DOCSLIB.ORG

Illegitimate DNA Integration in Mammalian Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Illegitimate DNA Integration in Mammalian Cells Gene Therapy (2003) 10, 1791–1799 & 2003 Nature Publishing Group All rights reserved 0969-7128/03 $25.00 www.nature.com/gt REVIEW Illegitimate DNA integration in mammalian cells HWu¨ rtele1, KCE Little2 and P Chartrand2,3 1Programme de Biologie Mole´culaire, Universite´ de Montre´al, Montre´al, Canada; 2Department of Medicine, Division of Experimental Medicine, McGill University, Montre´al, Que´bec, Canada; and 3Centre Hospitalier de l’Universite´ de Montre´al and De´partement de Pathologie et de Biologie Cellulaire, Universite´ de Montre´al, Montre´al, Que´bec, Canada Foreign DNA integration is one of the most widely exploited therapy procedures can result in illegitimate integration of cellular processes in molecular biology. Its technical use introduced sequences and thus pose a risk of unforeseeable permits us to alter a cellular genome by incorporating a genomic alterations. The choice of insertion site, the degree fragment of foreign DNA into the chromosomal DNA. This to which the foreign DNA and endogenous locus are modified process employs the cell’s own endogenous DNA modifica- before or during integration, and the resulting impact on tion and repair machinery. Two main classes of integration structure, expression, and stability of the genome are all mechanisms exist: those that draw on sequence similarity factors of illegitimate DNA integration that must be con- between the foreign and genomic sequences to carry out sidered, in particular when designing genetic therapies. homology-directed modifications, and the nonhomologous or Gene Therapy (2003) 10, 1791–1799. doi:10.1038/ ‘illegitimate’ insertion of foreign DNA into the genome. Gene sj.gt.3302074 Keywords: illegitimate DNA integration; DNA repair; transgenesis; recombination; mutagenesis Introduction timate integration. Homology-dependent genome mod- ifications rely on mechanisms that make use of sequence The development of methods to manipulate and modify similarities between the incoming DNA and the targeted the genome is one key achievement of molecular biology. locus to induce homologous recombination. These Foreign DNA integration is one of those widely used processes usually give rise to predictable results, such techniques, allowing us to modify a cell’s genetic that the configurations of the modified loci, and of the content. The integration process begins with the delivery integrated DNA, can be predefined by the investigators. of the DNA to the cell. Many transfection procedures Techniques employing these mechanisms have numer- have been developed that enable DNA to enter into the ous applications.11 Among others, small fragment homo- cytoplasm, but its passage into the nucleus is mainly logous recombination (SFHR) employs short (400– mediated by cellular processes.1,2 After its entry into the 800 bp) DNA fragments to modify any locus and can nucleus, a large proportion of the foreign DNA is rapidly be used to correct punctual mutations.12 Other techni- degraded or diluted among subsequent cell divisions.3 ques, such as classic gene targeting, are routinely used to However, molecules containing an origin of replication introduce DNA to a specific site or to knock-out genes.13 (typically derived from viruses) can persist for long However, while these methods hold great promise for periods as extrachromosomally replicating episomes the field of gene therapy, and for the development of under certain conditions (such as expression of viral experimental tools to investigate genome dynamics, we tumour antigens or association with the nuclear matrix).4 must take into account the fact that a significant Alternatively, in approximately one cell per thousand, proportion of cells integrate DNA into their genomes the introduced foreign DNA will integrate into chromo- via homology-independent means, collectively referred somal DNA (although this figure may vary somewhat to as illegitimate integration. Illegitimate integration depending on cell type).5,6 This phenomenon is not events are usually more frequent than homology- limited to laboratory transfections as many natural directed integration: the ratio of homology versus non- cellular processes, such as integration of DNA from homology-dependent integration can be anywhere from apoptotic bodies,7 repair of chromosomal lesions by 4:1 to 1:1 000 000, depending on experimental conditions insertion of mitochondrial DNA,8 or retrotransposition and cell types, but illegitimate integration is typically events, give rise to de novo integration of DNA.9,10 Thus 1000–10 000 times more frequent than targeted integra- DNA integration may be seen as an ongoing natural tion (see Smith14 and references therein). These mechan- process, which can be