High Perfluorooctanoic Acid Exposure Induces Autophagy Blockage and Disturbs Intracellular Vesicle Fusion in the Liver

Total Page:16

File Type:pdf, Size:1020Kb

High Perfluorooctanoic Acid Exposure Induces Autophagy Blockage and Disturbs Intracellular Vesicle Fusion in the Liver Arch Toxicol (2017) 91:247–258 DOI 10.1007/s00204-016-1675-1 MOLECULAR TOXICOLOGY High perfluorooctanoic acid exposure induces autophagy blockage and disturbs intracellular vesicle fusion in the liver Shengmin Yan1 · Hongxia Zhang1 · Xuejiang Guo2 · Jianshe Wang1 · Jiayin Dai1 Received: 25 October 2015 / Accepted: 28 January 2016 / Published online: 15 February 2016 © Springer-Verlag Berlin Heidelberg 2016 Abstract Perfluorooctanoic acid (PFOA) has been PFOA on cell viability. Although these findings demon- shown to cause hepatotoxicity and other toxicological strate that PFOA blocked autophagy and disturbed intracel- effects. Though PPARα activation by PFOA in the liver lular vesicle fusion in the liver, the changes in autophagy has been well accepted as an important mechanism of were observed only at high cytotoxic concentrations of PFOA-induced hepatotoxicity, several pieces of evidence PFOA, suggesting that autophagy may not be a primary have shown that the hepatotoxic effects of PFOA may not target or mode of toxicity. Furthermore, since altered liver be fully explained by PPARα activation. In this study, we autophagy was not observed at concentrations of PFOA observed autophagosome accumulation in mouse livers as associated with human exposures, the relevance of these well as HepG2 cells after PFOA exposure. Further in vitro findings must be questioned. study revealed that the accumulation of autophagosomes was not caused by autophagic flux stimulation. In addition, Keywords Perfluorooctanoic acid · Autophagy · we observed that PFOA exposure affected the proteolytic Proteome · Vesicle fusion activity of HepG2 cells while significant dysfunction of lysosomes was not detected. Quantitative proteomic analy- sis of crude lysosomal fractions from HepG2 cells treated Introduction with PFOA revealed that 54 differentially expressed pro- teins were related to autophagy or vesicular trafficking and Perfluoroalkyl acids (PFAAs) are widely used anthropo- fusion. The proteomic results were further validated in the genic compounds, which have been incorporated into many cells in vitro and livers in vivo after PFOA exposure, which products over the past six decades due to their unique physi- implied potential dysfunction at the late stage of autophagy. cal and chemical characteristics (Lau et al. 2007; Lind- However, in HepG2 cells, it seemed that further inhibi- strom et al. 2011). Because many of these compounds fit tion of autophagy did not significantly alter the effects of the defining characteristics of persistent organic pollutants (POPs), concerns regarding their impact on human health and the environment have increased (Lindstrom et al. 2011). Electronic supplementary material The online version of this As one of the most widely known PFAAs, the toxicologi- article (doi:10.1007/s00204-016-1675-1) contains supplementary cal effects of perfluorooctanoic acid (PFOA) have been material, which is available to authorized users. extensively studied, with hepatotoxicity found in rodents * Jiayin Dai even at low-dose exposure (Lau et al. 2007; Yan et al. 2014). [email protected] Medical surveillance studies have also found PFOA expo- sure to be positively associated with serum alanine ami- 1 Key Laboratory of Animal Ecology and Conservation notransferase (ALT) levels and negatively related to serum Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China high-density lipoprotein (HDL) levels in fluorochemical production workers (Gallo et al. 2012; Wang et al. 2012). 