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https://www.readbyqxmd.com/read/29759185/a-fast-sample-processing-strategy-for-large-scale-profiling-of-human-urine-phosphoproteome-by-mass-spectrometry
#1
Xinyuan Zhao, Wanjun Zhang, Tong Liu, Hangyan Dong, Junjie Huang, Changqing Sun, Guangshun Wang, Xiaohong Qian, Weijie Qin
Liquid biopsies using body fluids have gained much attention in recent years due to their multiple advantages in clinical diagnosis, such as less/non-invasive collection, suitability for longitudinal disease monitoring, and better representation of tumor heterogeneity. As an attractive choice for liquid biopsy, urine proteins and their post-translational modifications (PTMs) have the potential to offer significant insights into physiological variations and pathological changes in the human body. However, due to the intrinsically large variability of urine proteins and their PTMs among different individuals, there is a high demand for strategies for high-throughput analysis of a large number of samples to obtain a comprehensive view and a reliable reference interval of the urine proteome...
August 1, 2018: Talanta
https://www.readbyqxmd.com/read/29752463/personalization-of-prostate-cancer-therapy-through-phosphoproteomics
#2
REVIEW
Wei Yang, Michael R Freeman, Natasha Kyprianou
Castration-resistant prostate cancer (CRPC) remains incurable despite the approval of several new treatments. Identification of new biomarkers and therapeutic targets to enable personalization of CRPC therapy, with the aim of maximizing therapeutic responses and minimizing toxicity in patients, is urgently needed. Prostate cancer progression and therapeutic resistance are frequently driven by aberrantly activated kinase signalling pathways that are amenable to pharmacological inhibition. Personalized phosphoproteomics, which enables the analysis of signalling networks in individual tumours, is a promising approach to advance personalized therapy by discovering biomarkers of pathway activity and clinically actionable targets...
May 11, 2018: Nature Reviews. Urology
https://www.readbyqxmd.com/read/29743597/mastl-overexpression-promotes-chromosome-instability-and-metastasis-in-breast-cancer
#3
Samuel Rogers, Rachael A McCloy, Benjamin L Parker, David Gallego-Ortega, Andrew M K Law, Venessa T Chin, James R W Conway, Dirk Fey, Ewan K A Millar, Sandra O'Toole, Niantao Deng, Alexander Swarbrick, Paul D Chastain, Anthony J Cesare, Paul Timpson, C Elizabeth Caldon, David R Croucher, David E James, D Neil Watkins, Andrew Burgess
MASTL kinase is essential for correct progression through mitosis, with loss of MASTL causing chromosome segregation errors, mitotic collapse and failure of cytokinesis. However, in cancer MASTL is most commonly amplified and overexpressed. This correlates with increased chromosome instability in breast cancer and poor patient survival in breast, ovarian and lung cancer. Global phosphoproteomic analysis of immortalised breast MCF10A cells engineered to overexpressed MASTL revealed disruption to desmosomes, actin cytoskeleton, PI3K/AKT/mTOR and p38 stress kinase signalling pathways...
May 10, 2018: Oncogene
https://www.readbyqxmd.com/read/29741879/reanalysis-of-global-proteomic-and-phosphoproteomic-data-identified-a-large-number-of-glycopeptides
#4
Yingwei Hu, Punit Shah, David J Clark, Minghui Ao, Hui Zhang
Protein glycosylation plays fundamental roles in many cellular processes, and previous reports have shown dysregulation to be associated with several human diseases, including diabetes, cancer, and neurodegenerative disorders. Despite the vital role of glycosylation for proper protein function, the analysis of glycoproteins has been lagged behind to other protein modifications. In this study, we describe the re-analysis of global proteomic data from breast cancer xenograft tissues using recently developed software package GPQuest 2...
May 9, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29734811/streamlined-tandem-mass-tag-sl-tmt-protocol-an-efficient-strategy-for-quantitative-phospho-proteome-profiling-using-tandem-mass-tag-synchronous-precursor-selection-ms3
#5
José Navarrete-Perea, Qing Yu, Steven P Gygi, Joao A Paulo
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol...
