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Proximity ligation assay

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https://www.readbyqxmd.com/read/28783179/reciprocal-antagonism-between-the-netrin-1-receptor-uncoordinated-phenotype-5a-unc5a-and-the-hepatitis-c-virus
#1
M-L Plissonnier, T Lahlali, M Raab, M Michelet, C Romero-López, M Rivoire, K Strebhardt, D Durantel, M Levrero, P Mehlen, F Zoulim, R Parent
Hepatitis C virus (HCV) infection is a leading cause of hepatocellular carcinoma (HCC), mainly through cirrhosis induction, spurring research for a deeper understanding of HCV versus host interactions in cirrhosis. The present study investigated crosstalks between HCV infection and UNC5A, a netrin-1 dependence receptor that is inactivated in cancer. UNC5A and HCV parameters were monitored in patients samples (n=550) as well as in in vitro. In patients, UNC5A mRNA expression is significantly decreased in clinical HCV(+) specimens irrespective of the viral genotype, but not in (HBV)(+) liver biopsies, as compared to uninfected samples...
August 7, 2017: Oncogene
https://www.readbyqxmd.com/read/28782625/shifted-golgi-targeting-of-glycosyltransferases-and-%C3%AE-mannosidase-ia-from-giantin-to-gm130-grasp65-results-in-formation-of-high-mannose-n-glycans-in-aggressive-prostate-cancer-cells
#2
Ganapati Bhat, Vishwanath-Reddy Hothpet, Ming-Fong Lin, Pi-Wan Cheng
BACKGROUND: There is a pressing need for biomarkers that can distinguish indolent from aggressive prostate cancer to prevent over-treatment of patients with indolent tumor. METHODS: Golgi targeting of glycosyltransferases was characterized by confocal microscopy after knockdown of GM130, giantin, or both. N-glycans on a trans-Golgi enzyme β4galactosyltransferase-1 isolated by immunoprecipitation from androgen-sensitive and independent prostate cancer cells were determined by matrix-assisted laser desorption-time of flight-mass spectrometry...
August 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28771231/fgfr1-is-critical-for-the-anti-endothelial-mesenchymal-transition-effect-of-n-acetyl-seryl-aspartyl-lysyl-proline-via-induction-of-the-map4k4-pathway
#3
Jinpeng Li, Sen Shi, Swayam Prakash Srivastava, Munehiro Kitada, Takako Nagai, Kyoko Nitta, Miyuki Kohno, Keizo Kanasaki, Daisuke Koya
Endothelial-to-mesenchymal transition (EndMT) has been shown to contribute to organ fibrogenesis, and we have reported that the anti-EndMT effect of N-acetyl-seryl-aspartyl-lysyl-proline (AcSDKP) is associated with restoring expression of diabetes-suppressed fibroblast growth factor receptor (FGFR), the key anti-EndMT molecule. FGFR1 is the key inhibitor of EndMT via the suppression of the transforming growth factor β (TGFβ) signaling pathway, and mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) inhibits integrin β1, a key factor in activating TGFβ signaling and EndMT...
August 3, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28764767/monoamine-oxidase-b-is-elevated-in-alzheimer-disease-neurons-is-associated-with-%C3%AE-secretase-and-regulates-neuronal-amyloid-%C3%AE-peptide-levels
#4
Sophia Schedin-Weiss, Mitsuhiro Inoue, Lenka Hromadkova, Yasuhiro Teranishi, Natsuko Goto Yamamoto, Birgitta Wiehager, Nenad Bogdanovic, Bengt Winblad, Anna Sandebring-Matton, Susanne Frykman, Lars O Tjernberg
BACKGROUND: Increased levels of the pathogenic amyloid β-peptide (Aβ), released from its precursor by the transmembrane protease γ-secretase, are found in Alzheimer disease (AD) brains. Interestingly, monoamine oxidase B (MAO-B) activity is also increased in AD brain, but its role in AD pathogenesis is not known. Recent neuroimaging studies have shown that the increased MAO-B expression in AD brain starts several years before the onset of the disease. Here, we show a potential connection between MAO-B, γ-secretase and Aβ in neurons...
August 1, 2017: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28758625/the-dengue-virus-non-structural-protein-1-ns1-is-secreted-from-infected-mosquito-cells-via-a-non-classical-caveolin-1-dependent-pathway
#5
Ana C Alcalá, Raiza Hernández-Bravo, Fernando Medina, David S Coll, Jose L Zambrano, Rosa M Del Angel, Juan E Ludert
Dengue virus NS1 is a glycoprotein of 46-50 kDa that is conserved among flaviviruses, associates as a dimer to cell membranes and is secreted as a hexamer to the extracellular milieu. Recent evidence showed that NS1 is secreted efficiently from infected mosquito cells. To explore the secretory route of NS1 in mosquito cells, infected cells were treated with brefeldin A (BFA) and methyl-beta-cyclodextrin (MβCD). The results showed that MβCD, but not BFA, significantly reduced the release of NS1. Moreover, silencing the expression of caveolin-1 (CAV1; a key component of the caveolar system that transports cholesterol inside the cell), but not SAR1 (a GTPase that participates in the classical secretory pathway), also results in a significant reduction of the secretion of NS1...
