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https://www.readbyqxmd.com/read/28346509/systematic-identification-of-phosphorylation-mediated-protein-interaction-switches
#1
Matthew J Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P Roth, Anne-Claude Gavin, Peer Bork, Robert B Russell
Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions...
March 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28346425/chip-stub1-regulates-the-warburg-effect-by-promoting-degradation-of-pkm2-in-ovarian-carcinoma
#2
Y Shang, J He, Y Wang, Q Feng, Y Zhang, J Guo, J Li, S Li, Y Wang, G Yan, F Ren, Y Shi, J Xu, N Zeps, Y Zhai, D He, Z Chang
Tumor cells preferentially adopt aerobic glycolysis for their energy supply, a phenomenon known as the Warburg effect. It remains a matter of debate as to how the Warburg effect is regulated during tumor progression. Here, we show that CHIP (carboxyl terminus of Hsc70-interacting protein), a U-box E3 ligase, suppresses tumor progression in ovarian carcinomas by inhibiting aerobic glycolysis. While CHIP is downregulated in ovarian carcinoma, induced expression of CHIP results in significant inhibition of the tumor growth examined by in vitro and in vivo experiments...
March 27, 2017: Oncogene
https://www.readbyqxmd.com/read/28345649/proteomic-analysis-indicates-that-mitochondrial-energy-metabolism-in-skeletal-muscle-tissue-is-negatively-correlated-with-feed-efficiency-in-pigs
#3
Liangliang Fu, Yueyuan Xu, Ye Hou, Xiaolong Qi, Lian Zhou, Huiying Liu, Yu Luan, Lu Jing, Yuanxin Miao, Shuhong Zhao, Huazhen Liu, Xinyun Li
Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345601/towards-reproducible-mrm-based-biomarker-discovery-using-dried-blood-spots
#4
Sureyya Ozcan, Jason D Cooper, Santiago G Lago, Diarmuid Kenny, Nitin Rustogi, Pawel Stocki, Sabine Bahn
There is an increasing interest in the use of dried blood spot (DBS) sampling and multiple reaction monitoring in proteomics. Although several groups have explored the utility of DBS by focusing on protein detection, the reproducibility of the approach and whether it can be used for biomarker discovery in high throughput studies is yet to be determined. We assessed the reproducibility of multiplexed targeted protein measurements in DBS compared to serum. Eighty-two medium to high abundance proteins were monitored in a number of technical and biological replicates...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345587/derivation-of-functional-human-astrocytes-from-cerebral-organoids
#5
Rômulo Sperduto Dezonne, Rafaela Costa Sartore, Juliana Minardi Nascimento, Verônica M Saia-Cereda, Luciana Ferreira Romão, Soniza Vieira Alves-Leon, Jorge Marcondes de Souza, Daniel Martins-de-Souza, Stevens Kastrup Rehen, Flávia Carvalho Alcantara Gomes
Astrocytes play a critical role in the development and homeostasis of the central nervous system (CNS). Astrocyte dysfunction results in several neurological and degenerative diseases. However, a major challenge to our understanding of astrocyte physiology and pathology is the restriction of studies to animal models, human post-mortem brain tissues, or samples obtained from invasive surgical procedures. Here, we report a protocol to generate human functional astrocytes from cerebral organoids derived from human pluripotent stem cells...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345451/the-impact-of-advanced-proteomics-in-the-search-for-markers-and-therapeutic-targets-of-bladder-cancer
#6
Hongshuo Zhang, Yue Fan, Lingling Xia, Chunhui Gao, Xin Tong, Hanfu Wang, Lili Sun, Tuo Ji, Mingyu Jin, Bing Gu, Bo Fan
Bladder cancer is the most common cancer of the urinary tract and can be avoided through proper surveillance and monitoring. Several genetic factors are known to contribute to the progression of bladder cancer, many of which produce molecules that serve as cancer biomarkers. Blood, urine, and tissue are commonly analyzed for the presence of biomarkers, which can be derived from either the nucleus or the mitochondria. Recent advances in proteomics have facilitated the high-throughput profiling of data generated from bladder cancer-related proteins or peptides in parallel with high sensitivity and specificity, providing a wealth of information for biomarker discovery and validation...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345336/proteomic-identification-of-eef1a1-as-a-molecular-target-of-curcumol-for-suppressing-metastasis-of-mda-mb-231-cells
#7
Hongyi Qi, Ling Ning, Zanyang Yu, Guojun Dou, Li Li
Curcumol, a major volatile component in Rhizoma Curcumae, exhibited potent anti-metastatic effect on breast cancer cells. However, its molecular mechanism remains poorly understood. In this study, we employed a 2-DE based proteomics to investigate the cellular targets of curcumol in MDA-MB-231 cells, and identified 10 differentially expressed proteins. Moreover, Gene Ontology analysis revealed that those proteins mainly get involved in 9 types of cellular components, 7 different biological processes and 9 kinds of molecular functions, and 35 pathways (p < 0...