harnessed to artificially introduce isms give rise to much less predictable integrated modifications to a cell’s genetic content. structures, as one usually cannot preselect the genomic DNA can become integrated into chromosomes by two site of integration, nor the resulting foreign DNA– main processes: homology-dependent means and illegi- chromosome structure. The conditions governing how the cell chooses which mode of integration to employ are Correspondence: Dr P Chartrand, 1560 Sherbrooke Est, Montreal, Que´bec, unclear, but may be dictated by cell cycle-dependent Canada H2L 4M1 availability of DNA-modifying machinery: homology- Received 10 December 2002; accepted 28 March 2003 dependent machinery is available mainly in G2/S, while Illegitimate DNA integration HWu¨rtele et al 1792 homology-independent means are present during most suggesting that viral factors can also be involved in the of the cell cycle (see below).15 integration.18–20 Thus, some viral DNA integration events It must therefore be stressed that DNA often integrates appear to be identical in nature to any type of foreign into the genome in ways that we do not fully understand, DNA integration (for example SV40 DNA), while those nor totally control. In the context of gene therapy, it is depending on viral-encoded machinery are clearly likely that local or systemic delivery of DNA to cells will different. These types of virus-specific events will not eventually result in illegitimate integration of DNA be considered here, but it should be noted that many of molecules. This appears to happen at a low fre- the mechanisms involved in the illegitimate integration quency.16,17 However, we will see in this review that of foreign DNA could also be involved, at one point or the resultant integrated structure can be surprisingly another, in viral DNA integration. complex and unpredictable compared to the expected structure of targeted integration, making it difficult to evaluate the risks inherent in these events (see Figure 1). Extrachromosomal DNA is often modified A brief note regarding the source of integrating DNA before integration into chromosomal DNA discussed in this review, since much of the early work done on illegitimate integration described the integration The first part of this article addresses the status of foreign of viral DNA. Viral DNA per se appears to integrate into DNA before, during or shortly after integration (see the genome in the same way as any foreign DNA. Figure 2a). As mentioned earlier, it has been shown that However, available data suggest that viral-encoded most transfected DNA is rapidly degraded upon integrases (such as with retroviruses) may target incom- introduction into cells. Molecules that are not degraded ing DNA to particular genomic loci, and influence (at can be modified extrachromosomally in many different least in part) the mechanisms of integration. Indeed, ways. Homologous recombination can modify extra- characterization of retroviral integration processes has chromosomal DNA very efficiently using either inter- or shown only a partial dependence on host cell factors, intramolecular sequence homology and can result in multiple products depending on the organization of the sequences sharing identity.21–26 The end products of extrachromosomal homologous recombination are simi- lar to those obtained during chromosomal homologous recombination, suggesting that at least some mechanisms are shared by the two processes.27–31 Transfected DNA can also be mutated at high frequency (on the order of 1%) by homology-indepen- dent means including point mutations, deletions, and more complex rearrangements such as insertion of genomic DNA.32–34 (see also our unpublished work). Linear extrachromosomal DNA can also be efficiently circularized in the nucleus, and different molecules can be joined together to form concatamers35 by processes referred to as nonhomologous end joining (NHEJ). NHEJ often involves short sequence homology between the joined ends, and additions or deletions of approximately 25 nucleotides or less at the junctions.34,36,37 Similar processes have been shown to occur during chromoso- mal double-strand break (DSB) repair,27,29,38 which again suggests that extrachromosomal and chromosomal re- pair are mediated by similar cellular machinery. Integrated DNA is modified in the same ways as extrachromosomal DNA Studies aimed at characterizing integrated foreign DNA reveal modifications very similar to those observed in nonintegrating extrachromosomal DNA. However, it must be kept in mind that it is not known whether the integrated DNA was modified before or during integra- Figure 1 Difference between homology-directed genome modification and tion, since the observations are typically made after the illegitimate DNA integration. (a) The chromosome structure resulting integration has taken place.