July 31, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28744553/brag2a-a-guanine-nucleotide-exchange-factor-for-arf6-is-a-component-of-the-dystrophin-associated-glycoprotein-complex-at-the-photoreceptor-terminal
#6
Hiroyuki Sakagami, Osamu Katsumata, Yoshinobu Hara, Toshikuni Sasaoka, Masahiro Fukaya
Purpose: Mutations in genes encoding the dystrophin-associated glycoprotein complex (DGC) can cause muscular dystrophy and disturb synaptic transmission in the photoreceptor ribbon synapse. However, the molecular composition and specific functions of the photoreceptor DGC remain unknown. Brefeldin A-resistant Arf-GEF 2 (BRAG2), also known as IQSEC1, is a guanine nucleotide exchange factor for ADP-ribosylation factor 6 (Arf6), a critical GTPase that regulates endosomal trafficking and actin cytoskeleton remodeling...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28742858/reduction-of-endoplasmic-reticulum-mitochondria-interactions-in-beta-cells-from-patients-with-type-2-diabetes
#7
Charles Thivolet, Guillaume Vial, Romeo Cassel, Jennifer Rieusset, Anne-Marie Madec
Type 2 diabetes develops when beta cells are not able to fulfill insulin needs. The role of the endoplasmic reticulum-mitochondria junction in coordinating the functions of these two organelles throughout the natural history of type 2 diabetes is determinant and may explain the alterations of insulin biosynthesis. Our goal was to study endoplasmic reticulum and mitochondrial interactions in human beta cells from organ donors with type 2 diabetes. Pancreas samples were obtained via the network for pancreatic organ donors with diabetes (nPOD) based on disease status with 12 subjects with type 2 diabetes and 9 non-diabetic controls...
2017: PloS One
https://www.readbyqxmd.com/read/28742097/mrtadfinder-a-network-modularity-based-approach-to-identify-topologically-associating-domains-in-multiple-resolutions
#8
Koon-Kiu Yan, Shaoke Lou, Mark Gerstein
Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs). From a visual examination of the chromosomal contact map, however, it is clear that the organization of the domains is not simple or obvious. Instead, TADs exhibit various length scales and, in many cases, a nested arrangement. Here, by exploiting the resemblance between TADs in a chromosomal contact map and densely connected modules in a network, we formulate TAD identification as a network optimization problem and propose an algorithm, MrTADFinder, to identify TADs from intra-chromosomal contact maps...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28736577/optimization-of-proximity-ligation-assay-pla-for-detection-of-protein-interactions-and-fusion-proteins-in-non-adherent-cells-application-to-pre-b-lymphocytes
#9
Lydie Debaize, Hélène Jakobczyk, Anne-Gaëlle Rio, Virginie Gandemer, Marie-Bérengère Troadec
BACKGROUND: Genetic abnormalities, including chromosomal translocations, are described for many hematological malignancies. From the clinical perspective, detection of chromosomal abnormalities is relevant not only for diagnostic and treatment purposes but also for prognostic risk assessment. From the translational research perspective, the identification of fusion proteins and protein interactions has allowed crucial breakthroughs in understanding the pathogenesis of malignancies and consequently major achievements in targeted therapy...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28734077/integrative-studies-implicate-matrix-metalloproteinase-12-as-a-culprit-gene-for-large-artery-atherosclerotic-stroke
#10
Hovsep Mahdessian, Ljubica Perisic Matic, Mariette Lengquist, Karl Gertow, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E Humphries, Rainer Rauramaa, Ulf de Faire, Andries J Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Elena Tremoli, Anders Hamsten, Per Eriksson, Ulf Hedin, Anders Mälarstig
BACKGROUND: Ischemic stroke and coronary heart disease are important contributors to the global disease burden and share atherosclerosis as the main underlying cause. Recent evidence from a genome-wide association study (GWAS) suggested that single nucleotide polymorphisms (SNP) near the MMP12 gene at chromosome 11q22.3 were associated with large-vessel ischemic stroke. Here we evaluated and extended these results by examining the relationship between MMP12 and atherosclerosis in clinical and experimental studies...