2 State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, Activation of peroxisome proliferator-activated receptor α People’s Republic of China (PPARα) has been widely accepted as a critical mechanism 1 3 248 Arch Toxicol (2017) 91:247–258 for PFOA-induced hepatomegaly and disturbance of lipid Earlier reviewed studies suggest that autophagy also metabolism (Lau et al. 2007; Takacs and Abbott 2007), plays an important physiological role in the liver, particu- and our previous study observed significant activation of larly in regard to energy and nutrient balance, misfolded PPARα in livers of mice exposed to PFOA for 28 days (Yan proteins removal, and major subcellular organelle turno- et al. 2015). However, liver weight increase as well as per- ver under normal and pathophysiological conditions (Rau- turbation of fatty acid metabolism still could be observed tou et al. 2010; Yin et al. 2008). However, little is known in PFOA-exposed PPARα-null mice (Minata et al. 2010; about the connection between autophagy and the toxico- Rosen et al. 2008; Wolf et al. 2008), and this evidence logical effects of PFOA. In the present study, we assessed implies that there may be potential mechanisms other than the occurrence of autophagy and its potential relevance to PPARα activation in PFOA-induced hepatotoxicity. hepatotoxic effects after PFOA exposure. We demonstrated Autophagy is an evolutionarily conserved catabolic that the dysfunction of lysosome–autophagosome fusion cellular process dependent on lysosomes for its execu- led to the blockage of autophagy after PFOA exposure. tion and includes macroautophagy, microautophagy, and chaperone-mediated autophagy (Kim and Lee 2014; Malhi et al. 2010). Macroautophagy (referred to as autophagy Materials and methods hereafter) is characterized by the formation of a double- membrane-bound structure that sequesters cellular orga- Animal treatment nelles or cytoplasm into a structure called the autophago- some, which then fuses with the lysosome for degradation Male Balb/c mice (aged 6–8 weeks) were purchased from of the sequestered material (Kim and Lee 2014; Malhi et al. Beijing Vital River Experimental Animals Centre (Beijing, 2010). At least four major protein complexes are required China), with all experimental manipulations described in for the formation of autophagosomes: Atg1–Unc-51-like our previous study (Yan et al. 2014). Briefly, mice were kinase (ULK) complex, which initiates formation; class randomly divided into six groups and dosed with either III phosphatidylinositol 3-kinase (PI3K) or Vps34 com- Milli-Q water or PFOA diluted in Milli-Q water at doses plexes, which are required for autophagosome nucleation; of 0.08, 0.31, 1.25, 5, and 20 mg/kg/day via gavage for autophagy-related (Atg) protein 9 (Atg9) and its traffick- 28 days. The PFOA doses were chosen based on earlier ing machinery, which may play an important role in deliv- toxicological studies and our previous experiments (Yan ering vesicles and lipids to expand the autophagosome et al. 2014). All animal treatments were approved by the membranes at all stages; and ubiquitin-like proteins Atg12 Committee on the Ethics of Animal Experiments from the and Atg8/LC3 and their conjugation machinery, which Institute of Zoology, Chinese Academy of Sciences (Permit are required for autophagosome expansion and closure Number: EET-015-08-2012) and in accordance with the (Dall’Armi et al. 2013; Lamb et al. 2013). Guiding Principles in the Use of Animals in Toxicology, Autophagy occurs at low basal levels in most cells and which were adopted by the Society of Toxicology in 1989. contributes to the regular turnover of cytoplasmic compo- Full materials and methods were described in supple- nents (Rautou et al. 2010; Shintani and