A Systematic Review on the Implications of O-Linked Glycan Branching and Truncating Enzymes on Cancer Progression and Metastasis
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Targeted Metabolic Labeling of Yeast N-Glycans with Unnatural Sugars
Targeted metabolic labeling of yeast N-glycans with unnatural sugars Mark A. Breidenbacha, Jennifer E. G. Gallagherb, David S. Kingc, Brian P. Smarta, Peng Wua,2, and Carolyn R. Bertozzia,b,c,d,1 aDepartments of Chemistry; bMolecular and Cell Biology; and cHoward Hughes Medical Institute, University of California, Berkeley, CA 94720; and dThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Edited by David A. Tirrell, California Institute of Technology, Pasadena, CA, and approved December 23, 2009 (received for review September 30, 2009) Metabolic labeling of glycans with synthetic sugar analogs has and mass spectrometric analyses of proteins displaying the nonna- emerged as an attractive means for introducing nonnatural chemi- tural chemical functionality (5, 6). cal functionality into glycoproteins. However, the complexities of While existing glycan labeling methodology is suitable for stud- glycan biosynthesis prevent the installation of nonnatural moieties ies that require only stochastic insertion of analogs at low levels, at defined, predictable locations within glycoproteins at high levels the technique is inadequate for applications in which specific of incorporation. Here, we demonstrate that the conserved monosaccharides must be reliably targeted for metabolic replace- N-acetyglucosamine (GlcNAc) residues within chitobiose cores of ment. For example, high-efficiency and predictable installation of N-glycans in the model organism Saccharomyces cerevisiae can sugar analogs could dramatically facilitate biophysical studies of be specifically targeted for metabolic replacement by unnatural glycoprotein structure and function via site-specific introduction sugars. We introduced an exogenous GlcNAc salvage pathway into of fluorophores and heavy atoms. Unfortunately, site-specific me- yeast, allowing cells to metabolize GlcNAc provided as a supple- tabolic labeling of glycans is hindered by multiple factors. -
High Affinity Biomolecular Interactions That Can Mediate Binding of Pathogenic Bacteria to Host Cells
Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells Christopher J. Daya,1, Elizabeth N. Tranb, Evgeny A. Semchenkoa, Greg Trama, Lauren E. Hartley-Tassella, Preston S. K. Nga, Rebecca M. Kinga, Rachel Ulanovskya, Sarah McAtamneya, Michael A. Apicellac, Joe Tiralongoa, Renato Moronab,2, Victoria Korolika,2, and Michael P. Jenningsa,1,2 aInstitute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, QLD 4222, Australia; bSchool of Biological Sciences, Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA 5005, Australia; and cDepartment of Microbiology, University of Iowa, Iowa City, IA 52242 Edited by Rino Rappuoli, GSK Vaccines, Siena, Italy, and approved November 10, 2015 (received for review November 3, 2014) Cells from all domains of life express glycan structures attached to Interestingly, there are specific reports of several bacteria lipids and proteins on their surface, called glycoconjugates. Cell-to- expressing truncated surface polysaccharides and oligosaccharides cell contact mediated by glycan:glycan interactions have been that are significantly less adherent than wild-type equivalents considered to be low-affinity interactions that precede high- (10, 11), or that their adherence can be blocked by extracted affinity protein–glycan or protein–protein interactions. In several LOS/LPS (10), indicating a role for bacterial surface glycans in pathogenic bacteria, truncation of surface glycans, lipooligosac- adherence to host cells. This decreased adherence of rough strains charide (LOS), or lipopolysaccharide (LPS) have been reported to or blocking of adherence using the free lipooligosaccharide (LOS)/ significantly reduce bacterial adherence to host cells. Here, we lipopolysaccharide (LPS) in both cell-based and animal infection show that the saccharide component of LOS/LPS have direct, models has been noted in a range of Gram-negative bacteria in- high-affinity interactions with host glycans. -
Enzymatic Encoding Methods for Efficient Synthesis Of