July 22, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28731464/trophoblast-survival-signaling-during-human-placentation-requires-hsp70-activation-of-mmp2-mediated-hbegf-shedding
#11
Chandni V Jain, Philip Jessmon, Charbel T Barrak, Alan D Bolnick, Brian A Kilburn, Michael Hertz, D Randall Armant
Survival of trophoblast cells in the low oxygen environment of human placentation requires metalloproteinase-mediated shedding of HBEGF and downstream signaling. A matrix metalloproteinase (MMP) antibody array and quantitative RT-PCR revealed upregulation of MMP2 post-transcriptionally in human first trimester HTR-8/SVneo trophoblast cells and placental villous explants exposed to 2% O2. Specific MMP inhibitors established the requirement for MMP2 in HBEGF shedding and upregulation. Because α-amanitin inhibited the upregulation of HBEGF, differentially expressed genes were identified by next-generation sequencing of RNA from trophoblast cells cultured at 2% O2 for 0, 1, 2 and 4 h...
July 21, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28708592/a-peptidomimetic-with-a-chiral-switch-is-an-inhibitor-of-epidermal-growth-factor-receptor-heterodimerization
#12
Shanthi P Kanthala, Yong-Yu Liu, Sitanshu Singh, Rushikesh Sable, Sandeep Pallerla, Seetharama D Jois
Among different types of EGFR dimers, EGFR-HER2 and HER2-HER3 are well known in different types of cancers. Targeting dimerization of EGFR will have a significant impact on cancer therapies. A symmetric peptidomimetic was designed to inhibit the protein-protein interaction of EGFR. The peptidomimetic (Cyclo(1,10)PpR (R) Anapa-FDDF-(R)-Anapa)R, compound 18) was shown to exhibit antiproliferative activity with an IC50 of 194 nM in HER2-expressing breast cancer cell lines and 18 nM in lung cancer cell lines. The peptidomimetic has a Pro-Pro sequence in the structure to stabilize the β-turn and a β-amino acid, amino napthyl propionic acid...
July 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28678418/detection-of-extracellular-vesicles-using-proximity-ligation-assay-with-flow-cytometry-readout-exopla
#13
Liza Löf, Linda Arngården, Tonge Ebai, Ulf Landegren, Ola Söderberg, Masood Kamali-Moghaddam
Extracellular vesicles (EVs) are continuously released by most cells, and they carry surface markers of their cells of origin. Found in all body fluids, EVs function as conveyers of cellular information, and evidence implicates them as markers of disease. These characteristics make EVs attractive diagnostic targets. However, detection and characterization of EVs is challenging due to their small size. We've established a method, called ExoPLA, that allows individual EVs to be detected and characterized at high specificity and sensitivity...
July 5, 2017: Current Protocols in Cytometry
https://www.readbyqxmd.com/read/28676490/tgf-%C3%AE-promotes-pi3k-akt-signaling-and-prostate-cancer-cell-migration-through-the-traf6-mediated-ubiquitylation-of-p85%C3%AE
#14
Anahita Hamidi, Jie Song, Noopur Thakur, Susumu Itoh, Anders Marcusson, Anders Bergh, Carl-Henrik Heldin, Maréne Landström
Transforming growth factor-β (TGF-β) is a pluripotent cytokine that regulates cell fate and plasticity in normal tissues and tumors. The multifunctional cellular responses evoked by TGF-β are mediated by the canonical SMAD pathway and by noncanonical pathways, including mitogen-activated protein kinase (MAPK) pathways and the phosphatidylinositol 3'-kinase (PI3K)-protein kinase B (AKT) pathway. We found that TGF-β activated PI3K in a manner dependent on the activity of the E3 ubiquitin ligase tumor necrosis factor receptor-associated factor 6 (TRAF6)...
July 4, 2017: Science Signaling
https://www.readbyqxmd.com/read/28667186/analytically-sensitive-protein-detection-in-microtiter-plates-by-proximity-ligation-with-rolling-circle-amplification
#15
Tonge Ebai, Felipe Marques Souza de Oliveira, Liza Löf, Lotta Wik, Caroline Schweiger, Anders Larsson, Ulrich Keilholtz, Johannes Haybaeck, Ulf Landegren, Masood Kamali-Moghaddam
BACKGROUND: Detecting proteins at low concentrations in plasma can be crucial for early diagnosis. Current techniques used in clinical routine, such as sandwich ELISA, provide for protein detection because of a dependence on target recognition by pairs of antibodies, but detection of low protein concentrations is often called for. Proximity ligation assay with rolling circle amplification (PLARCA) is an adaptation of the proximity ligation assay (PLA) for analytically specific and sensitive protein detection via binding of target proteins by 3 antibodies, and signal amplification via rolling circle amplification (RCA) in microtiter wells, in a manner easily adapted to instrumentation in use in hospitals...
