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phosphoproteomics

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https://www.readbyqxmd.com/read/28220839/pten-status-is-a-crucial-determinant-of-the-functional-outcome-of-combined-mek-and-mtor-inhibition-in-cancer
#1
Michele Milella, Italia Falcone, Fabiana Conciatori, Silvia Matteoni, Andrea Sacconi, Teresa De Luca, Chiara Bazzichetto, Vincenzo Corbo, Michele Simbolo, Isabella Sperduti, Antonina Benfante, Anais Del Curatolo, Ursula Cesta Incani, Federico Malusa, Adriana Eramo, Giovanni Sette, Aldo Scarpa, Marina Konopleva, Michael Andreeff, James Andrew McCubrey, Giovanni Blandino, Matilde Todaro, Giorgio Stassi, Ruggero De Maria, Francesco Cognetti, Donatella Del Bufalo, Ludovica Ciuffreda
Combined MAPK/PI3K pathway inhibition represents an attractive, albeit toxic, therapeutic strategy in oncology. Since PTEN lies at the intersection of these two pathways, we investigated whether PTEN status determines the functional response to combined pathway inhibition. PTEN (gene, mRNA, and protein) status was extensively characterized in a panel of cancer cell lines and combined MEK/mTOR inhibition displayed highly synergistic pharmacologic interactions almost exclusively in PTEN-loss models. Genetic manipulation of PTEN status confirmed a mechanistic role for PTEN in determining the functional outcome of combined pathway blockade...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220420/identification-of-mapk-substrates-using-quantitative-phosphoproteomics
#2
Tong Zhang, Jacqueline D Schneider, Ning Zhu, Sixue Chen
Activation of mitogen-activated protein kinases (MAPKs) under diverse biotic and abiotic factors and identification of an array of downstream MAPK target proteins are hot topics in plant signal transduction. Through interactions with a plethora of substrate proteins, MAPK cascades regulate many physiological processes in the course of plant growth, development, and response to environmental factors. Identification and quantification of potential MAPK substrates are essential, but have been technically challenging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28213246/spinel-type-manganese-ferrite-mnfe2o4-microspheres-a-novel-affinity-probe-for-selective-and-fast-enrichment-of-phosphopeptides
#3
Xing-Yu Long, Jia-Yuan Li, Dong Sheng, Hong-Zhen Lian
The spinel-type magnetic manganese ferrite (MnFe2O4) microspheres synthesized by simple solvothermal method were used as a novel adsorbent for selective enrichment and effective isolation of phosphopeptides. The uniform MnFe2O4 magnetic affinity microspheres (MAMSs) had a narrow particle size distribution between 250 and 260nm, and displayed superparamagnetism with a saturation magnetization value of 67.0emu/g. Comprehensively, the possible formation mechanism of MnFe2O4 microspheres with ferric and manganous sources as dual precursors was elucidated by comparison with those of Fe3O4 nanoparticles and MnOOH nanosheets respectively with either ferric or manganous source as single precursor...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213213/titanium-iv-ion-modified-covalent-organic-frameworks-for-specific-enrichment-of-phosphopeptides
#4
Heping Wang, Fenglong Jiao, Fangyuan Gao, Yayao Lv, Qiong Wu, Yan Zhao, Yehua Shen, Yangjun Zhang, Xiaohong Qian
To date, plenty of new alternative materials for phosphopeptides enrichment prior to mass spectrometry (MS) analysis appear, especially immobilized metal ion affinity chromatography (IMAC) materials. The variable combinations with different metal ions, chelating ligands and solid supports offer full of optionality for IMAC. However, further improvement was predicted by the tedious and complex synthetic process. In this work, a novel covalent organic framework (COF)-based IMAC material (denoted TpPa-2-Ti(4+)) was prepared simply by direct immobilizing Ti (IV) into TpPa-2 COFs without any extra chelating ligands...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28211852/plasmodium-falciparum-crk4-directs-continuous-rounds-of-dna-replication-during-schizogony
#5
Markus Ganter, Jonathan M Goldberg, Jeffrey D Dvorin, Joao A Paulo, Jonas G King, Abhai K Tripathi, Aditya S Paul, Jing Yang, Isabelle Coppens, Rays H Y Jiang, Brendan Elsworth, David A Baker, Rhoel R Dinglasan, Steven P Gygi, Manoj T Duraisingh
Plasmodium parasites, the causative agents of malaria, have evolved a unique cell division cycle in the clinically relevant asexual blood stage of infection(1). DNA replication commences approximately halfway through the intracellular development following invasion and parasite growth. The schizont stage is associated with multiple rounds of DNA replication and nuclear division without cytokinesis, resulting in a multinucleated cell. Nuclei divide asynchronously through schizogony, with only the final round of DNA replication and segregation being synchronous and coordinated with daughter cell assembly(2,3)...