Load more

Recommended publications
  • The Human Genome Project
    TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences.
    [Show full text]
  • Genetics As Explanation: Limits to the Human Genome Project’ (2006, 2009)
    els a0026653.tex V2 - 08/29/2016 4:00 P.M. Page 1 Version 3 a0026653 Genetics as Explanation: Introductory article Article Contents Limits to the Human • Definitions • Metaphors and Programs Genome Project • Metaphors and Expectations • Genome is Not a Simple Program Irun R Cohen, The Weizmann Institute of Science, Rehovot, Israel • Microbes, Symbiosis and the Holobiont Henri Atlan, Ecole des Hautes Etudes en Sciences Sociales, Paris, France and Hadas- • Stem Cells Express Multiple Genes • sah University Hospital, Jerusalem, Israel Meaning: Line or Loop? AU:1 • Self-Organisation and Program Sol Efroni, Bar-Ilan University, Ramat Gan, Israel • Complexity, Reduction and Emergence • Evolving Genomes AU:2 Based in part on the previous versions of this eLS article ‘Genetics as Explanation: Limits to the Human Genome Project’ (2006, 2009). • The Environment and the Genome • Language Metaphor • Tool and Toolbox Metaphors • Conclusion Online posting date: 14th October 2016 Living organisms are composed of cells and all biological evolution, single organisms, populations of organisms, living cells contain a genome, the organism’s stock species, cells and molecules, heredity, embryonic development, of deoxyribonucleic acid (DNA). The role of the health and disease and life management. These are quite diverse genome has been likened to a computer program subjects, and the people who study them would seem to use the term gene in distinctly different ways. But genetics as a whole that encodes the organism’s development and its is organised by a single unifying principle, the deoxyribonucleic subsequent response to the environment. Thus, the acid (DNA) code; all would agree that the information borne by organism and its fate can be explained by genetics, a gene is linked to particular sequences of DNA.
    [Show full text]
  • Connecting Myelin-Related and Synaptic Dysfunction In
    www.nature.com/scientificreports OPEN Connecting myelin-related and synaptic dysfunction in schizophrenia with SNP-rich Received: 24 October 2016 Accepted: 27 February 2017 gene expression hubs Published: 07 April 2017 Hedi Hegyi Combining genome-wide mapping of SNP-rich regions in schizophrenics and gene expression data in all brain compartments across the human life span revealed that genes with promoters most frequently mutated in schizophrenia are expression hubs interacting with far more genes than the rest of the genome. We summed up the differentially methylated “expression neighbors” of genes that fall into one of 108 distinct schizophrenia-associated loci with high number of SNPs. Surprisingly, the number of expression neighbors of the genes in these loci were 35 times higher for the positively correlating genes (32 times higher for the negatively correlating ones) than for the rest of the ~16000 genes. While the genes in the 108 loci have little known impact in schizophrenia, we identified many more known schizophrenia-related important genes with a high degree of connectedness (e.g. MOBP, SYNGR1 and DGCR6), validating our approach. Both the most connected positive and negative hubs affected synapse-related genes the most, supporting the synaptic origin of schizophrenia. At least half of the top genes in both the correlating and anti-correlating categories are cancer-related, including oncogenes (RRAS and ALDOA), providing further insight into the observed inverse relationship between the two diseases. Gene expression correlation, protein-protein interaction and other high-throughput experiments in the post-genomic era have revealed that genes tend to form complex, scale-free networks where most genes have a few connections with others and a few have a high number of interactions, commonly referred to as “hubs”, estab- lishing them as important central genes in these gene networks1.
