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Molecular & Cellular Proteomics: MCP

Claudia Ctortecka, Vinayak Palve, Brent M Kuenzi, Bin Fang, Natalia J Sumi, Victoria Izumi, Silvia Novakova, Fumi Kinose, Lily L Remsing Rix, Eric B Haura, John Matthew Koomen, Uwe Rix
Lung cancer is associated with high prevalence and mortality, and despite significant successes with targeted drugs in genomically defined subsets of lung cancer and immunotherapy, the majority of patients currently does not benefit from these therapies. Through a targeted drug screen, we found the recently approved multi-kinase inhibitor midostaurin to have potent activity in several lung cancer cells independent of its intended target, PKC, or a specific genomic marker. To determine the underlying mechanism of action we applied a layered functional proteomics approach and a new data integration method...
September 14, 2018: Molecular & Cellular Proteomics: MCP
Brett Nixon, Geoffry N De Iuliis, Hanah M Hart, Wei Zhou, Andrea Mathe, Ilana Bernstein, Amanda L Anderson, Simone J Stanger, David A Skerrett-Byrne, M Fairuz B Jamaluddin, Juhura G Almazi, Elizabeth G Bromfield, Martin R Larsen, Matthew D Dun
The functional maturation of spermatozoa that is necessary to achieve fertilization occurs as they transit through the epididymis, a highly specialized region of the male reproductive tract. A defining feature of this maturation process is that it occurs in the complete absence of nuclear gene transcription or de novo protein translation in the spermatozoa. Rather, it is driven by sequential interactions between spermatozoa and the complex external milieu in which they are bathed within lumen of the epididymal tubule...
September 13, 2018: Molecular & Cellular Proteomics: MCP
Samantha Z Chia, Yu-Wen Lai, Daniel Yagoub, Sophie Lev, Joshua J Hamey, Chi Nam Ignatius Pang, Desmarini Desmarini, Zhiliang Chen, Julianne T Djordjevic, Melissa A Erce, Gene Hart-Smith, Marc R Wilkins
Hmt1p is the predominant arginine methyltransferase in Saccharomyces cerevisiae. Its substrate proteins are involved in transcription, transcriptional regulation, nucleocytoplasmic transport and RNA splicing. Hmt1p-catalysed methylation can also modulate protein-protein interactions. Hmt1p is conserved from unicellular eukaryotes through to mammals where its ortholog, PRMT1, is lethal upon knockout. In yeast, however, the effect of knockout on the transcriptome and proteome has not been described. Transcriptome analysis revealed downregulation of phosphate-responsive genes in hmt1Δ, including acid phosphatases PHO5, PHO11 and PHO12, phosphate transporters PHO84 and PHO89 and the vacuolar transporter chaperone VTC3...
September 11, 2018: Molecular & Cellular Proteomics: MCP
Tobias Busche, Mélanie Hillion, Vu Van Loi, David Berg, Birgit Walther, Torsten Semmler, Birgit Strommenger, Wolfgang Witte, Christiane Cuny, Alexander Mellmann, Mark A Holmes, Jörn Kalinowski, Lorenz Adrian, Jörg Bernhardt, Haike Antelmann
The spread of methicillin-resistant Staphylococcus aureus (MRSA) in the community, hospitals and in livestock is mediated by highly diverse virulence factors that include secreted toxins, superantigens, enzymes and surface-associated adhesins allowing host adaptation and colonization. Here, we combined proteogenomics, secretome and phenotype analyses to compare the secreted virulence factors in selected S. aureus isolates of the dominant human and livestock-associated genetic lineages CC8, CC22 and CC398. The proteogenomic comparison revealed 2181 core genes and 1306 accessory genes in 18 S...
September 10, 2018: Molecular & Cellular Proteomics: MCP
Dieter Vanderschaeghe, Leander Meuris, Tom Raes, Hendrik Grootaert, Annelies Van Hecke, Xavier Verhelst, Frederique Van de Velde, Bruno Lapauw, Hans Van Vlierberghe, Nico Callewaert
Over the past 30 years, it has been firmly established that a wide spectrum of (autoimmune) diseases such as rheumatoid arthritis, Crohn's and lupus, but also other pathologies like alcoholic and non-alcoholic steatohepatitis (ASH and NASH) are driven by chronic inflammation and are hallmarked by a reduced level of serum IgG galactosylation. IgG (under)galactosylation is a promising biomarker to assess disease severity, and monitor and adjust therapy. However, this biomarker has not been implemented in routine clinical chemistry due to a complex analytical procedure that necessitates IgG purification, which is difficult to perform and validate at high throughput...