(19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN, -
Metabolomics Analysis of Skeletal Muscles from FKRP-Deficient Mice
www.nature.com/scientificreports OPEN Metabolomics Analysis of Skeletal Muscles from FKRP-Defcient Mice Indicates Improvement After Gene Received: 21 March 2019 Accepted: 28 June 2019 Replacement Therapy Published: xx xx xxxx Charles Harvey Vannoy 1, Victoria Leroy1, Katarzyna Broniowska2 & Qi Long Lu1 Muscular dystrophy-dystroglycanopathies comprise a heterogeneous and complex group of disorders caused by loss-of-function mutations in a multitude of genes that disrupt the glycobiology of α-dystroglycan, thereby afecting its ability to function as a receptor for extracellular matrix proteins. Of the various genes involved, FKRP codes for a protein that plays a critical role in the maturation of a novel glycan found only on α-dystroglycan. Yet despite knowing the genetic cause of FKRP-related dystroglycanopathies, the molecular pathogenesis of disease and metabolic response to therapeutic intervention has not been fully elucidated. To address these challenges, we utilized mass spectrometry- based metabolomics to generate comprehensive metabolite profles of skeletal muscle across diseased, treated, and normal states. Notably, FKRP-defcient mice elicit diverse metabolic abnormalities in biomarkers of extracellular matrix remodeling and/or aging, pentoses/pentitols, glycolytic intermediates, and lipid metabolism. More importantly, the restoration of FKRP protein activity following AAV-mediated gene therapy induced a substantial correction of these metabolic impairments. While interconnections of the afected molecular mechanisms remain unclear, -
Glycosylation: Rising Potential for Prostate Cancer Evaluation
cancers Review Glycosylation: Rising Potential for Prostate Cancer Evaluation Anna Kałuza˙ * , Justyna Szczykutowicz and Mirosława Ferens-Sieczkowska Department of Chemistry and Immunochemistry, Wroclaw Medical University, Sklodowskiej-Curie 48/50, 50-369 Wroclaw, Poland; [email protected] (J.S.); [email protected] (M.F.-S.) * Correspondence: [email protected]; Tel.: +48-71-770-30-66 Simple Summary: Aberrant protein glycosylation is a well-known hallmark of cancer and is as- sociated with differential expression of enzymes such as glycosyltransferases and glycosidases. The altered expression of the enzymes triggers cancer cells to produce glycoproteins with specific cancer-related aberrations in glycan structures. Increasing number of data indicate that glycosylation patterns of PSA and other prostate-originated proteins exert a potential to distinguish between benign prostate disease and cancer as well as among different stages of prostate cancer development and aggressiveness. This review summarizes the alterations in glycan sialylation, fucosylation, truncated O-glycans, and LacdiNAc groups outlining their potential applications in non-invasive diagnostic procedures of prostate diseases. Further research is desired to develop more general algorithms exploiting glycobiology data for the improvement of prostate diseases evaluation. Abstract: Prostate cancer is the second most commonly diagnosed cancer among men. Alterations in protein glycosylation are confirmed to be a reliable hallmark of cancer. Prostate-specific antigen is the biomarker that is used most frequently for prostate cancer detection, although its lack of sensitivity and specificity results in many unnecessary biopsies. A wide range of glycosylation alterations in Citation: Kałuza,˙ A.; Szczykutowicz, prostate cancer cells, including increased sialylation and fucosylation, can modify protein function J.; Ferens-Sieczkowska, M. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Detecting Substrate Glycans of Fucosyltransferases on Glycoproteins with Fluorescent Fucose