March 27, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28345237/moving-to-translational-proteomics
#8
EDITORIAL
Akhilesh Pandey
No abstract text is available yet for this article.
March 2017: Proteomics
https://www.readbyqxmd.com/read/28345020/bacterial-carriers-for-glioblastoma-therapy
#9
Nalini Mehta, Johnathan G Lyon, Ketki Patil, Nassir Mokarram, Christine Kim, Ravi V Bellamkonda
Treatment of aggressive glioblastoma brain tumors is challenging, largely due to diffusion barriers preventing efficient drug dosing to tumors. To overcome these barriers, bacterial carriers that are actively motile and programmed to migrate and localize to tumor zones were designed. These carriers can induce apoptosis via hypoxia-controlled expression of a tumor suppressor protein p53 and a pro-apoptotic drug, Azurin. In a xenograft model of human glioblastoma in rats, bacterial carrier therapy conferred a significant survival benefit with 19% overall long-term survival of >100 days in treated animals relative to a median survival of 26 days in control untreated animals...
March 17, 2017: Molecular Therapy Oncolytics
https://www.readbyqxmd.com/read/28344861/zoledronic-acid-boosts-%C3%AE-%C3%AE-t-cell-activity-in-children-receiving-%C3%AE-%C3%AE-t-and-cd19-cell-depleted-grafts-from-an-hla-haplo-identical-donor
#10
A Bertaina, A Zorzoli, A Petretto, G Barbarito, E Inglese, P Merli, C Lavarello, L P Brescia, B De Angelis, G Tripodi, L Moretta, F Locatelli, I Airoldi
We demonstrated that γδ T cells of patients given HLA-haploidentical HSCT after removal of αβ(+) T cells and CD19(+) B cells are endowed with the capacity of killing leukemia cells after ex vivo treatment with zoledronic acid (ZOL). Thus, we tested the hypothesis that infusion of ZOL in patients receiving this type of graft may enhance γδ T-cell cytotoxic activity against leukemia cells. ZOL was infused every 28 d in 43 patients; most were treated at least twice. γδ T cells before and after ZOL treatments were studied in 33 of these 43 patients, till at least 7 mo after HSCT by high-resolution mass spectrometry, flow-cytometry, and degranulation assay...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344825/identification-of-filamin-a-and-b-as-potential-biomarkers-for-prostate-cancer
#11
Niven R Narain, Anne R Diers, Arleide Lee, Socheata Lao, Joyce Y Chan, Sally Schofield, Joe Andreazi, Rakibou Ouro-Djobo, Joaquin J Jimenez, Tracey Friss, Nikunj Tanna, Aditee Dalvi, Sihe Wang, Dustin Bunch, Yezhou Sun, Wenfang Wu, Khampaseuth Thapa, Stephane Gesta, Leonardo O Rodrigues, Viatcheslav R Akmaev, Vivek K Vishnudas, Rangaprasad Sarangarajan
AIM: A novel strategy for prostate cancer (PrCa) biomarker discovery is described. MATERIALS & METHODS: In vitro perturbation biology, proteomics and Bayesian causal analysis identified biomarkers that were validated in in vitro models and clinical specimens. RESULTS: Filamin-B (FLNB) and Keratin-19 were identified as biomarkers. Filamin-A (FLNA) was found to be causally linked to FLNB. Characterization of the biomarkers in a panel of cells revealed differential mRNA expression and regulation...