February 17, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28210003/differential-signaling-through-p190-and-p210-bcr-abl-fusion-proteins-revealed-by-interactome-and-phosphoproteome-analysis
#6
J A Cutler, R Tahir, S K Sreenivasamurthy, C Mitchell, S Renuse, R S Nirujogi, A H Patil, M Heydarian, X Wong, X Wu, T-C Huang, M-S Kim, K Reddy, A Pandey
Two major types of leukemogenic BCR-ABL fusion proteins are p190(BCR-ABL) and p210(BCR-ABL). Although the two fusion proteins are closely related, they can lead to different clinical outcomes. A thorough understanding of the signaling programs employed by these two fusion proteins is necessary to explain these clinical differences. We took an integrated approach by coupling protein-protein interaction analysis using biotinylation identification (BioID) with global phosphorylation analysis to investigate the differences in signaling between these two fusion proteins...
February 17, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28209619/lapatinib-resistance-in-breast-cancer-cells-is-accompanied-by-phosphorylation-mediated-reprogramming-of-glycolysis
#7
Benjamin Ruprecht, Esther A Zaal, Jana Zecha, Wei Wu, Celia R Berkers, Bernhard Kuster, Simone Lemeer
HER2/ERBB2-overexpressing breast cancers targeted effectively by the small molecule kinase inhibitor lapatinib frequently acquire resistance to this drug. In this study, we employed explorative mass spectrometry to profile proteomic, kinomic, and phosphoproteomic changes in an established model of lapatinib resistance to systematically investigate initial inhibitor response and subsequent reprogramming in resistance. The resulting dataset, which collectively contains quantitative data for >7,800 proteins, >300 protein kinases and >15,000 phosphopeptides, enabled deep insight into signaling recovery and molecular reprogramming upon resistance...
February 16, 2017: Cancer Research
https://www.readbyqxmd.com/read/28200105/benchmarking-substrate-based-kinase-activity-inference-using-phosphoproteomic-data
#8
Claudia Hernandez-Armenta, David Ochoa, Emanuel Gonçalves, Julio Saez-Rodriguez, Pedro Beltrao
No abstract text is available yet for this article.
