Lysyl Hydroxylases. Studies on Recombinant Lysyl Hydroxylases and Mouse Lines Lacking Lysyl Hydroxylase 1 Or Lysyl Hydroxylase 3
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Boards' Fodder
boards’ fodder Cosmeceuticals Contributed by Elisabeth Hurliman, MD, PhD; Jennifer Hayes, MD; Hilary Reich MD; and Sarah Schram, MD. INGREDIENT FUNCTION MECHANISM ASSOCIATIONS/SIDE EFFECTS Vitamin A/ Antioxidant (reduces free Affects gene transcription Comedolysis epidermal thickening, dermal Derivatives (retinal, radicals, lowers concentration differentiation and growth of regeneration, pigment lightening retinol, retinoic of matrix metalloproteinases cells in the skin acid, provitamin reduces collagen degradation) Side effects: Irritation, erythema, desquamation A, asthaxanthin, Normalizes follicular Elisabeth Hurliman, lutein) epithelial differentiation and keratinization MD, PhD, is a PGY-4 dermatology resident Vitamin C (L Secondary endogenous Ascorbic acid: necessary L-ascorbic acid + alpha-tocopherol (vitamin E)= ascorbic acid, antioxidant in skin cofactor for prolylhydroxylase UVA and UVB protection at University of tetrahexyldecyl and lysyl hydroxylase Minnesota department ascorbate) Lightens pigment Zinc, resveratrol, L-ergothioneine and tyrosine add of dermatology. (affects melanogenesis) L-ascorbic acid: scavenges to vitamin C bioavailability free oxygen radicals, Protects Vitamin E from oxidation stimulates collagen synthesis Improves skin texture and hydration May interrupt melanogenesis by interacting with copper ions Vitamin E/ Primary endogenous antioxidant Prevents lipid peroxidation; Alpha tocopherol is the most physiologically Tocopherols, in skin scavenges free oxygen active isomer Jennifer Hayes, MD, Tocotrienols -
New Concepts in Basement Membrane Biology Willi Halfter1, Philipp Oertle2, Christophe A
REVIEW ARTICLE New concepts in basement membrane biology Willi Halfter1, Philipp Oertle2, Christophe A. Monnier2,*, Leon Camenzind2, Magaly Reyes-Lua1, Huaiyu Hu3, Joseph Candiello4, Anatalia Labilloy5,†, Manimalha Balasubramani6, Paul Bernhard Henrich1 and Marija Plodinec2,7 1 Department of Ophthalmology, University Hospital Basel, Switzerland 2 Biozentrum and the Swiss Nanoscience Institute, University of Basel, Switzerland 3 Department of Neurobiology and Physiology, Upstate University Hospital, SUNY University, Syracuse, NY, USA 4 Department of Bioengeneering, University of Pittsburgh, PA, USA 5 Department of Renal Physiology, University of Pittsburgh, PA, USA 6 Proteomics Core Facility of the University of Pittsburgh, PA, USA 7 Department of Pathology, University Hospital Basel, Switzerland Keywords Basement membranes (BMs) are thin sheets of extracellular matrix that basal lamina; basement membrane; outline epithelia, muscle fibers, blood vessels and peripheral nerves. The biomechanical properties; collagen IV; current view of BM structure and functions is based mainly on transmis- laminin; membrane asymmetry; nidogen; sion electron microscopy imaging, in vitro protein binding assays, and phe- perlecan notype analysis of human patients, mutant mice and invertebrata. Correspondence Recently, MS-based protein analysis, biomechanical testing and cell adhe- W. Halfter, Department of Ophthalmology, sion assays with in vivo derived BMs have led to new and unexpected University Hospital Basel, Mittlere insights. Proteomic analysis combined with ultrastructural studies showed Strasse 91, 4031 Basel, Switzerland that many BMs undergo compositional and structural changes with Fax: +41 61 267 21 09 advancing age. Atomic force microscopy measurements in combination Tel: +49 7624 982528 with phenotype analysis have revealed an altered mechanical stiffness that E-mail: [email protected] M. -
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, -
Mutant IDH, (R)-2-Hydroxyglutarate, and Cancer