May 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29731745/autophosphorylation-mechanism-of-the-ser-thr-kinase-stk1-from-staphylococcus-aureus
#6
Weihao Zheng, Xiaodan Cai, Shuiming Li, Zigang Li
The eukaryotic-like Ser/Thr kinase Stk1 is crucial for virulence, cell wall biosynthesis, and drug susceptibility in methicillin-resistant Staphylococcus aureus ( S. aureus ) (MRSA). Importantly, MRSA lacking Stk1 become sensitive to β-lactam antibiotics, implying that Stk1 could be an alternative target for combination therapy. However, the autophosphorylation mechanism of Stk1 remains elusive. Using a phosphoproteomic study, we identified six in vivo phosphorylated activation loop residues (Ser159, Thr161, Ser162, Thr164, Thr166, and Thr172) of Stk1, which are also phosphorylated in vitro ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29721955/how-excessive-cgmp-impacts-metabolic-proteins-in-retinas-at-the-onset-of-degeneration
#7
Jianhai Du, Jie An, Jonathan D Linton, Yekai Wang, James B Hurley
Aryl-hydrocarbon receptor interacting protein-like 1 (AIPL1) is essential to stabilize cGMP phosphodiesterase 6 (PDE6) in rod photoreceptors. Mutation of AIPL1 leads to loss of PDE6, accumulation of intracellular cGMP, and rapid degeneration of rods. To understand the metabolic basis for the photoreceptor degeneration caused by excessive cGMP, we performed proteomics and phosphoproteomics analyses on retinas from AIPL1-/- mice at the onset of rod cell death. AIPL1-/- retinas have about 18 times less than normal PDE6a and no detectable PDE6b...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29719593/whole-exome-sequencing-identifies-mtor-and-keap1-as-potential-targets-for-radiosensitization-of-hnscc-cells-refractory-to-egfr-and-%C3%AE-1-integrin-inhibition
#8
Erik Klapproth, Ellen Dickreuter, Falk Zakrzewski, Michael Seifert, Andreas Petzold, Andreas Dahl, Evelin Schröck, Barbara Klink, Nils Cordes
Intrinsic and acquired resistances are major obstacles in cancer therapy. Genetic characterization is commonly used to identify predictive or prognostic biomarker signatures and potential cancer targets in samples from therapy-naïve patients. By far less common are such investigations to identify specific, predictive and/or prognostic gene signatures in patients or cancer cells refractory to a specific molecular-targeted intervention. This, however, might have a great value to foster the development of tailored, personalized cancer therapy...
April 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29717265/identification-of-a-met-eif4g1-translational-regulation-axis-that-controls-hif-1%C3%AE-levels-under-hypoxia
#9
Astrid A Glück, Eleonora Orlando, Dominic Leiser, Michaela Poliaková, Lluís Nisa, Aurélie Quintin, Jacopo Gavini, Deborah M Stroka, Sabina Berezowska, Lukas Bubendorf, Andree Blaukat, Daniel M Aebersold, Michaela Medová, Yitzhak Zimmer
Poor oxygenation is a common hallmark of solid cancers that strongly associates with aggressive tumor progression and treatment resistance. While a hypoxia-inducible factor 1α (HIF-1α)-associated transcriptional overexpression of the hepatocyte growth factor (HGF) receptor tyrosine kinase (RTK) MET has been previously documented, any regulation of the HIF-1α system through MET downstream signaling in hypoxic tumors has not been yet described. By using MET-driven in vitro as well as ex vivo tumor organotypic fresh tissue models we report that MET targeting results in depletion of HIF-1α and its various downstream targets...