February 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28194157/comparative-phosphoproteomic-analysis-under-high-nitrogen-fertilizer-reveals-central-phosphoproteins-promoting-wheat-grain-starch-and-protein-synthesis
#9
Shoumin Zhen, Xiong Deng, Ming Zhang, Gengrui Zhu, Dongwen Lv, Yaping Wang, Dong Zhu, Yueming Yan
Nitrogen (N) is a macronutrient important for plant growth and development. It also strongly influences starch and protein synthesis, closely related to grain yield and quality. We performed the first comparative phosphoproteomic analysis of developing wheat grains in response to high-N fertilizer. Physiological and biochemical analyses showed that application of high-N fertilizer resulted in significant increases in leaf length and area, chlorophyll content, the activity of key enzymes in leaves such as nitrate reductase (NR), and in grains such as sucrose phosphate synthase (SPS), sucrose synthase (SuSy), and ADP glucose pyrophosphorylase (AGPase)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28193068/high-confidence-sequencing-of-phosphopeptides-by-electron-transfer-dissociation-mass-spectrometry-using-dinuclear-zinc-ii-complex
#10
Daiki Asakawa, Issey Osaka
Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS(2)) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn2L)(3+) (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS(2) analysis...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28192934/sensitive-approaches-for-the-assay-of-the-global-protein-tyrosine-phosphorylation-in-complex-samples-using-a-mutated-sh2-domain
#11
Yanan Li, Yan Wang, Mingming Dong, Hanfa Zou, Mingliang Ye
Temporal tyrosine phosphorylation (pTyr) plays a crucial role in numerous cellular functions. The characterization of the tyrosine phosphorylation states of cells is of great interest for understanding the underlying mechanisms. In this study, we developed sensitive and cost-effective methods for the assay of the global protein tyrosine phosphorylation in complex samples by using a novel engineered pTyr binding protein, Src SH2 domain triple-point mutant (Trm-SH2). Taking the advantage of the pan-specific interaction of Trm-SH2 to pTyr, a high throughput approach was developed to determine the total protein tyrosine phosphorylation level in a sample...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192900/biphasic-affinity-chromatographic-approach-for-deep-tyrosine-phosphoproteome-analysis
#12
Zhenzhen Deng, Mingming Dong, Yan Wang, Jing Dong, Shawn S-C Li, Hanfa Zou, Mingliang Ye
Tyrosine phosphorylation (pTyr) is important for normal physiology and implicated in many human diseases, particularly cancer. Identification of pTyr sites is critical to dissecting signaling pathways and understanding disease pathologies. However, compared with serine/threonine phosphorylation (pSer/pThr), the analysis of pTyr at the proteome level is more challenging due to its low abundance. Here, we developed a biphasic affinity chromatographic approach where Src SH2 superbinder was coupled with NeutrAvidin affinity chromatography, for tyrosine phosphoproteome analysis...
February 1, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192239/super-silac-mix-coupled-with-sim-aims-assays-for-targeted-verification-of-phosphopeptides-discovered-in-a-large-scale-phosphoproteome-analysis-of-hepatocellular-carcinoma
#13
Yu-Tsun Lin, Kun-Yi Chien, Chia-Chun Wu, Wen-Yu Chang, Lichieh Julie Chu, Min-Chi Chen, Chau-Ting Yeh, Jau-Song Yu
: Plentiful studies have established a close association between aberrant phosphorylation and hepatocellular carcinoma (HCC). Here, we applied a quantitative phosphoproteomics platform combining dimethylation labeling and online 3D strong cation exchange chromatography (SCX)-titanium oxide (TiO2)/RP-LTQ-Orbitrap to compare phosphoproteomes between three pairs of HCC tissues and non-tumor counterparts. This analysis yielded 7868 quantifiable phosphopeptides and numerous up- or down-regulated candidates...
February 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28190389/phosphoproteomics-protein-phosphorylation-in-regulation-of-seed-germination-and-plant-growth
#14
Xiaojian Yin, Xin Wang, Setsuko Komatsu
Seed germination and plant growth are key stages in the plant life cycle and they are affected by abiotic stresses. Protein phosphorylation is commonly involved in key regulatory process, which mediates plant growth/development and stress responses. In plant, phosphoproteins play roles in stress responses and provide basic backbone in complex signaling networks. The mechanism of plant responses to abiotic stresses has been uncovered through study of protein phosphorylation. Recently, the methods for enrichment of phosphopeptides and phosphoproteins have been developed...
February 9, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28190387/engineering-crops-for-future-a-phosphoproteomics-approach
#15
Vinay Kumar, Tushar Khare, Mansi Sharma, Shabir Hussain Wani
Abiotic stresses like salinity, drought, heat, metal, radiation and oxidative stress, and especially their combinations are major limiting factors for growth and productivity of the crops. Various molecular and biochemical processes governing the plant responses to abiotic stresses have often been investigated and hold the key for producing high-yielding and abiotic stress-tolerant crops. Plant responses to abiotic stresses are dynamic and intricate, and vary with type, level, and duration of the stress involved, as well as on the type of tissue under stress...
9, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28188525/high-ph-reversed-phase-micro-columns-for-simple-sensitive-and-efficient-fractionation-of-proteome-and-tmt-labeled-phosphoproteome-digests
#16
Benjamin Ruprecht, Jana Zecha, Daniel P Zolg, Bernhard Kuster
Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun digested proteomes. While a multitude of methods has been established for off-line peptide separation using HPLC columns, their use can be limited particularly when sample quantities are scarce. In this protocol, we describe an approach which combines high pH reversed-phase peptide separation into few fractions in StageTip micro-columns...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28188522/optimized-enrichment-of-phosphoproteomes-by-fe-imac-column-chromatography
#17
Benjamin Ruprecht, Heiner Koch, Petra Domasinska, Martin Frejno, Bernhard Kuster, Simone Lemeer
Phosphorylation is among the most important post-translational modifications of proteins and has numerous regulatory functions across all domains of life. However, phosphorylation is often substoichiometric, requiring selective and sensitive methods to enrich phosphorylated peptides from complex cellular digests. Various methods have been devised for this purpose and we have recently described a Fe-IMAC HPLC column chromatography setup which is capable of comprehensive, reproducible, and selective enrichment of phosphopeptides out of complex peptide mixtures...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28188228/time-resolved-phosphoproteome-analysis-of-paradoxical-raf-activation-reveals-novel-targets-of-erk
#18
Peter Kubiniok, Hugo Lavoie, Marc Therrien, Pierre Thibault
Small molecules targeting aberrant RAF activity, like Vemurafenib (PLX4032), are highly effective against cancers harboring the V600E BRAF mutation, and are now approved for clinical use against metastatic melanoma. However, in tissues showing elevated RAS activity and in RAS-mutant tumors, these inhibitors stimulate RAF dimerization, resulting in inhibitor resistance and downstream paradoxical ERK activation. To understand the global signaling response of cancer cells to RAF inhibitors, we profiled the temporal changes of the phosphoproteome of two colon cancer cell lines (Colo205 and HCT116) that respond differently to Vemurafenib...
February 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28179408/time-resolved-global-and-chromatin-proteomics-during-herpes-simplex-virus-hsv-1-infection
#19
Katarzyna Kulej, Daphne C Avgousti, Simone Sidoli, Christin Herrmann, Ashley N Della Fera, Eui Tae Kim, Benjamin A Garcia, Matthew D Weitzman
Herpes simplex virus (HSV-1) lytic infection results in global changes to the host cell proteome and the proteins associated with host chromatin. We present a system level characterization of proteome dynamics during infection by performing a multi-dimensional analysis during HSV-1 lytic infection of human foreskin fibroblast (HFF) cells. Our study includes identification and quantification of the host and viral proteomes, phosphoproteomes, chromatin bound proteomes and post-translational modifications (PTMs) on cellular histones during infection...
February 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28176443/quantitative-phosphoproteomic-analysis-reveals-system-wide-signaling-pathways-regulated-by-site-specific-phosphorylation-on-keratin-8-in-skin-squamous-cell-carcinoma-derived-cell-line
#20
Richa Tiwari, Indrajit Sahu, Bihari Lal Soni, Gajanan J Sathe, Keshava K Datta, Pankaj Thapa, Shruti Sinha, Chella Krishna Vadivel, Bharti Dhaka, Harsha Gowda, Milind M Vaidya
Keratin 8/18, a simple epithelia specific keratin pair, is often aberrantly expressed in squamous cell carcinomas (SCC) where its expression is correlated with increased invasion and poor prognosis. Majority of Keratin 8 (K8) functions are governed by its phosphorylation at Serine(73) (head-domain) and Serine(431) (tail-domain) residues. Although, deregulation of K8 phosphorylation is associated with progression of different carcinomas, its role in skin-SCC and the underlying mechanism is obscure. In this direction, we performed TMT-based quantitative phosphoproteomics by expressing K8 wild type, phosphodead and phosphomimetic mutants in K8-deficient A431 cells...
February 7, 2017: Proteomics
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