Klionsky 2004). It mentary information. can be rapidly induced by a change in environmental condi- tions, such as nutrient depletion, growth factor withdrawal, or high bioenergetic demands (Rautou et al. 2010; Shintani Results and Klionsky 2004). In conditions of nutrient deprivation, several cellular signaling pathways are modulated upon dif- PFOA exposure induced autophagosome accumulation ferent nutrient deficiencies, which lead to the initiation of autophagosome formation (Kim and Lee 2014). Autophagy Consistent with the serum ALT levels in our previous report has also been suggested to interplay with apoptosis, which (Yan et al. 2014), the histopathology results with H&E has been well reviewed elsewhere (Delgado et al. 2014; staining also showed significant hepatocyte swelling and Marino et al. 2014). Evidence from mice with systemic or lipid deposits in mice after 28-day exposure, especially tissue-specific deletion of autophagy-related (Atg) genes at high doses of PFOA (Fig. S1). Microtubule-associated suggests that autophagy dysfunction might contribute to protein light chain 3 (LC3) conversion (LC3 I to LC3 II) certain disease phenotypes, such as cancer, neurodegenera- was detected by Western blotting to investigate the occur- tion, liver disease, and metabolic disease (Jiang and Miz- rence of autophagosome accumulation. Both LC3A II and ushima 2014; Shintani and Klionsky 2004). The possible LC3B II were accumulated in livers of mice after 28-day roles of autophagy in health and disease can serve to pro- exposure to PFOA, especially at the middle dose of PFOA tect cells but may also contribute to cell damage (Shintani (Fig. 1a, b). Several autophagy-related genes, especially and Klionsky 2004). Atg12, were stimulated in mouse livers by PFOA (Fig. S2). 1 3 Arch Toxicol (2017) 91:247–258 249 Fig. 1 PFOA exposure induced autophagosome accumulation in levels were analyzed from whole lysates of HepG2 cells after 72 h of mouse livers and HepG2 cells. a LC3A, LC3B, Atg12–Atg5, and exposure to PFOA. Long indicates the representative images of long p62 protein levels were analyzed from whole lysates of livers after exposures, and short indicates short exposures. Band densities of
Recommended publications
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • A Trafficome-Wide Rnai Screen Reveals Deployment of Early and Late Secretory Host Proteins and the Entire Late Endo-/Lysosomal V
    bioRxiv preprint doi: https://doi.org/10.1101/848549; this version posted November 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 A trafficome-wide RNAi screen reveals deployment of early and late 2 secretory host proteins and the entire late endo-/lysosomal vesicle fusion 3 machinery by intracellular Salmonella 4 5 Alexander Kehl1,4, Vera Göser1, Tatjana Reuter1, Viktoria Liss1, Maximilian Franke1, 6 Christopher John1, Christian P. Richter2, Jörg Deiwick1 and Michael Hensel1, 7 8 1Division of Microbiology, University of Osnabrück, Osnabrück, Germany; 2Division of Biophysics, University 9 of Osnabrück, Osnabrück, Germany, 3CellNanOs – Center for Cellular Nanoanalytics, Fachbereich 10 Biologie/Chemie, Universität Osnabrück, Osnabrück, Germany; 4current address: Institute for Hygiene, 11 University of Münster, Münster, Germany 12 13 Running title: Host factors for SIF formation 14 Keywords: siRNA knockdown, live cell imaging, Salmonella-containing vacuole, Salmonella- 15 induced filaments 16 17 Address for correspondence: 18 Alexander Kehl 19 Institute for Hygiene 20 University of Münster 21 Robert-Koch-Str. 4148149 Münster, Germany 22 Tel.: +49(0)251/83-55233 23 E-mail: [email protected] 24 25 or bioRxiv preprint doi: https://doi.org/10.1101/848549; this version posted November 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license.