May 2, 2018: Oncogene
https://www.readbyqxmd.com/read/29717210/exploring-intrinsically-disordered-proteins-in-chlamydomonas-reinhardtii
#10
Zhang Yizhi, Launay Hélène, Schramm Antoine, Lebrun Régine, Gontero Brigitte
The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29691806/phosphoproteome-profiling-revealed-abnormally-phosphorylated-ampk-and-atf2-involved-in-glucose-metabolism-and-tumorigenesis-of-gh-pas
#11
S Zhao, J Feng, C Li, H Gao, P Lv, J Li, Q Liu, Y He, H Wang, L Gong, D Li, Y Zhang
PURPOSE: Protein phosphorylation plays a key role in tumorigenesis and progression. However, little is known about the phosphoproteome profiles of growth hormone-secreting pituitary adenomas (GH-PAs). The aim of this study was to identify critical biomarkers and signaling pathways that might play important roles in GH-PAs and may, therefore, represent potential therapeutic targets. METHODS: The differential phosphoprotein expression patterns involved in GH-PAs were investigated by nano-LC-MS/MS in a group of samples...
April 24, 2018: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/29688323/silac-based-phosphoproteomics-reveals-new-pp2a-cdc55-regulated-processes-in-budding-yeast
#12
Barbara Baro, Soraya Játiva, Inés Calabria, Judith Vinaixa, Joan-Josep Bech-Serra, Carolina de LaTorre, João Rodrigues, María Luisa Hernáez, Concha Gil, Silvia Barceló-Batllori, Martin R Larsen, Ethel Queralt
Background: Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast, however few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells. Results: We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actin-cytoskeleton organization...
April 24, 2018: GigaScience
https://www.readbyqxmd.com/read/29684792/global-effects-of-ddx3-inhibition-on-cell-cycle-regulation-identified-by-a-combined-phosphoproteomics-and-single-cell-tracking-approach
#13
Marise R Heerma van Voss, Kai Kammers, Farhad Vesuna, Justin Brilliant, Yehudit Bergman, Saritha Tantravedi, Xinyan Wu, Robert N Cole, Andrew Holland, Paul J van Diest, Venu Raman
DDX3 is an RNA helicase with oncogenic properties. The small molecule inhibitor RK-33 is designed to fit into the ATP binding cleft of DDX3 and hereby block its activity. RK-33 has shown potent activity in preclinical cancer models. However, the mechanism behind the antineoplastic activity of RK-33 remains largely unknown. In this study we used a dual phosphoproteomic and single cell tracking approach to evaluate the effect of RK-33 on cancer cells. MDA-MB-435 cells were treated for 24 hours with RK-33 or vehicle control...
April 20, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29678115/characterization-of-plasmodium-falciparum-atypical-kinase-pfpk7-dependent-phosphoproteome
#14
Brittany N Pease, Edward L Huttlin, Mark P Jedrychowski, Dominique Dorin-Semblat, Daniela Sebastiani, Daniel T Segarra, Bracken F Roberts, Ratna Chakrabarti, Christian Doerig, Steven P Gygi, Debopam Chakrabarti
PfPK7 is an "orphan" kinase displaying regions of homology to multiple protein kinase families. PfPK7 functions in regulating parasite proliferation/development as evident from the phenotype analysis of knockout parasites. Despite this regulatory role, the functions of PfPK7 in signaling pathways are not known. To better understand PfPK7-regulated phosphorylation events, we performed isobaric tag-based quantitative comparative phosphoproteomics of the schizont and segmenter stages from wild-type and pfpk7- parasite lines...
April 20, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29677473/signaling-and-function-of-interleukin-2-in-t-lymphocytes
#15
Sarah H Ross, Doreen A Cantrell
The discovery of interleukin-2 (IL-2) changed the molecular understanding of how the immune system is controlled. IL-2 is a pleiotropic cytokine, and dissecting the signaling pathways that allow IL-2 to control the differentiation and homeostasis of both pro- and anti-inflammatory T cells is fundamental to determining the molecular details of immune regulation. The IL-2 receptor couples to JAK tyrosine kinases and activates the STAT5 transcription factors. However, IL-2 does much more than control transcriptional programs; it is a key regulator of T cell metabolic programs...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29669986/quantitative-analyses-of-the-metaphase-to-anaphase-transition-reveal-differential-kinetic-regulation-for-securin-and-cyclin-b1
#16
Makoto Konishi, Norihisa Shindo, Masataka Komiya, Kozo Tanaka, Takehiko Itoh, Toru Hirota
Separation of sister chromatids is a drastic and irreversible step in the cell cycle. The key biochemistry behind this event is the proteolysis mediated by the ubiquitin ligase called the anaphase promoting complex, or APC/C. Securin and cyclin B1 are the two established substrates for APC/C whose degradation releases separase and inactivates cyclin B1-dependent kinase 1 (cdk1), respectively, at the metaphase-to-anaphase transition. In this study, we have combined biochemical quantifications with mathematical simulations to characterize the kinetic regulation of securin and cyclin B1, in the cytoplasmic and chromosomal compartments, and found that they are differentially distributed and degraded with different rates...
