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proteomics pathway analysis

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https://www.readbyqxmd.com/read/29340031/analyzing-the-influence-of-kinase-inhibitors-on-dna-repair-by-differential-proteomics-of-chromatin-interacting-proteins-and-nuclear-phospho-proteins
#1
Lisa Gleißner, Marcel Kwiatkowski, Laura Myllynen, Pascal Steffen, Cordula Petersen, Kai Rothkamm, Hartmut Schlüter, Malte Kriegs
The combination of radiotherapy and pharmacological inhibition of cellular signal transduction pathways offers promising strategies for enhanced cancer cell inactivation. However, the molecular effects of kinase inhibitors especially on DNA damage detection and repair after X-irradiation have to be understood to facilitate the development of efficient and personalized treatment regimens. Therefore, we applied differential proteomics for analyzing inhibitor-induced changes in either chromatin-bound or phosphorylated nuclear proteins...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339515/mers-cov-and-h5n1-influenza-virus-antagonize-antigen-presentation-by-altering-the-epigenetic-landscape
#2
Vineet D Menachery, Alexandra Schäfer, Kristin E Burnum-Johnson, Hugh D Mitchell, Amie J Eisfeld, Kevin B Walters, Carrie D Nicora, Samuel O Purvine, Cameron P Casey, Matthew E Monroe, Karl K Weitz, Kelly G Stratton, Bobbie-Jo M Webb-Robertson, Lisa E Gralinski, Thomas O Metz, Richard D Smith, Katrina M Waters, Amy C Sims, Yoshihiro Kawaoka, Ralph S Baric
Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ-dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339483/hells-and-cdca7-comprise-a-bipartite-nucleosome-remodeling-complex-defective-in-icf-syndrome
#3
Christopher Jenness, Simona Giunta, Manuel M Müller, Hiroshi Kimura, Tom W Muir, Hironori Funabiki
Mutations in CDCA7, the SNF2 family protein HELLS (LSH), or the DNA methyltransferase DNMT3b cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. While it has been speculated that DNA methylation defects cause this disease, little is known about the molecular function of CDCA7 and its functional relationship to HELLS and DNMT3b. Systematic analysis of how the cell cycle, H3K9 methylation, and the mitotic kinase Aurora B affect proteomic profiles of chromatin in Xenopus egg extracts revealed that HELLS and CDCA7 form a stoichiometric complex on chromatin, in a manner sensitive to Aurora B...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29337282/comparative-proteome-analysis-of-monolayer-and-spheroid-culture-of-canine-osteosarcoma-cells
#4
Christiane Gebhard, Ingrid Miller, Karin Hummel, Martina Neschi Née Ondrovics, Sarah Schlosser, Ingrid Walter
Osteosarcoma is an aggressive bone tumor with high metastasis rate in the lungs and affects both humans and dogs in a similar way. Three-dimensional tumor cell cultures mimic the in vivo situation of micro-tumors and metastases and are therefore better experimental in vitro models than the often applied two-dimensional monolayer cultures. The aim of the present study was to perform comparative proteomics of standard monolayer cultures of canine osteosarcoma cells (D17) and three-dimensional spheroid cultures, to better characterize the 3D model before starting with experiments like migration assays...
January 11, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29332228/comparative-evaluation-of-the-aqueous-humor-proteome-of-primary-angle-closure-and-primary-open-angle-glaucomas-and-age-related-cataract-eyes
#5
Inderjeet Kaur, Jasbir Kaur, K Sooraj, Sandeep Goswami, Rohit Saxena, Virander Singh Chauhan, Ramanjit Sihota
PURPOSE: To analyze and compare the total proteome of aqueous humor (AH) from patients having primary angle closure glaucoma (PACG), primary open angle glaucoma (POAG) and age-related cataract. MATERIALS AND METHODOLOGY: Aqueous humor was collected from age-matched PACG, POAG and cataract patients who underwent surgery, and it was immediately stored at - 80 °C until analysis. From each sample, 25 µg of total protein was subjected to trypsin digestion and subsequently LC-MS/MS analysis was performed for the deep proteome analysis...