    [Show full text]
  • Γ-SNAP Stimulates Disassembly of Endosomal SNARE Complexes and Regulates Endocytic Trafficking Pathways
    © 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 128, 2781-2794 doi:10.1242/jcs.158634 RESEARCH ARTICLE γ-SNAP stimulates disassembly of endosomal SNARE complexes and regulates endocytic trafficking pathways Hiroki Inoue1,*, Yuka Matsuzaki1, Ayaka Tanaka1, Kaori Hosoi1, Kaoru Ichimura2, Kohei Arasaki1, Yuichi Wakana1, Kenichi Asano1, Masato Tanaka1, Daisuke Okuzaki3, Akitsugu Yamamoto2, Katsuko Tani1 and Mitsuo Tagaya1,* ABSTRACT specific organelles and transport vesicles, and mediates membrane Soluble N-ethylmaleimide-sensitive factor attachment protein transport in specific endocytic and exocytic routes. For example, receptors (SNAREs) that reside in the target membranes and SNAREs such as syntaxin (STX)4, STX7 and STX18 catalyze transport vesicles assemble into specific SNARE complexes to membrane fusion in the plasma membrane, endosomes and drive membrane fusion. N-ethylmaleimide-sensitive factor (NSF) and lysosomes, and the endoplasmic reticulum (ER), respectively its attachment protein, α-SNAP (encoded by NAPA), catalyze (Hatsuzawa et al., 2000; Sumitani et al., 1995; Wong et al., 1998). disassembly of the SNARE complexes in the secretory and SNARE proteins are classified into four groups, Qa, Qb, Qc and R, endocytic pathways to recycle them for the next round of fusion according to the sequence similarity of the SNARE motif and its events. γ-SNAP (encoded by NAPG) is a SNAP isoform, but its flanking regions (Hong, 2005; Jahn and Scheller, 2006). In most function in SNARE-mediated membrane trafficking remains cases, Qa-, Qb- and Qc-SNAREs reside in target membranes and thus unknown. Here, we show that γ-SNAP regulates the endosomal are also called target (t)-SNAREs.
    [Show full text]
  • Understanding the Immunological Consequences Of
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
    [Show full text]
  • A Meta-Learning Approach for Genomic Survival Analysis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.21.053918; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A meta-learning approach for genomic survival analysis Yeping Lina Qiu1;2, Hong Zheng2, Arnout Devos3, Olivier Gevaert2;4;∗ 1Department of Electrical Engineering, Stanford University 2Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University 3School of Computer and Communication Sciences, Swiss Federal Institute of Technology Lausanne (EPFL) 4Department of Biomedical Data Science, Stanford University ∗To whom correspondence should be addressed: [email protected] Abstract RNA sequencing has emerged as a promising approach in cancer prognosis as sequencing data becomes more easily and affordably accessible. However, it remains challenging to build good predictive models especially when the sample size is limited and the number of features is high, which is a common situation in biomedical settings. To address these limitations, we propose a meta-learning framework based on neural networks for survival analysis and evaluate it in a genomic cancer research setting. We demonstrate that, compared to regular transfer- learning, meta-learning is a significantly more effective paradigm to leverage high-dimensional data that is relevant but not directly related to the problem of interest. Specifically, meta-learning explicitly constructs a model, from abundant data of relevant tasks, to learn a new task with few samples effectively. For the application of predicting cancer survival outcome, we also show that the meta- learning framework with a few samples is able to achieve competitive performance with learning from scratch with a significantly larger number of samples.
    [Show full text]
  • Molecular Characterization of the Cytotoxic Mechanism of Multiwall
    NANO LETTERS 2005 Molecular Characterization of the Vol. 5, No. 12 Cytotoxic Mechanism of Multiwall 2448-2464 Carbon Nanotubes and Nano-Onions on Human Skin Fibroblast Lianghao Ding,†,‡ Jackie Stilwell,†,‡ Tingting Zhang,†,‡,§ Omeed Elboudwarej,† Huijian Jiang,†,| John P. Selegue,⊥ Patrick A. Cooke,#,¶ Joe W. Gray,†,+ and Fanqing Frank Chen*,†,+ Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Chemistry, UniVersity of Kentucky, Lexington, Kentucky 40506-0055, Affymetrix Inc., 3380 Central Expressway, Santa Clara, California 95051, and Department of Laboratory Medicine and the ComprehensiVe Cancer Center, UniVersity of California, San Francisco, California 94143 Received September 1, 2005; Revised Manuscript Received October 18, 2005 ABSTRACT The increasing use of nanotechnology in consumer products and medical applications underlies the importance of understanding its potential toxic effects to people and the environment. Although both fullerene and carbon nanotubes have been demonstrated to accumulate to cytotoxic levels within organs of various animal models and cell types and carbon nanomaterials have been exploited for cancer therapies, the molecular and cellular mechanisms for cytotoxicity of this class of nanomaterial are not yet fully apparent. To address this question, we have performed whole genome expression array analysis and high content image analysis based phenotypic measurements on human skin fibroblast cell populations exposed to multiwall carbon nano-onions (MWCNOs) and multiwall carbon nanotubes (MWCNTs). Here we demonstrate that exposing cells to MWCNOs and MWCNTs at cytotoxic doses induces cell cycle arrest and increases apoptosis/necrosis. Expression array analysis indicates that multiple cellular pathways are perturbed after exposure to these nanomaterials at these doses, with material-specific toxigenomic profiles observed.