2018: Biomedical Research
https://www.readbyqxmd.com/read/29666759/phosphoproteomic-insights-into-processes-influenced-by-the-kinase-like-protein-dia1-c3orf58
#17
Agnieszka Hareza, Magda Bakun, Bianka Świderska, Małgorzata Dudkiewicz, Alicja Koscielny, Anna Bajur, Jacek Jaworski, Michał Dadlez, Krzysztof Pawłowski
Many kinases are still 'orphans,' which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography-tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated...
2018: PeerJ
https://www.readbyqxmd.com/read/29661693/phosphorylation-of-beta-3-adrenergic-receptor-at-serine-247-by-erk-map-kinase-drives-lipolysis-in-obese-adipocytes
#18
Shangyu Hong, Wei Song, Peter-James H Zushin, Bingyang Liu, Mark P Jedrychowski, Amir I Mina, Zhaoming Deng, Dimitrije Cabarkapa, Jessica A Hall, Colin J Palmer, Hassan Aliakbarian, John Szpyt, Steven P Gygi, Ali Tavakkoli, Lydia Lynch, Norbert Perrimon, Alexander S Banks
OBJECTIVE: The inappropriate release of free fatty acids from obese adipose tissue stores has detrimental effects on metabolism, but key molecular mechanisms controlling FFA release from adipocytes remain undefined. Although obesity promotes systemic inflammation, we find activation of the inflammation-associated Mitogen Activated Protein kinase ERK occurs specifically in adipose tissues of obese mice, and provide evidence that adipocyte ERK activation may explain exaggerated adipose tissue lipolysis observed in obesity...
March 29, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29655704/a-library-of-phosphoproteomic-and-chromatin-signatures-for-characterizing-cellular-responses-to-drug-perturbations
#19
Lev Litichevskiy, Ryan Peckner, Jennifer G Abelin, Jacob K Asiedu, Amanda L Creech, John F Davis, Desiree Davison, Caitlin M Dunning, Jarrett D Egertson, Shawn Egri, Joshua Gould, Tak Ko, Sarah A Johnson, David L Lahr, Daniel Lam, Zihan Liu, Nicholas J Lyons, Xiaodong Lu, Brendan X MacLean, Alison E Mungenast, Adam Officer, Ted E Natoli, Malvina Papanastasiou, Jinal Patel, Vagisha Sharma, Courtney Toder, Andrew A Tubelli, Jennie Z Young, Steven A Carr, Todd R Golub, Aravind Subramanian, Michael J MacCoss, Li-Huei Tsai, Jacob D Jaffe
Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP)...
April 10, 2018: Cell Systems
https://www.readbyqxmd.com/read/29650682/phosphoproteome-dynamics-during-mitotic-exit-in-budding-yeast
#20
Sandra A Touati, Meghna Kataria, Andrew W Jones, Ambrosius P Snijders, Frank Uhlmann
The cell division cycle culminates in mitosis when two daughter cells are born. As cyclin-dependent kinase (Cdk) activity reaches its peak, the anaphase-promoting complex/cyclosome (APC/C) is activated to trigger sister chromatid separation and mitotic spindle elongation, followed by spindle disassembly and cytokinesis. Degradation of mitotic cyclins and activation of Cdk-counteracting phosphatases are thought to cause protein dephosphorylation to control these sequential events. Here, we use budding yeast to analyze phosphorylation dynamics of 3,456 phosphosites on 1,101 proteins with high temporal resolution as cells progress synchronously through mitosis...
April 12, 2018: EMBO Journal
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