    [Show full text]
  • A New Entrez Database Transitioning from Locuslink to Entrez
    NCBI News National Center for Biotechnology Information National Library of Medicine National Institutes of Health Spring 2004 Department of Health and Human Services Transitioning from LocusLink to Entrez Gene Cancer Chromosomes: a New Entrez Database A gene-based view of annotated The Entrez Gene help document genomes is essential to capitalize on provides tips to ease the transition Three databases, the NCI/NCBI the increase in the sequencing and for LocusLink users to the current SKY (Spectral Karyotyping)/M- analysis of model genomes. The Entrez Gene database. FISH (Multiplex-FISH) and CGH Entrez Gene database has been (Comparative Genomic The default display format for developed to supply key connections Hybridization) Database, the NCI Entrez Gene is the graphics display between maps, sequences, expression Mitelman Database of Chromosome shown in Figure 1 for BMP7, which profiles, structure, function, homolo- Aberrations in Cancer, and the NCI resembles the traditional view of a gy data, and the scientific literature. Recurrent Chromosome Aberrations LocusLink record. The array of col- Unique identifiers are assigned to in Cancer databases are now integrat- ored boxes at the head of LocusLink genes with defining sequence, genes ed into NCBI’s Entrez system as the reports that provide links to gene- with known map positions, and “Cancer Chromosomes” database. related resources is replaced by the genes inferred from phenotypic Cancer Chromosomes supports “Links” menu in Gene, which information. These gene identifiers searches for cytogenetic, clinical, or includes additional links, such as are tracked, and functional informa- reference information using the flexi- those to Books, GEO, UniSTS, and tion is added when available.
    [Show full text]
  • ALK, the Chromosome 2 Gene Locus Altered by the T(2;5) in Non
    Oncogene (1997) 14, 2175 ± 2188 1997 Stockton Press All rights reserved 0950 ± 9232/97 $12.00 ALK, the chromosome 2 gene locus altered by the t(2;5) in non-Hodgkin's lymphoma, encodes a novel neural receptor tyrosine kinase that is highly related to leukocyte tyrosine kinase (LTK) Stephan W Morris1,2,4, Clayton Naeve3, Prasad Mathew5, Payton L James1, Mark N Kirstein1, Xiaoli Cui1 and David P Witte6,7 Departments of 1Experimental Oncology, 2Hematology-Oncology and 3Virology and Molecular Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105; 4Department of Pediatrics, University of Tennessee College of Medicine, Memphis, Tennessee 38163; 5Department of Pediatrics, Medical College of Ohio, Toledo, Ohio 43699; 6Department of Pathology, University of Cincinnati College of Medicine and 7Division of Pathology, Children's Hospital Research Foundation, Cincinnati, Ohio 45229, USA Anaplastic Lymphoma Kinase (ALK) was originally Introduction identi®ed as a member of the insulin receptor subfamily of receptor tyrosine kinases that acquires transforming Diverse cellular processes such as division, differentia- capability when truncated and fused to nucleophosmin tion, survival, metabolism, and motility can all be (NPM) in the t(2;5) chromosomal rearrangement regulated through binding of cognate ligands to their associated with non-Hodgkin's lymphoma, but further speci®c receptor tyrosine kinases (RTKs) (reviewed in insights into its normal structure and function are Schlessinger and Ullrich, 1992; Fantl et al., 1993). The lacking. Here, we characterize a full-length normal common structural features of the RTKs include an human ALK cDNA and its product, and determine the extracellular ligand-binding region, a hydrophobic pattern of expression of its murine homologue in membrane-spanning segment and a cytoplasmic do- embryonic and adult tissues as a ®rst step toward the main that carries the catalytic function.