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer Julie-Aurore Losman1 and William G. Kaelin Jr.1,2,3 1Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA; 2Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Mutations in metabolic enzymes, including isocitrate whether altered cellular metabolism is a cause of cancer dehydrogenase 1 (IDH1) and IDH2, in cancer strongly or merely an adaptive response of cancer cells in the face implicate altered metabolism in tumorigenesis. IDH1 of accelerated cell proliferation is still a topic of some and IDH2 catalyze the interconversion of isocitrate and debate. 2-oxoglutarate (2OG). 2OG is a TCA cycle intermediate The recent identification of cancer-associated muta- and an essential cofactor for many enzymes, including tions in three metabolic enzymes suggests that altered JmjC domain-containing histone demethylases, TET cellular metabolism can indeed be a cause of some 5-methylcytosine hydroxylases, and EglN prolyl-4-hydrox- cancers (Pollard et al. 2003; King et al. 2006; Raimundo ylases. Cancer-associated IDH mutations alter the enzymes et al. 2011). Two of these enzymes, fumarate hydratase such that they reduce 2OG to the structurally similar (FH) and succinate dehydrogenase (SDH), are bone fide metabolite (R)-2-hydroxyglutarate [(R)-2HG]. Here we tumor suppressors, and loss-of-function mutations in FH review what is known about the molecular mechanisms and SDH have been identified in various cancers, in- of transformation by mutant IDH and discuss their im- cluding renal cell carcinomas and paragangliomas. -
Ophthalmological Features Associated with COL4A1 Mutations
OPHTHALMIC MOLECULAR GENETICS SECTION EDITOR: JANEY L. WIGGS, MD, PhD Ophthalmological Features Associated With COL4A1 Mutations Isabelle Coupry, PhD; Igor Sibon, MD, PhD; Bruno Mortemousque, MD; Franc¸ois Rouanet, MD; Manuele Mine, PharmD, PhD; Cyril Goizet, MD, PhD Objective: To investigate the wide variability of ocular Conclusions: The COL4A1 mutations may be associ- manifestations associated with mutations in the COL4A1 ated with various ophthalmologic developmental anoma- gene that encodes collagen IV␣1. lies of anterior segment dysgenesis type, which are reminiscent of Axenfeld-Rieger anomalies (ARA). Cere- Methods: We clinically evaluated 7 patients from 2 un- brovascular disorders should be added to the list of signs related families in whom ocular features segregated with potentially associated with ARA. COL4A1 mutations that were identified by direct se- quencing. Clinical Relevance: These data suggest that cerebral magnetic resonance imaging may be recommended in Results: The G2159A transition (c.2159GϾA) that leads the clinical treatment of patients with apparently iso- tothemissensemutationp.Gly720Aspwasidentifiedinfam- lated ARA, even when neurological symptoms or signs ily A. An ocular phenotype of variable severity was observed are lacking. in all affected relatives. The missense mutation c.2263GϾA, p.Gly755Arg was identified in family B. One patient from family B also displayed notable ocular features. Arch Ophthalmol. 2010;128(4):483-489 NEW FORM OF HEREDITARY constellation of ocular findings that in- cerebrovascular disorder clude anomalies of the anterior chamber was recently associated angle and aqueous drainage structures (iri- with mutations in the dogoniodysgenesis), iris hypoplasia, ec- COL4A1 gene that en- centric pupil (corectopia), iris tears (poly- Acodes collagen IV␣1.1,2 Mutations in coria), and iridocorneal adhesions COL4A1 were initially associated with ce- traversing the anterior chamber. -
Page Numbers in Bold Indicate Main Discus- Sion of Topic. Page Numbers