January 13, 2018: International Ophthalmology
https://www.readbyqxmd.com/read/29330215/mir-195-regulates-metabolism-in-failing-myocardium-via-alterations-in-sirt3-expression-and-mitochondrial-protein-acetylation
#6
Xiaokan Zhang, Ruiping Ji, Xianghai Liao, Estibaliz Castillero, Peter J Kennel, Danielle L Brunjes, Marcus Franz, Sven Möbius-Winkler, Konstantinos Drosatos, Isaac George, Emily I Chen, Paolo C Colombo, P Christian Schulze
Background -Heart failure (HF) leads to mitochondrial dysfunction and metabolic abnormalities of the failing myocardium coupled with an energy-depleted state and cardiac remodeling. The mitochondrial deacetylase sirtuin 3 (SIRT3) plays a pivotal role in the maintenance of mitochondrial function through regulating the mitochondrial acetylome. Interestingly, unique cardiac and systemic miRNAs have been shown to play an important role in cardiac remodeling by modulating key signaling elements in the myocardium...
January 12, 2018: Circulation
https://www.readbyqxmd.com/read/29326176/combinatorial-omics-analysis-reveals-perturbed-lysosomal-homeostasis-in-collagen-vii-deficient-keratinocytes
#7
Kerstin Thriene, Björn Andreas Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nyström, Thomas Reinheckel, Rolf Backofen, Cristina Has, Leena Bruckner-Tuderman, Joern Dengjel
The extracellular matrix protein collagen VII is part of the microenvironment of stratified epithelia and critical in organismal homeostasis. Mutations in the encoding gene COL7A1 lead to the skin disorder dystrophic epidermolysis bullosa (DEB), are linked to skin fragility and progressive inflammation-driven fibrosis that facilitates aggressive skin cancer. So far, these changes have been linked to mesenchymal alterations, the epithelial consequences of collagen VII loss remaining under-addressed. As epithelial dysfunction is a principal initiator of fibrosis, we performed a comprehensive transcriptome and proteome profiling of primary human keratinocytes to generate global and detailed images of dysregulated epidermal molecular pathways linked to loss of collagen VII...
January 11, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29325990/quantitative-proteomics-reveals-a-role-of-jaz7-in-plant-defense-response-to-pseudomonas-syringae-dc3000
#8
Tong Zhang, Li Meng, Wenwen Kong, Zepeng Yin, Yang Wang, Jacqueline D Schneider, Sixue Chen
Jasmonate ZIM-domain (JAZ) proteins are key transcriptional repressors regulating various biological processes. Although many studies have studied JAZ proteins by genetic and biochemical analyses, little is known about JAZ7-associated global protein networks and how JAZ7 contributes to bacterial pathogen defense. In this study, we aim to fill this knowledge gap by conducting unbiased large-scale quantitative proteomics using tandem mass tags (TMT). We compared the proteomes of a JAZ7 knock-out line, a JAZ7 overexpression line, as well as the wild type Arabidopsis plants in the presence and absence of Pseudomonas syringae DC3000 infection...