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.28.919860; this version posted January 29, 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. Detecting substrate glycans of fucosyltransferases on glycoproteins with fluorescent fucose Key words: Fucose/Fucosylation/fucosyltransferase/core-fucose/glycosylation Supplementary Data Included: Supplemental Fig.1 to Fig. 2 Zhengliang L Wu1*, Mark Whitaker, Anthony D Person1, Vassili Kalabokis1 1Bio-techne, R&D Systems, Inc. 614 McKinley Place N.E. Minneapolis, MN, 55413, USA *Correspondence: Phone: 612-656-4544. Email: [email protected], bioRxiv preprint doi: https://doi.org/10.1101/2020.01.28.919860; this version posted January 29, 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. Abstract Like sialylation, fucose usually locates at the non-reducing ends of various glycans on glycoproteins and constitutes important glycan epitopes. Detecting the substrate glycans of fucosyltransferases is important for understanding how these glycan epitopes are regulated in response to different growth conditions and external stimuli. Here we report the detection of these glycans via enzymatic incorporation of fluorescent tagged fucose using fucosyltransferases including FUT2, FUT6, FUT7, and FUT8 and FUT9. More specifically, we describe the detection of substrate glycans of FUT8 and FUT9 on therapeutic antibodies and the detection of high mannose glycans on glycoproteins by enzymatic conversion of high mannose glycans to the substrate glycans of FUT8. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Reciprocal Monoallelic Expression of ASAR Lncrna Genes Controls Replication Timing of Human Chromosome 6
Downloaded from rnajournal.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Reciprocal monoallelic expression of ASAR lncRNA genes 2 controls replication timing of human chromosome 6. 3 4 Michael Heskett1, Leslie G. Smith2, Paul Spellman1, and Mathew J. Thayer2* 5 6 1Department of Chemical Physiology and Biochemistry 7 Oregon Health & Science University 8 3181 S. W. Sam Jackson Park Road 9 Portland, Oregon 97239, USA 10 11 2Department of Chemical Physiology and Biochemistry 12 Oregon Health & Science University 13 3181 S. W. Sam Jackson Park Road 14 Portland, Oregon 97239, USA 15 16 *Corresponding author. 17 ORCID: 0000-0001-6483-1661 18 TEL: (503) 494-2447 19 FAX: (503) 494-7368 20 Email:[email protected] 21 22 Running Title: ASAR lincRNA genes on chromosome 6 23 Key Words: Replication timing, cis-acting element, non-coding RNA 1 Downloaded from rnajournal.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press 24 Abstract 25 DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal 26 order known as the replication timing program. We previously found that disruption of the 27 noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing 28 and delayed mitotic chromosome condensation of human chromosomes 6 and 15, 29 respectively. ASAR6 and ASAR15 display random monoallelic expression, and display 30 asynchronous replication between alleles that is coordinated with other random 31 monoallelic genes on their respective chromosomes. Disruption of the expressed allele, 32 but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously 33 silent alleles of linked monoallelic genes, and structural instability of human chromosome 34 6. -
Fucosyltransferase 8 As a Functional Regulator of Nonsmall Cell Lung Cancer
Fucosyltransferase 8 as a functional regulator of nonsmall cell lung cancer Chien-Yu Chena,b, Yi-Hua Janb, Yi-Hsiu Juanc, Chih-Jen Yangd, Ming-Shyan Huangd, Chong-Jen Yuc, Pan-Chyr Yangc, Michael Hsiaob, Tsui-Ling Hsub,1, and Chi-Huey Wongb,1 aInstitute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan; bGenomics Research Center, Academia Sinica, Taipei 115, Taiwan; cDepartment of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan; and dDepartment of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan Contributed by Chi-Huey Wong, November 26, 2012 (sent for review August 17, 2012) The up-regulation of fucosyltransferase 8 (FUT8), the only enzyme downstream signaling. Furthermore, the increase in core fuco- catalyzing α1,6-fucosylation in mammals, has been observed in sylation on E-cadherin has been shown to strengthen cell–cell several malignant cancers including liver, ovarian, thyroid, and co- adhesion (10). lorectal cancers. However, the pathological role and the regulatory Both transgenic and knockout mouse models have been gen- mechanism of FUT8 in cancers remain largely unknown. In the cur- erated to study the physiological role of FUT8 (7, 11, 12). Ec- rent study, we report that the expression of FUT8 is up-regulated in topic expression of FUT8 in mice results in an accumulation of