June 30, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28659344/guanylyl-cyclase-sensitivity-to-nitric-oxide-is-protected-by-a-thiol-oxidation-driven-interaction-with-thioredoxin1
#16
Can Huang, Maryam Alapa, Ping Shu, Narayan Nagarajan, Changgong Wu, Junichi Sadoshima, Vladyslav Kholodovych, Hong Li, Annie Beuve
Nitric oxide (NO) modulates many physiological events through production of cGMP from its receptor, the NO-sensitive guanylyl cyclase (GC1). NO also appears to function in a cGMP independent manner, via S-nitrosation (SNO), a redox-based modification of cysteine thiols. Previously we have shown that S-nitrosated GC1 (SNO-GC1) is desensitized to NO stimulation following prolonged NO exposure or under oxidative/nitrosative stress. In animal models of nitrate tolerance and angiotensin II-induced hypertension, decreased vasodilation in response to NO correlates with GC1 thiol oxidation, but the physiological mechanism that resensitizes GC1 to NO and restores basal activity is unknown...
June 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28654064/detection-and-visualization-of-dna-damage-induced-protein-complexes-in-suspension-cell-cultures-using-the-proximity-ligation-assay
#17
Mahnoush Bahjat, Timon A Bloedjes, Amélie van der Veen, Guus de Wilde, Chiel Maas, Jeroen E J Guikema
The DNA damage response orchestrates the repair of DNA lesions that occur spontaneously, are caused by genotoxic stress, or appear in the context of programmed DNA breaks in lymphocytes. The Ataxia-Telangiectasia Mutated kinase (ATM), ATM- and Rad3-Related kinase (ATR) and the catalytic subunit of DNA-dependent Protein Kinase (DNA-PKcs) are among the first that are activated upon induction of DNA damage, and are central regulators of a network that controls DNA repair, apoptosis and cell survival. As part of a tumor-suppressive pathway, ATM and ATR activate p53 through phosphorylation, thereby regulating the transcriptional activity of p53...
June 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28644885/organic-anion-transporting-polypeptide-1b3-can-form-homo-and-hetero-oligomers
#18
Yuchen Zhang, Kelli H Boxberger, Bruno Hagenbuch
OATP1B3 is a 12 transmembrane domain protein expressed at the basolateral membrane of human hepatocytes where it mediates the uptake of numerous drugs and endogenous compounds. Previous western blot results suggest the formation of OATP1B3 multimers. In order to better understand the function of OATP1B3 under normal physiological conditions, we investigated its oligomerization status. We transiently transfected OATP1B3 with a C-terminal His-, FLAG- or HA-tag in HEK293 cells and used co-immunoprecipitation and a Proximity Ligation Assay to detect interactions between the different constructs...
2017: PloS One
https://www.readbyqxmd.com/read/28644055/regulation-of-transient-receptor-potential-melastatin-4-channel-by-sarcoplasmic-reticulum-inositol-trisphosphate-receptors-role-in-human-detrusor-smooth-muscle-function
#19
Aaron Provence, Eric S Rovner, Georgi V Petkov
We recently reported key physiologic roles for Ca(2+)-activated transient receptor potential melastatin 4 (TRPM4) channels in detrusor smooth muscle (DSM). However, the Ca(2+)-signaling mechanisms governing TRPM4 channel activity in human DSM cells are unexplored. As the TRPM4 channels are activated by Ca(2+), inositol 1,4,5-trisphosphate receptor (IP3R)-mediated Ca(2+) release from the sarcoplasmic reticulum represents a potential Ca(2+) source for TRPM4 channel activation. We used clinically-characterized human DSM tissues to investigate the molecular and functional interactions of the IP3Rs and TRPM4 channels...
June 23, 2017: Channels
https://www.readbyqxmd.com/read/28642261/transforming-growth-factor-beta-stimulates-smad1-5-signaling-in-pulmonary-artery-smooth-muscle-cells-and-fibroblasts-of-the-newborn-mouse-through-alk1
#20
Huili Zhang, Lili Du, Ying Zhong, Kathleen C Flanders, Jesse D Roberts
The intracellular signaling mechanisms through which TGFβ regulates pulmonary development are incompletely understood. Canonical TGFβ signaling involves Smad2/3 phosphorylation, Smad2/3·Smad4 complex formation and nuclear localization, and gene regulation. Here we show that physiologically relevant TGFβ1 levels also stimulate Smad1/5 phosphorylation, typically a mediator of bone morphogenetic protein (BMP) signaling, in mouse pup pulmonary artery smooth muscle cells (mPASMC) and lung fibroblasts and other interstitial lung cell lines...
June 22, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
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