168397_P489-520.qxd7.0:34 Index 6-2-04 26p 2010.4.5 10:03 AM Page 489 source of, 109, 109f pairing with thymine, 396f, 397, 398f in tricarboxylic acid cycle, 109–111, 109f Adenine arabinoside (vidarabine, araA), 409 Acetyl CoA-ACP acetyltransferase, 184 Adenine phosphoribosyltransferase (APRT), Index Acetyl CoA carboxylase, 183, 185f, 190 296, 296f in absorptive/fed state, 324 Adenosine deaminase (ADA), 299 allosteric activation of, 183–184, 184f deficiency of, 298, 300f, 301–302 allosteric inactivation of, 183, 184f gene therapy for, 485, 486f dephosphorylation of, 184 Adenosine diphosphate (ADP) in fasting, 330 in ATP synthesis, 73, 77–78, 78f Page numbers in bold indicate main discus- hormonal regulation of, 184, 184f isocitrate dehydrogenase activation by, sion of topic. Page numbers followed by f long-term regulation of, 184 112 denote figures. “See” cross-references direct phosphorylation of, 183–184 transport of, to inner mitochondrial short-term regulation of, 183–184, 184f membrane, 79 the reader to the synonymous term. “See Acetyl CoA carboxylase-2 (ACC2), 191 in tricarboxylic acid cycle regulation, 114, also” cross-references direct the reader to N4-Acetylcytosine, 292f 114f related topics. [Note: Positional and configura- N-Acetyl-D-glucosamine, 142 in urea cycle, 255–256 N-Acetylgalactosamine (GalNAc), 160, 168 ribosylation, 95 tional designations in chemical names (for N-Acetylglucosamindase deficiency, 164f Adenosine monophosphate (AMP; also called example, “3-“, “α”, “N-“, “D-“) are ignored in N-Acetylglucosamine (GlcNAc), -
Meta-Analyses of Expression Profiling Data in the Postmortem
META-ANALYSES OF EXPRESSION PROFILING DATA IN THE POSTMORTEM HUMAN BRAIN by Meeta Mistry B.Sc., McMaster University, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2012 © Meeta Mistry, 2012 Abstract Schizophrenia is a severe psychiatric illness for which the precise etiology remains unknown. Studies using postmortem human brain have become increasingly important in schizophrenia research, providing an opportunity to directly investigate the diseased brain tissue. Gene expression profiling technologies have been used by a number of groups to explore the postmortem human brain and seek genes which show changes in expression correlated with schizophrenia. While this has been a valuable means of generating hypotheses, there is a general lack of consensus in the findings across studies. Expression profiling of postmortem human brain tissue is difficult due to the effect of various factors that can confound the data. The first aim of this thesis was to use control postmortem human cortex for identification of expression changes associated with several factors, specifically: age, sex, brain pH and postmortem interval. I conducted a meta-analysis across the control arm of eleven microarray datasets (representing over 400 subjects), and identified a signature of genes associated with each factor. These genes provide critical information towards the identification of problematic genes when investigating postmortem human brain in schizophrenia and other neuropsychiatric illnesses. The second aim of this thesis was to evaluate gene expression patterns in the prefrontal cortex associated with schizophrenia by exploring two methods of analysis: differential expression and coexpression. -
A Collagen Glucosyltransferase Drives Lung Adenocarcinoma Progression in Mice
ARTICLE https://doi.org/10.1038/s42003-021-01982-w OPEN A collagen glucosyltransferase drives lung adenocarcinoma progression in mice Hou-Fu Guo 1, Neus Bota-Rabassedas 1, Masahiko Terajima 2, B. Leticia Rodriguez1, Don L. Gibbons 1, Yulong Chen1, Priyam Banerjee1, Chi-Lin Tsai 3, Xiaochao Tan1, Xin Liu1, Jiang Yu1, Michal Tokmina-Roszyk4, Roma Stawikowska4, Gregg B. Fields4, Mitchell D. Miller 5, Xiaoyan Wang3, Juhoon Lee6,7, Kevin N. Dalby6,7, Chad J. Creighton 8,9, George N. Phillips Jr 5,10, John A. Tainer 3, Mitsuo Yamauchi2 & ✉ Jonathan M. Kurie 1 Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and 1234567890():,; is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen’s amino- and carboxy-terminal telopeptides to create stable collagen cross-links. Here, we