    [Show full text]
  • Murine Perinatal Beta Cell Proliferation and the Differentiation of Human Stem Cell Derived Insulin Expressing Cells Require NEUROD1
    Page 1 of 105 Diabetes Murine perinatal beta cell proliferation and the differentiation of human stem cell derived insulin expressing cells require NEUROD1 Anthony I. Romer,1,2 Ruth A. Singer1,3, Lina Sui2, Dieter Egli,2* and Lori Sussel1,4* 1Department of Genetics and Development, Columbia University, New York, NY 10032, USA 2Department of Pediatrics, Columbia University, New York, NY 10032, USA 3Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY 10032, USA 4Department of Pediatrics, University of Colorado Denver School of Medicine, Denver, CO 80045, USA *Co-Corresponding Authors Dieter Egli 1150 St. Nicholas Avenue New York, NY 10032 [email protected] Lori Sussel 1775 Aurora Ct. Aurora, CO 80045 [email protected] Word Count: Abstract= 149; Body= 4773 Total Paper Figures= 7, Total Supplemental Tables= 4, Total Supplemental Figures= 5 Diabetes Publish Ahead of Print, published online September 13, 2019 Diabetes Page 2 of 105 Abstract Inactivation of the β cell transcription factor NEUROD1 causes diabetes in mice and humans. In this study, we uncovered novel functions of Neurod1 during murine islet cell development and during the differentiation of human embryonic stem cells (HESCs) into insulin-producing cells. In mice, we determined that Neurod1 is required for perinatal proliferation of alpha and beta cells. Surprisingly, apoptosis only makes a minor contribution to beta cell loss when Neurod1 is deleted. Inactivation of NEUROD1 in HESCs severely impaired their differentiation from pancreatic progenitors into insulin expressing (HESC-beta) cells; however survival or proliferation was not affected at the time points analyzed. NEUROD1 was also required in HESC-beta cells for the full activation of an essential beta cell transcription factor network.
    [Show full text]
  • Network-Assisted Analysis of Primary Sjögren's Syndrome GWAS Data In
    Network-assisted analysis of primary Sjögren’s syndrome GWAS data in Han Chinese Kechi Fang, Kunlin Zhang, Jing Wang* Address: Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China. Email: Kechi Fang – [email protected]; Kunlin Zhang – [email protected]; Jing Wang – [email protected] *Corresponding author 1 Supplementary materials Page 3 – Page 5: Supplementary Figure S1. The direct network formed by the module genes from DAPPLE. Page 6: Supplementary Figure S2. Transcript expression heatmap. Page 7: Supplementary Figure S3. Transcript enrichment heatmap. Page 8: Supplementary Figure S4. Workflow of network-assisted analysis of pSS GWAS data to identify candidate genes. Page 9 – Page 734: Supplementary Table S1. A full list of PPI pairs involved in the node-weighted pSS interactome. Page 735 – Page 737: Supplementary Table S2. Detailed information about module genes and sigMHC-genes. Page 738: Supplementary Table S3. GO terms enriched by module genes. 2 NFKBIE CFLAR NFKB1 STAT4 JUN HSF1 CCDC90B SUMO2 STAT1 PAFAH1B3 NMI GTF2I 2e−04 CDKN2C LAMA4 8e−04 HDAC1 EED 0.002 WWOX PSMD7 0.008 TP53 PSMA1 HR 0.02 RPA1 0.08 UBC ARID3A PTTG1 0.2 TSC22D4 ERH NIF3L1 0.4 MAD2L1 DMRTB1 1 ERBB4 PRMT2 FXR2 MBL2 CBS UHRF2 PCNP VTA1 3 DNMT3B DNMT1 RBBP4 DNMT3A RFC3 DDB1 THRA CBX5 EED NR2F2 RAD9A HUS1 RFC4 DDB2 HDAC2 HCFC1 CDC45L PPP1CA MLLSMARCA2 PGR SP3 EZH2 CSNK2B HIST1H4C HIST1H4F HNRNPUL1 HR HIST4H4 TAF1C HIST1H4A ENSG00000206300 APEX1 TFDP1 RHOA ENSG00000206406 RPF2 E2F4 HIST1H4IHIST1H4B HIST1H4D
    [Show full text]