September 6, 2018: Molecular & Cellular Proteomics: MCP
Nikolina Sostaric, Francis J O'Reilly, Piero Giansanti, Albert J R Heck, Anne-Claude Gavin, Vera van Noort
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA...
September 4, 2018: Molecular & Cellular Proteomics: MCP
Vivian Delcourt, Mylène Brunelle, Annie V Roy, Jean-Francois Jacques, Michel Salzet, Isabelle Fournier, Xavier Roucou
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from a same gene is unknown. MIEF1, a gene recently identified as a dual-coding gene, harbours a CDS and a newly annotated and actively translated altORF located in the 5'UTR ...
September 4, 2018: Molecular & Cellular Proteomics: MCP
Liangcai Zhao, Minjian Dong, Mengqian Ren, Chen Li, Hong Zheng, Hongchang Gao
Diabetes mellitus causes brain structure changes and cognitive decline, and it has been estimated that diabetes doubles the risk for dementia. Until now, the pathogenic mechanism of diabetes-associated cognitive decline (DACD) has remained unclear. Using metabolomics, we show that lactate levels increased over time in the hippocampus of rats with streptozotocin-induced diabetes, as compared to age-matched control rats. Additionally, mRNA levels, protein levels, and enzymatic activity of lactate dehydrogenase-A (LDH-A) were significantly up-regulated, suggesting increased glycolysis activity...
August 31, 2018: Molecular & Cellular Proteomics: MCP
Kwangwon Lee, Andrew Haddad, Abdullah Osme, Chunki Kim, Ahmad Borzou, Sergei Ilchenko, Daniela Allende, Srinivasan Dasarathy, Arthur J McCullough, Rovshan G Sadygov, Takhar Kasumov
Nonalcoholic fatty liver disease (NAFLD) is associated with hepatic mitochondrial dysfunction characterized by reduced ATP synthesis. We applied the 2H2O-metabolic labeling approach to test the hypothesis that the reduced stability of oxidative phosphorylation proteins contributes to mitochondrial dysfunction in a diet-induced mouse model of NAFLD. A high fat diet containing cholesterol (a so-called Western diet (WD)) led to hepatic oxidative stress, steatosis, inflammation and mild fibrosis, all markers of NAFLD, in low density cholesterol (LDL) receptor deficient (LDLR-/-) mice...
August 31, 2018: Molecular & Cellular Proteomics: MCP
Roman Mylonas, Ilan Beer, Christian Iseli, Chloe Chong, Hui-Song Pak, David Gfeller, George Coukos, Ioannis Xenarios, Markus Müller, Michal Bassani-Sternberg
Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters...
August 31, 2018: Molecular & Cellular Proteomics: MCP
Sylvia Varland, Henriette Aksnes, Fedor Kryuchkov, Francis Impens, Delphi Van Haver, Veronique Jonckheere, Mathias Ziegler, Kris Gevaert, Petra Van Damme, Thomas Arnesen
N-terminal acetylation (Nt-acetylation) is a highly abundant protein modification in eukaryotes and impacts a wide range of cellular processes, including protein quality control and stress tolerance. Despite its prevalence, the mechanisms regulating Nt-acetylation are still nebulous. Here, we present the first global study of Nt-acetylation in yeast cells as they progress to stationary phase in response to nutrient starvation. Surprisingly, we found that yeast cells maintain their global Nt-acetylation levels upon nutrient depletion, despite a marked decrease in acetyl-CoA levels...
August 27, 2018: Molecular & Cellular Proteomics: MCP
Asrar Ali Khan, Jenny Hansson, Peter Weber, Sophia Foehr, Jeroen Krijgsveld, Stephan Herzig, Marcel Scheideler
The adipose organ, including white and brown adipose tissues, is an important player in systemic energy homeostasis, storing excess energy in form of lipids while releasing energy upon various energy demands. Recent studies have demonstrated that white and brown adipocytes also function as endocrine cells and regulate systemic metabolism by secreting factors that act locally and systemically. However, a comparative proteomic analysis of secreted factors from white and brown adipocytes and their responsiveness to adrenergic stimulation has not been reported yet...
August 22, 2018: Molecular & Cellular Proteomics: MCP
Zi-Qi Shen, Bei Shi, Tian-Ren Wang, Jiao Jiao, Xuejun Shang, Qi-Jun Wu, Yi-Ming Zhou, Tie-Feng Cao, Qiang Du, Xiu-Xia Wang, Da Li
Semen samples from men after a short ejaculatory abstinence show improved sperm quality and result in increased pregnancy rates, but the underlying mechanisms remain unclear. Herein, we report that ejaculates from short (1-3 hours) compared with long (3-7 days) periods of abstinence showed increases in motile sperm count, sperm vitality, normal sperm morphology, acrosome reaction capacity, total antioxidant capacity, sperm mitochondrial membrane potential, high DNA stainability, and a decrease in the sperm DNA fragmentation index (P < 0...