show that electrostatic interac- tions between the LH domain active site and collagen determine the unique telopeptidyl lysyl hydroxylase (tLH) activity of LH2. However, CRISPR/Cas-9-mediated inactivation of tLH activity does not fully recapitulate the inhibitory effect of LH2 knock out on LUAD growth and metastasis in mice, suggesting that LH2 drives LUAD progression, in part, through a tLH- independent mechanism. Protein homology modeling and biochemical studies identify an LH2 isoform (LH2b) that has previously undetected collagen galactosylhydroxylysyl glucosyl- transferase (GGT) activity determined by a loop that enhances UDP-glucose-binding in the GLT active site and is encoded by alternatively spliced exon 13 A. -
Hypoxia-Inducible Factors and RAB22A Mediate Formation of Microvesicles That Stimulate Breast Cancer Invasion and Metastasis
Hypoxia-inducible factors and RAB22A mediate formation of microvesicles that stimulate breast cancer invasion and metastasis Ting Wanga,b, Daniele M. Gilkesb,c, Naoharu Takanob,c, Lisha Xiangb,c, Weibo Luob,d, Corey J. Bishope, Pallavi Chaturvedib,c, Jordan J. Greene, and Gregg L. Semenzab,c,d,f,g,h,i,1 aDepartment of Hematology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; and bVascular Program, Institute for Cell Engineering, cMcKusick-Nathans Institute of Genetic Medicine, and Departments of dBiological Chemistry, eBiomedical Engineering, fOncology, gPediatrics, hMedicine, and iRadiation Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 Contributed by Gregg L. Semenza, May 30, 2014 (sent for review May 2, 2014) Extracellular vesicles such as exosomes and microvesicles (MVs) melanoma cells into the peripheral blood of mice induced are shed by cancer cells, are detected in the plasma of cancer prometastatic behavior of bone marrow cells, and the small patients, and promote cancer progression, but the molecular mech- GTPase RAB27A was required for exosome biogenesis in mel- anisms regulating their production are not well understood. Intra- anoma cells (10). In HeLa cells, RAB27A and RAB27B were tumoral hypoxia is common in advanced breast cancers and each required for exosome biogenesis, based on different loss-of- is associated with an increased risk of metastasis and patient function phenotypes (11). RAB27A loss of function in 4T1 breast mortality that is mediated in part by the activation of hypoxia- cancer cells inhibited both primary tumor growth and lung me- inducible factors (HIFs). In this paper, we report that exposure of tastasis (12). -
Collagen Type XVIII (H-140): Sc-25720
SANTA CRUZ BIOTECHNOLOGY, INC. Collagen Type XVIII (H-140): sc-25720 The Power to Question BACKGROUND APPLICATIONS Type XV and XVIII collagens form the new subgroup MULTIPLEXIN, within the Collagen Type XVIII (H-140) is recommended for detection of Collagen α1 diverse family of collagens, which contains nineteen distinct types of collagens Type XVIII of mouse, rat and human origin by Western Blotting (starting found in vertebrates. Both type XV and XVIII collagens are characterized by dilution 1:200, dilution range 1:100-1:1000), immunoprecipitation [1–2 µg extensive interruptions in their collagenous sequences. Members of the MUL- per 100–500 µg of total protein (1 ml of cell lysate)] and immunofluores- TIPLEXIN subgroup contain polypeptides with multiple triple-helical domains cence (starting dilution 1:50, dilution range 1:50-1:500). separated and flanked by non-triple-helical regions. Type XV is predominantly Suitable for use as control antibody for Collagen Type XVIII siRNA (h): expressed in internal organs such as adrenal gland, kidney and pancreas. Type sc-43072 and Collagen Type XVIII siRNA (m): sc-43073. XVIII encodes two different α1 chains, which have different signal peptides and variant N-terminal non-collagenous NC1 domains of 495 and 303 amino Molecular Weight of Collagen Type XVIII: 20-22 kDa. acids. The long variant NC1-434 Type XVIII mRNAs are prominently expressed Positive Controls: rat C6 glioblastoma, human PBL or rat lung extract: sc-2396. in liver, while the variant NC1-303 mRNAs are predominantly expressed in heart, kidney, placenta, prostate, ovaries, skeletal muscle and small intestine. RECOMMENDED SECONDARY REAGENTS Endostatin is a fragment of the C-terminal domain NC1 of collagen XV and XVIII that inhibits angiogenesis and tumor growth. -