nonsmall cell lung cancer (NSCLC) and correlates with tumor me- lipid droplets in hepatocytes and proximal renal tubular cells. tastasis, disease recurrence, and poor survival in patients with This steatosis-like phenotype observed in transgenic mice is NSCLC. Knocking down FUT8 in aggressive lung cancer cell lines linked to the activity of liver lysosomal acid lipase, which becomes significantly inhibits their malignant behaviors including in vitro inactive when over core-fucosylated (11), suggesting that excess invasion and cell proliferation, as well as in vivo metastasis and core fucosylation may lead to a breakdown of normal lipid me- tumor growth. -
(12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
US 20030082511A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown et al. (43) Pub. Date: May 1, 2003 (54) IDENTIFICATION OF MODULATORY Publication Classification MOLECULES USING INDUCIBLE PROMOTERS (51) Int. Cl." ............................... C12O 1/00; C12O 1/68 (52) U.S. Cl. ..................................................... 435/4; 435/6 (76) Inventors: Steven J. Brown, San Diego, CA (US); Damien J. Dunnington, San Diego, CA (US); Imran Clark, San Diego, CA (57) ABSTRACT (US) Correspondence Address: Methods for identifying an ion channel modulator, a target David B. Waller & Associates membrane receptor modulator molecule, and other modula 5677 Oberlin Drive tory molecules are disclosed, as well as cells and vectors for Suit 214 use in those methods. A polynucleotide encoding target is San Diego, CA 92121 (US) provided in a cell under control of an inducible promoter, and candidate modulatory molecules are contacted with the (21) Appl. No.: 09/965,201 cell after induction of the promoter to ascertain whether a change in a measurable physiological parameter occurs as a (22) Filed: Sep. 25, 2001 result of the candidate modulatory molecule. Patent Application Publication May 1, 2003 Sheet 1 of 8 US 2003/0082511 A1 KCNC1 cDNA F.G. 1 Patent Application Publication May 1, 2003 Sheet 2 of 8 US 2003/0082511 A1 49 - -9 G C EH H EH N t R M h so as se W M M MP N FIG.2 Patent Application Publication May 1, 2003 Sheet 3 of 8 US 2003/0082511 A1 FG. 3 Patent Application Publication May 1, 2003 Sheet 4 of 8 US 2003/0082511 A1 KCNC1 ITREXCHO KC 150 mM KC 2000000 so 100 mM induced Uninduced Steady state O 100 200 300 400 500 600 700 Time (seconds) FIG. -
Dissertation / Doctoral Thesis
DISSERTATION / DOCTORAL THESIS Titel der Dissertation / Title of the Doctoral Thesis “In-depth mass spectrometry-based proteome profiling of inflammation-related processes” verfasst von / submitted by Andrea Bileck, MSc angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Doktorin der Naturwissenschaften (Dr.rer.nat.) Doctor of Sciences (Dr.rer.nat.) Wien, 2016 / Vienna 2016 Studienkennzahl lt. Studienblatt / degree programme code as it appears on the student A 796 605 419 record sheet: Dissertationsgebiet lt. Studienblatt / Chemie / Chemistry field of study as it appears on the student record sheet: Betreut von / Supervisor: Univ. Prof. Dr. Christopher Gerner II This doctoral thesis is based on the following publications and manuscripts: Comprehensive assessment of proteins regulated by dexamethasone reveals novel effects in primary human peripheral blood mononuclear cells Andrea Bileck, Dominique Kreutz, Besnik Muqaku, Astrid Slany, Christopher Gerner Journal of Proteome Research, 2014, 13, (12), 5989-6000 Impact of a synthetic cannabinoid (CP-47,497-C8) on protein expression in human cells: evidence for induction of inflammation and DNA damage Andrea Bileck, Franziska Ferk, Halh Al-Serori, Verena J. Koller, Besnik Muqaku, Alexander Haslberger, Volker Auwärter, Christopher Gerner, Siegfried Knasmüller Archives of Toxicology, 2015, doi:10.1007/s00204-015-1569-7 Shotgun proteomics of primary human cells enables the analysis of signaling pathways and nuclear translocations related to inflammation Andrea Bileck, Rupert L. Mayer, Dominique Kreutz, Tamara Weiss, Astrid Slany, Christopher Gerner Journal of Proteome Research, 2015, manuscript under revision Contribution of human fibroblasts and endothelial cells to the hallmarks of inflammation as determined by proteome profiling Astrid Slany, Andrea Bileck, Dominique Kreutz, Rupert L.