August 20, 2018: Molecular & Cellular Proteomics: MCP
Alba Hykollari, Daniel Malzl, Barbara Eckmair, Jorick Vanbeselaere, Patrick Scheidl, Chunsheng Jin, Niclas G Karlsson, Iain B H Wilson, Katharina Paschinger
Royal jelly has received attention due to its necessity for the development of queen honeybees as well as claims of benefits on human health; this product of the hypopharyngeal glands of worker bees contains a large number of proteins, some of which have been claimed to have various biological effects only in their glycosylated state. However, although there have been glycomic and glycoproteomic analyses in the past, none of the glycan structures previously defined would appear to have potential to trigger specific biological functions...
August 13, 2018: Molecular & Cellular Proteomics: MCP
Nicolai Bache, Philipp Emanuel Geyer, Dorte B Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V Treit, Sophia Doll, Igor Paron, Johannes Bruno Müller, Florian Meier, Jesper V Olsen, Ole Vorm, Matthias Mann
To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop...
August 13, 2018: Molecular & Cellular Proteomics: MCP
Jiradej Makjaroen, Poorichaya Somparn, Kenneth Hodge, Witthaya Poomipak, Nattiya Hirankarn, Trairak Pisitkun
Interferon lambda (IFN-λ) is a relatively unexplored, yet promising anti-viral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B virus infection (CHB), with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ's downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Alok K Shah, Gunter Hartel, Ian Brown, Clay Winterford, Renhua Na, Kim-Anh Lê Cao, Bradley A Spicer, Michelle A Dunstone, Wayne A Phillips, Reginald V Lord, Andrew P Barbour, David I Watson, Virendra Joshi, David C Whiteman, Michelle M Hill
Esophageal adenocarcinoma (EAC) is thought to develop from asymptomatic Barrett's esophagus (BE) with a low annual rate of conversion. Current endoscopy surveillance for BE patients is probably not cost-effective. Previously, we discovered serum glycoprotein biomarker candidates which could discriminate BE patients from EAC. Here, we aimed to validate candidate serum glycoprotein biomarkers in independent cohorts, and to develop a biomarker candidate panel for BE surveillance. Serum glycoprotein biomarker candidates were measured in 301 serum samples collected from Australia (4 states) and USA (1 clinic) using previously established lectin magnetic bead array (LeMBA) coupled multiple reaction monitoring mass spectrometry (MRM-MS) tier 3 assay...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Christina Schiza, Dimitrios Korbakis, Efstratia Panteleli, Keith Jarvi, Andrei P Drabovich, Eleftherios P Diamandis
TEX101 is a testis-specific protein expressed exclusively in male germ cells and is a validated biomarker of male infertility. Studies in mice suggest that TEX101 is a cell-surface chaperone which regulates, through protein-protein interactions, the maturation of proteins involved in spermatozoa transit and oocyte binding. Male TEX101-null mice are sterile. Here, we identified by co-immunoprecipitation-mass spectrometry the interactome of human TEX101 in testicular tissues and spermatozoa. The testis-specific cell-surface dipeptidase 3 (DPEP3) emerged as the top hit...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Julien Mariethoz, Davide Alocci, Alessandra Gastaldello, Oliver Horlacher, Elisabeth Gasteiger, Miguel Rojas-Macias, Niclas G Karlsson, Nicolle Packer, Frederique Lisacek
Glycomics@ExPASy ( is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralise web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (a) popularising the use of bioinformatics in glycobiology and (b) emphasising the relationship between glycobiology and protein-oriented bioinformatics resources...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Alexander B Saltzman, Mei Leng, Bhoomi Bhatt, Purba Singh, Doug W Chan, Lacey E Dobrolecki, Hamssika Chandrasekaran, Jong Min Choi, Antrix Jain, Sung Yun Jung, Michael T Lewis, Matthew J Ellis, Anna Malovannaya
In quantitative mass spectrometry, the method by which peptides are grouped into proteins can have dramatic effects on downstream analyses. Here we describe gpGrouper, an inference and quantitation algorithm that offers an alternative method for assignment of protein groups by gene locus and improves pseudo-absolute iBAQ quantitation by weighted distribution of shared peptide areas. We experimentally show that distributing shared peptide quantities based on unique peptide peak ratios improves quantitation accuracy in comparison to conventional winner-take-all scenarios...
August 9, 2018: Molecular & Cellular Proteomics: MCP
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