March 2017: Future Science OA
https://www.readbyqxmd.com/read/28344590/proteome-profiling-of-paulownia-seedlings-infected-with-phytoplasma
#12
Xibing Cao, Guoqiang Fan, Yanpeng Dong, Zhenli Zhao, Minjie Deng, Zhe Wang, Wenshan Liu
Phytoplasma is an insect-transmitted pathogen that causes witches' broom disease in many plants. Paulownia witches' broom is one of the most destructive diseases threatening Paulownia production. The molecular mechanisms associated with this disease have been investigated by transcriptome sequencing, but changes in protein abundance have not been investigated with isobaric tags for relative and absolute quantitation. Previous results have shown that methyl methane sulfonate (MMS) can help Paulownia seedlings recover from the symptoms of witches' broom and reinstate a healthy morphology...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28344575/identification-of-capsid-coat-related-protein-folds-and-their-utility-for-virus-classification
#13
Arshan Nasir, Gustavo Caetano-Anollés
The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28344541/olfm4-kng1-and-sec24c-identified-by-proteomics-and-immunohistochemistry-as-potential-markers-of-early-colorectal-cancer-stages
#14
Florence Quesada-Calvo, Charlotte Massot, Virginie Bertrand, Rémi Longuespée, Noëlla Blétard, Joan Somja, Gabriel Mazzucchelli, Nicolas Smargiasso, Dominique Baiwir, Marie-Claire De Pauw-Gillet, Philippe Delvenne, Michel Malaise, Carla Coimbra Marques, Marc Polus, Edwin De Pauw, Marie-Alice Meuwis, Edouard Louis
BACKGROUND: Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is important for reducing CRC incidence and increasing patient's survival. METHODS: We analysed 76 colorectal tissue samples originated from early CRC stages, normal or inflamed mucosa by label-free proteomics. The characterisation of three selected biomarker candidates was performed by immunohistochemistry on an independent set of precancerous and cancerous lesions harbouring increasing CRC stages...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28344315/proteomic-characterization-of-human-multiple-myeloma-bone-marrow-extracellular-matrix
#15
S V Glavey, A Naba, S Manier, K Clauser, S Tahri, J Park, M R Reagan, M Moschetta, Y Mishima, M Gambella, A Rocci, A Sacco, M E O'Dwyer, J M Asara, A Palumbo, A M Roccaro, R O Hynes, I M Ghobrial
The extracellular matrix (ECM) is a major component of the tumor microenvironment, contributing to the regulation of cell survival, proliferation, differentiation and metastasis. In multiple myeloma (MM), interactions between MM cells and the bone marrow (BM) microenvironment, including the BM ECM, are critical to the pathogenesis of the disease and the development of drug resistance. Nevertheless, composition of the ECM in MM and its role in supporting MM pathogenesis has not been reported. We have applied a novel proteomic-based strategy and defined the BM ECM composition in patients with monoclonal gammopathy of undetermined significance (MGUS), newly diagnosed and relapsed MM compared to healthy donor-derived BM ECM...
March 27, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28344024/putative-model-based-on-itraq-proteomics-for-spirulina-morphogenesis-mechanisms
#16
Fu-Shuang Wang, Shi-Rui Dong, Hong-Yu Zhang, Su-Ying Wang
The morphology of Spirulina during cultivation is susceptible to external interferences, but the morphogenesis mechanism is still unclear. Here the proteomic changes of linear Spirulina and spiral Spirulina were comparatively investigated via isobaric tag for relative and absolute quantitation (iTRAQ). Totally 165 and 167 differences in proteins expression were screened out from the TJSD2/TJSD3 and TJBC4-1/TJBC4-2 groups, respectively. Gene ontology and metabolic pathway analysis of differences in proteins expression uncovered the metabolic pathways (photosynthesis, carbon fixation, sugar metabolism) that were significantly enriched with the proteins correlated with Spirulina morphogenesis...
March 23, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28343581/proteomic-analysis-of-physiological-function-response-to-hot-summer-in-liver-from-lactating-dairy-cows
#17
Qiangjun Wang, Xiaowei Zhao, Zijun Zhang, Huiling Zhao, Dongwei Huang, Guanglong Cheng, Yongxin Yang
Lactation performance of dairy cattle is susceptible to heat stress. The liver is one of the most crucial organs affected by high temperature in dairy cows. However, the physiological adaption by the liver to hot summer conditions has not been well elucidated in lactating dairy cows. In the present study, proteomic analysis of the liver in dairy cows in spring and hot summer was performed using a label-free method. In total, 127 differentially expressed proteins were identified; most of the upregulated proteins were involved in protein metabolic processes and responses to stimuli, whereas most of the downregulated proteins were related to oxidation-reduction...
April 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28343541/predicting-clinical-outcomes-using-proteomics-in%C3%A2-non-small-cell-lung-cancer-the-past-present-and%C3%A2-future
#18
EDITORIAL
Ross A Soo, Alex A Adjei
No abstract text is available yet for this article.
April 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#19
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28342851/site-specific-photocoupling-of-pbpa-mutated-scfv-antibodies-for-use-in-affinity-proteomics
#20
Mattias Brofelth, Lars Wagner Städe, Anna Isinger Ekstrand, Linn Petersson Edfeldt, Rebeka Kovačič, Thorbjørn Terndrup Nielsen, Kim Lambertsen Larsen, Laurent Duroux, Christer Wingren
Recombinant antibody libraries can provide a source of renewable and high-performing binders tailored for use in affinity proteomics. In this context, the process of generating site-specific 1:1 tagging/functionalization and/or orientated surface immobilization of antibodies has, however, proved to be challenging. Hence, novel ways of generating such engineered antibodies for use in affinity proteomics could have a major impact on array performance. In this study, we have further tailored the design of human recombinant scFv antibodies for site-specific photocoupling through the use of an unnatural amino acid (UAA) and the Dock'n'Flash technology...
March 22, 2017: Biochimica et Biophysica Acta
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