  • Cellular Functions of NSF: Not Just Snaps and Snares
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 581 (2007) 2140–2149 Minireview Cellular functions of NSF: Not just SNAPs and SNAREs Chunxia Zhaoa, John T. Slevinb, Sidney W. Whitehearta,* a Departmental of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, 741 South Limestone, BBSRB B261, Lexington, KY 40536, USA b Neurology Service, Department of Veterans Affairs Medical Center, Departments of Neurology and Molecular and Biomedical Pharmacology, University of Kentucky Medical Center, Lexington, KY 40536, USA Received 13 February 2007; accepted 7 March 2007 Available online 21 March 2007 Edited by Thomas So¨llner cargo selection and vesicle production through a budding pro- Abstract N-ethylmaleimide sensitive factor (NSF) is an ATP- ases associated with various cellular activities protein (AAA), cess. The subsequent vesicle transport and targeting process broadly required for intracellular membrane fusion. NSF func- concludes with specific membrane fusion of the vesicle to its tions as a SNAP receptor (SNARE) chaperone which binds, target membrane. Early molecular analysis of vesicular traf- through soluble NSF attachment proteins (SNAPs), to SNARE ficking between Golgi cisternae identified an essential N-ethyl- complexes and utilizes the energy of ATP hydrolysis to disas- maleimide sensitive factor (NSF) [1]. Subsequent studies semble them thus facilitating SNARE recycling. While this is identified NSF adaptors, soluble NSF attachment proteins a major function of NSF, it does seem to interact with other pro- (SNAPs) [2], and SNAP receptors [3] (SNAREs). The charac- teins, such as the AMPA receptor subunit, GluR2, and b2-AR terization of these proteins has lead to a detailed picture of the and is thought to affect their trafficking patterns.
    [Show full text]
  • Identification of Significant Pathways in Gastric Cancer Based on Protein-Protein Interaction Networks and Cluster Analysis
    Genetics and Molecular Biology, 35, 3, 701-708 (2012) Copyright © 2012, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Research Article Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis Kongwang Hu1 and Feihu Chen2 1Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Anhui, P.R. China. 2School of Pharmacology, Anhui Medical University, Anhui, P.R. China. Abstract Gastric cancer is one of the most common and lethal cancers worldwide. However, despite its clinical importance, the regulatory mechanisms involved in the aggressiveness of this cancer are still poorly understood. A better under- standing of the biology, genetics and molecular mechanisms of gastric cancer would be useful in developing novel targeted approaches for treating this disease. In this study we used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in gastric cancer. A primary immunodefi- ciency pathway, focal adhesion, ECM-receptor interactions and the metabolism of xenobiotics by cytochrome P450 were identified as four important pathways associated with the progression of gastric cancer. The genes in these pathways, e.g., ZAP70, IGLL1, CD79A, COL6A3, COL3A1, COL1A1, CYP2C18 and CYP2C9, may be considered as potential therapeutic targets for gastric cancer. Key words: graph clustering, pathway crosstalk, protein-protein interaction network. Received: March 12, 2012; Accepted: May 4, 2012. Introduction mal persons (Offerhaus et al., 1992). b-catenin is fre- Gastric cancer is one of the most common malignan- quently mutated in gastric cancer (Clements et al., 2002). In cies worldwide (Lin et al., 2007b).