Inherited Connective Tissue Disorders of Collagens: Lessons from Targeted Mutagenesis
13 Inherited Connective Tissue Disorders of Collagens: Lessons from Targeted Mutagenesis Christelle Bonod-Bidaud and Florence Ruggiero Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon, UMR CNRS 5242, University Lyon 1, France 1. Introduction The extracellular matrix (ECM) is the cell structural environment in tissues and organs. The ECM is a dynamic structure that it is constantly remodelled. It contributes to tissue integrity and mechanical properties. It is also essential for maintaining tissue homeostasis, morphogenesis and differentiation, which it does, through specific interactions with cells. The ECM is composed of a mixture of water and macromolecules classified into four main categories: collagens, proteoglycans, elastic proteins, and non-collagenous glycoproteins (also called adhesive glycoproteins). The nature, concentration and ratio of the different ECM components are all important factors in the regulation of the assembly of complex tissue-specific networks tuned to meet mechanical and biological requirements of tissues. Collagens form a superfamily of 28 trimeric proteins, distinguishable from the other ECM components by their particular abundance in tissues (collagens represent up to 80-90% of total proteins in skin, tendon and bones) and their capacity to self-assemble into supramolecular organized structures (the best known being the banded fibers). The collagen superfamily is highly complex and shows a remarkable diversity in structure, tissue distribution and function (Ricard-Blum and Ruggiero, 2005). The importance -
List of Publications Taina Pihlajaniemi
List of publications Taina Pihlajaniemi 1 April, 2016 A Peer-reviewed scientific articles Journal article (refereed), original research; review article, literature review, systematic review; book section, chapters in research books; conference proceedings A.1 Savolainen E-R, Kero M, Pihlajaniemi T, and Kivirikko KI. Deficiency of galactosylhydroxylysyl glucosyltransferase, an enzyme of collagen synthesis, in a family with dominant epidermolysis bullosa simplex. N Engl J Med 304: 197-204, 1981 A.2 Pihlajaniemi T, Myllylä R, Alitalo K, Vaheri A, and Kivirikko KI. Post-translational modifications in the biosynthesis of type IV collagen by a human tumor cell line. Biochemistry 20: 7409-7415, 1981 A.3 Anttinen H, Puistola U, Pihlajaniemi T, and Kivirikko KI. Differences between proline and lysine hydroxylations in their inhibition by zinc or by ascorbate deficiency during collagen synthesis in various cell types. Biochim Biophys Acta 674: 336-344, 1981 A.4 Pihlajaniemi T, Myllylä R, Kivirikko KI, and Tryggvason K. Effects of streptozotocin diabetes, glucose, and insulin on the metabolism of type IV collagen and proteoglycan in murine basement membrane-forming EHS tumor tissue. J Biol Chem 257: 14914-14920, 1982 A.5 de Wet WJ, Pihlajaniemi T, Myers J, Kelly TE, and Prockop DJ. Synthesis of a shortened pro- 2(I) chain and decreased synthesis of pro- 2(I) chains in a proband with osteogenesis imperfecta. J Biol Chem 258: 7721-7728, 1983 A.6 Oikarinen J, Pihlajaniemi T, Hämäläinen L, and Kivirikko KI. Cortisol decreases the cellular concentration of translatable procollagen mRNA species in cultured human skin fibroblasts. Biochim Biophys Acta 741: 297-302, 1983 A.7 Myllylä R, Koivu J, Pihlajaniemi T, and Kivirikko KI.