January 8, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29324904/prohibitin-plays-a-critical-role-in-enterovirus-71-neuropathogenesis
#9
Issac Horng Khit Too, Isabelle Bonne, Eng Lee Tan, Justin Jang Hann Chu, Sylvie Alonso
A close relative of poliovirus, enterovirus 71 (EV71) is regarded as an important neurotropic virus of serious public health concern. EV71 causes Hand, Foot and Mouth Disease and has been associated with neurological complications in young children. Our limited understanding of the mechanisms involved in its neuropathogenesis has hampered the development of effective therapeutic options. Here, using a two-dimensional proteomics approach combined with mass spectrometry, we have identified a unique panel of host proteins that were differentially and dynamically modulated during EV71 infection of motor-neuron NSC-34 cells, which are found at the neuromuscular junctions where EV71 is believed to enter the central nervous system...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29323127/differential-proteomics-of-lesional-vs-non-lesional-biopsies-revealed-non-immune-mechanisms-of-alopecia-areata
#10
Kanchalit Thanomkitti, Rattiyaporn Kanlaya, Kedsarin Fong-Ngern, Chompunoot Kapincharanon, Kanyarat Sueksakit, Prangwalai Chanchaem, Rattapon Thuangtong, Visith Thongboonkerd
Alopecia areata (AA) is one of the common hair disorders for which treatment is frequently ineffective and associated with relapsing episodes. Better understanding of disease mechanisms and novel therapeutic targets are thus required. From 10 AA patients, quantitative proteomics using LTQ-Orbitrap-XL mass spectrometer revealed 104 down-regulated, 4 absent, 3 up-regulated and 11 newly present proteins in lesional vs. non-lesional biopsies. Among these, the decreased levels of α-tubulin, vimentin, heat shock protein 70 (HSP70), HSP90, annexin A2 and α-enolase were successfully confirmed by Western blotting...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#11
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321808/itraq-based-proteomic-analysis-to-identify-the-molecular-mechanism-of-zhibai-dihuang-granule-in-the-yin-deficiency-heat-syndrome-rats
#12
Chang-Ming Liu, Jing Chen, Su Yang, Ting-Ting Jiang, Zhong-Liang Chen, Hui-Hui Tu, Lian-Gen Mao, Yu-Ting Hu, Lin Gan, Zhong-Jie Li, Ji-Cheng Li
Background: Zhibai Dihuang Granule (ZDG) is a traditional Chinese medicine which has been used to treat Yin-deficiency-heat (YDH) syndrome for thousands of years in China. However, little work has been conducted to explore the molecular mechanism of ZDG in YDH syndrome, and the processes of YDH syndrome prevention and treatment have been developed slowly. The present study was aimed to explore the therapeutic mechanism of ZDG on YDH syndrome. Methods: The YDH syndrome rats were induced by hot Chinese herbs, then treated by ZDG orally for 1 week...
2018: Chinese Medicine
https://www.readbyqxmd.com/read/29321553/prediction-of-co-expression-genes-and-integrative-analysis-of-gene-microarray-and-proteomics-profile-of-keshan-disease
#13
Sen Wang, Rui Yan, Bin Wang, Peiru Du, Wuhong Tan, Mikko J Lammi, Xiong Guo
Keshan disease (KD) is a kind of endemic cardiomyopathy which has a high mortality. However, molecular mechanism in the pathogenesis of KD remains poorly understood. Serum samples were collected from 112 KD patients and 112 normal controls. Gene microarray was used to screen differently expressed genes. Genevestigator was applied to forecast co-expression genes of significant gene. iTRAQ proteomics analysis was used to verify significant genes and their co-expression genes. GO, COG, IPA and STRING were applied to undertake function categorization, pathway and network analysis separately...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321187/infection-by-the-helminth-parasite-fasciola-hepatica-requires-rapid-regulation-of-metabolic-virulence-and-invasive-factors-to-adjust-to-its-mammalian-host
#14
Krystyna Cwiklinski, Heather Jewhurst, Paul McVeigh, Tara Barbour, Aaron G Maule, Jose Tort, Sandra M O'Neill, Mark W Robinson, Sheila Donnelly, John P Dalton
The parasite Fasciola hepatica infects a broad range of mammals with impunity.  Following ingestion of parasites (metacercariae) by the host, newly excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall and migrate to the liver.  Successful infection takes just a few hours and involves negotiating hurdles presented by host macromolecules, tissues and micro-environments, as well as the immune system.  Here, transcriptome and proteome analysis of ex vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude of metabolic and developmental alterations that take place in order for the parasite to establish infection...