    [Show full text]
  • Featured Articles : Neuroscience Gateway
    FEATURED ARTICLES With friends like these... Neuroscience Gateway (May 2007) | doi:10.1038/aba1747 Using a proteomics approach, researchers identify 234 proteins that bind to the protein associated with Huntington's disease and may modify disease progression. Powerful people involved in scandals often take their associates down with them when they fall from grace. Similarly, some mutant proteins involved in neurodegeneration bind and sequester proteins important in cellular function in inclusion bodies that clog cellular functions. Huntington's disease is a fatal neurodegenerative disorder caused by the polyglutamine expansion of the huntingtin protein, which forms potentially toxic cellular aggregates. Kaltenbach et al. identify over 200 proteins, including several potential therapeutic targets, that bind to normal and polyglutamine-expanded huntingtin in a high-throughput proteomics screen reported in PLoS Genetics. Normally, the amino terminus of huntingtin contains several repeats of the amino acid glutamine. In people with Huntington's disease, the huntingtin polyglutamine tract contains more than 35 glutamines. Symptoms of Huntington's disease, including involuntary movements (chorea), muscle rigidity and cognitive dysfuntion, begin during middle age. There is no cure, and most patients die within 15 years of symptom onset. The authors screened for proteins in mouse and human brain that interact with normal and polyglutamine-expanded huntingtin by affinity purification followed by mass spectrometry and yeast two- hybrid. They used 'baits' from various regions of huntingtin protein. Regardless of the number of glutamine repeats, only baits from the amino terminus of huntingtin (amino acids 1 to 90) formed complexes with other proteins. After stringent filtering, affinity purification identified 130 and yeast two-hybrid identified 104 mouse and human proteins that bound to normal or polyglutamine-expanded huntingtin.
    [Show full text]
  • Interaction Networks of Weibel-Palade Body Regulators Syntaxin-3 and Syntaxin Binding Protein 5 in Endothelial Cells T
    Journal of Proteomics 205 (2019) 103417 Contents lists available at ScienceDirect Journal of Proteomics journal homepage: www.elsevier.com/locate/jprot Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells T Maaike Schillemansa,1, Ellie Karampinia,1, Arie J. Hoogendijka, Maryam Wahedia, ⁎ Floris P.J. van Alphenb, Maartje van den Biggelaara, Jan Voorberga,c, Ruben Bieringsa,d, a Molecular and Cellular Hemostasis, Amsterdam UMC, University of Amsterdam, The Netherlands b Research Facilities, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, The Netherlands c Experimental Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands d Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands ARTICLE INFO ABSTRACT Keywords: The endothelium stores the hemostatic protein Von Willebrand factor (VWF) in endothelial storage organelles Endothelial cells called Weibel-Palade bodies (WPBs). During maturation, WPBs recruit a complex of Rab GTPases and effectors Weibel-Palade body that associate with components of the SNARE machinery that control WPB exocytosis. Recent genome wide SNARE protein association studies have found links between genetic variations in the SNAREs syntaxin-2 (STX2) and syntaxin Syntaxin binding protein 5 (STXBP5) and VWF plasma levels, suggesting a role for SNARE proteins in regulating VWF Protein-protein interactions release. Moreover, we have previously identified the SNARE proteins syntaxin-3 and STXBP1 as regulators of WPB release. In this study we used an unbiased iterative interactomic approach to identify new components of the WPB exocytotic machinery. An interactome screen of syntaxin-3 identifies a number of SNAREs and SNARE associated proteins (STXBP2, STXBP5, SNAP23, NAPA and NSF).
    [Show full text]