshitoshi Hirao, Suguru Saito, Hidehiko Fujinaka, Shigeru Miyazaki, Bo Xu, Ali F Quadery, Amr Elguoshy, Keiko Yamamoto, Tadashi Yamamoto
Diabetic mellitus (DM) is a disease that affects glucose homeostasis and causes complications, such as diabetic nephropathy (DN). For early diagnosis of DN, microalbuminuria is currently one of the most frequently used biomarkers. However, more early diagnostic biomarkers are desired in addition to microalbuminuria. In this study, we performed comprehensive proteomics analysis of urine proteomes of diabetic mellitus patients without microalbuminuria and healthy volunteers to compare the protein profiles by mass spectrometry...
February 6, 2018: Proteomes
He Wang, Dandan Ma, Xiaoyi Zhang, Shuaimei Xu, Tingting Ning, Buling Wu
OBJECTIVE: This study aimed to compare the proteomic profiling of human dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs) under in vitro osteogenic induction, which imitates the microenvironment during osteo-/odontogenesis of DPSCs and PDLSCs. DESIGN: The proteomic profiles of osteoinduced DPSCs and PDLSCs from a single donor were compared using the isobaric tag for relative and absolute quantitation (iTRAQ) technique and subsequent bioinformatics analysis...
February 3, 2018: Archives of Oral Biology
Thidathip Wongsurawat, Chin Cheng Woo, Antonis Giannakakis, Xiao Yun Lin, Esther Sok Hwee Cheow, Chuen Neng Lee, Mark Richards, Siu Kwan Sze, Intawat Nookaew, Vladimir A Kuznetsov, Vitaly Sorokin
BACKGROUND AND AIMS: We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Providing a robust transcriptomic signature, we aim to highlight the most likely aberrant pathway(s) in MI VSMCs. METHODS AND RESULTS: Laser-captured microdissection (LCM) was used to obtain VSMCs from aortic wall tissues harvested during coronary artery bypass surgery. Microarray gene analysis was applied to analyse VSMCs from 17 MI and 19 non-MI patients...
January 29, 2018: Atherosclerosis
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