January 10, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29317699/inflammatory-proteomic-network-analysis-of-statin-treated-and-lipopolysaccharide-activated-macrophages
#15
Abu Hena M Kamal, Jayanta K Chakrabarty, S M Nashir Udden, Md Hasan Zaki, Saiful M Chowdhury
A significant component of immune biology research is the investigation of protein encoding genes that play central roles in contributing inflammatory response. A gel-free quantitative bottom-up proteomics study was performed on immune cell macrophages after the combined treatment of lipopolysaccharide (LPS) and statin drugs using mass spectrometry and a detailed bioinformatics analyses were conducted. Systematic bioinformatics analysis was applied for discovering novel relationships among proteins and effects of statin and lipopolysaccharide in macrophage cells...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317657/blood-plasma-igg-n-glycome-biosignatures-associated-with-major-depressive-disorder-symptom-severity-and-the-antidepressant-response
#16
Dong Ik Park, Jerko Štambuk, Genadij Razdorov, Maja Pučić-Baković, Daniel Martins-de-Souza, Gordan Lauc, Christoph W Turck
While N-linked glycosylation has been extensively studied in the context of inflammatory and metabolic disorders, its relationship with major depressive disorder (MDD) and antidepressant treatment response has not been investigated. In our exploratory study, we analysed N-glycan profiles in blood plasma samples collected from MDD patients (n = 18) and found gender-dependent correlations with severity of depressive symptoms prior to initiating antidepressant treatment. In addition, several N-glycosylation traits showed gender-dependent associations with clinical antidepressant response...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317357/novel-identified-aluminum-hydroxide-induced-pathways-proof-monocyte-activation-and-pro-inflammatory-preparedness
#17
Sietske Kooijman, Jolanda Brummelman, Cécile A C M van Els, Fabio Marino, Albert J R Heck, Geert P M Mommen, Bernard Metz, Gideon F A Kersten, Jeroen L A Pennings, Hugo D Meiring
Aluminum-based adjuvants are the most widely used adjuvants in human vaccines. A comprehensive understanding of the mechanism of action of aluminum adjuvants at the molecular level, however, is still elusive. Here, we unravel the effects of aluminum hydroxide Al(OH)3 by a systems-wide analysis of the Al(OH)3-induced monocyte response. Cell response analysis by cytokine release was combined with (targeted) transcriptome and full proteome analysis. Results from this comprehensive study revealed two novel pathways to become activated upon monocyte stimulation with Al(OH)3: the first pathway was IFNβ signaling possibly induced by DAMP sensing pathways like TLR or NOD1 activation, and second the HLA class I antigen processing and presentation pathway...
January 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29317355/identification-of-candidate-serum-biomarkers-of-childhood-onset-growth-hormone-deficiency-using-swath-ms-and-feature-selection
#18
Ignacio Ortea, Isabel Ruíz, Ramón Cañete, Javier Caballero-Villarraso, María Dolores Cañete
A typical clinical manifestation of growth hormone deficiency (GHD) is a short stature resulting from delayed growth, but GHD affects bone health, cardiovascular function and metabolic profile and therefore quality of life. Although early GH treatment during childhood has been shown to improve outcomes, no single biochemical parameter is currently available for the accurate diagnosis of GHD in children. There is hence a need for non-invasive biomarkers. In this study, the relative abundance of serum proteins from GHD children and healthy controls was measured by next-generation proteomics SWATH-MS technology...
January 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29316787/reprogramming-one-carbon-metabolic-pathways-to-decouple-l-serine-catabolism-from-cell-growth-in-corynebacterium-glutamicum
#19
Yun Zhang, Xiuling Shang, Shujuan Lai, Yu Zhang, Qitiao Hu, Xin Chai, Bo Wang, Shuwen Liu, Tingyi Wen
L-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of L-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple L-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with L-serine productivity. Attenuation of glyA transcription resulted in increased L-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes...
January 9, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29312565/dissect-new-mechanistic-insights-for-geniposide-efficacy-on-the-hepatoprotection-using-multiomics-approach
#20
Shi Qiu, Aihua Zhang, Tianlei Zhang, Hui Sun, Yu Guan, Guangli Yan, Xijun Wang
A multi-omics approach could yield in-depth mechanistic insights. Here, we performed an integrated analysis of miRNAome, proteome and metabolome, aimed to investigate the underlying mechanism of active product geniposide in ethanol-induced apoptosis. We found that integrative meta-analysis identified 28 miRNAs, 20 proteins and 7 metabolites significantly differentially expressed, respectively. Further analysis identified geniposide extensively regulated multiple metabolism pathways and the most important related pathway was citrate cycle (TCA cycle)...
December 12, 2017: Oncotarget
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