    [Show full text]
  • Genetic Nomenclature Zhiliang Hu Iowa State University, [email protected]
    Animal Science Publications Animal Science 2012 Genetic Nomenclature Zhiliang Hu Iowa State University, [email protected] James M. Reecy Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Animal Sciences Commons, and the Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ans_pubs/170. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Book Chapter is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genetic Nomenclature Abstract Genetics includes the study of genotypes, phenotypes and the mechanisms of genetic control between them. Genetic terms describe the processes, genes, alleles and traits with which genetic phenomena are described and examined. In this chapter we will concentrate on the discussions of genetic term standardizations and, at the end of the chapter, we will list some terms relevant to genetic processes and concepts in a Genetic Glossary. Disciplines Agriculture | Animal Sciences | Genetics Comments This is a chapter from The Genetics of the Dog, 2nd edition, chapter 23 (2012): 496. Posted with permission. This book chapter is available at Iowa State University
    [Show full text]
  • Viral Component of the Human Genome V
    ISSN 0026-8933, Molecular Biology, 2017, Vol. 51, No. 2, pp. 205–215. © Pleiades Publishing, Inc., 2017. Original Russian Text © V.M. Blinov, V.V. Zverev, G.S. Krasnov, F.P. Filatov, A.V. Shargunov, 2017, published in Molekulyarnaya Biologiya, 2017, Vol. 51, No. 2, pp. 240–250. REVIEWS UDC 578.264.9 Viral Component of the Human Genome V. M. Blinova, V. V. Zvereva, G. S. Krasnova, b, c, F. P. Filatova, d, *, and A. V. Shargunova aMechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia bEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111911 Russia cOrekhovich Research Institute of Biomedical Chemistry, Moscow, 119121 Russia dGamaleya Research Center of Epidemiology and Microbiology, Moscow, 123098 Russia *e-mail: [email protected] Received December 27, 2015; in final form, April 27, 2016 Abstract⎯Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. How- ever, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways.
    [Show full text]
  • Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse Janan T
    ILAR Journal, 2017, Vol. 58, No. 1, 17–41 doi: 10.1093/ilar/ilx013 Article Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse Janan T. Eppig Janan T. Eppig, PhD, is Professor Emeritus at The Jackson Laboratory in Bar Harbor, Maine. Address correspondence to Dr. Janan T. Eppig, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 or email [email protected] Abstract The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. Key words: database; genetics; genomics; human disease model; informatics; model organism; mouse; phenotypes Introduction strains and special purpose strains that have been developed The laboratory mouse is an essential model for understanding provide fertile ground for population studies and the potential human biology, health, and disease.
    [Show full text]
  • Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
    Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons.
    [Show full text]
  • The Proteins of Keratoconus: a Literature Review Exploring Their Contribution to the Pathophysiology of the Disease
    Adv Ther (2019) 36:2205–2222 https://doi.org/10.1007/s12325-019-01026-0 REVIEW The Proteins of Keratoconus: a Literature Review Exploring Their Contribution to the Pathophysiology of the Disease Eleftherios Loukovitis . Nikolaos Kozeis . Zisis Gatzioufas . Athina Kozei . Eleni Tsotridou . Maria Stoila . Spyros Koronis . Konstantinos Sfakianakis . Paris Tranos . Miltiadis Balidis . Zacharias Zachariadis . Dimitrios G. Mikropoulos . George Anogeianakis . Andreas Katsanos . Anastasios G. Konstas Received: June 11, 2019 / Published online: July 30, 2019 Ó The Author(s) 2019 ABSTRACT abnormalities primarily relate to the weakening of the corneal collagen. Their understanding is Introduction: Keratoconus (KC) is a complex, crucial and could contribute to effective man- genetically heterogeneous multifactorial agement of the disease, such as with the aid of degenerative disorder characterized by corneal corneal cross-linking (CXL). The present article ectasia and thinning. Its incidence is approxi- critically reviews the proteins involved in the mately 1/2000–1/50,000 in the general popula- pathophysiology of KC, with particular tion. KC is associated with moderate to high emphasis on the characteristics of collagen that myopia and irregular astigmatism, resulting in pertain to CXL. severe visual impairment. KC structural Methods: PubMed, MEDLINE, Google Scholar and GeneCards databases were screened for rel- evant articles published in English between January 2006 and June 2018. Keyword combi- Enhanced Digital Features To view enhanced digital nations of the words ‘‘keratoconus,’’ ‘‘risk features for this article go to https://doi.org/10.6084/ m9.figshare.8427200. E. Loukovitis K. Sfakianakis Hellenic Army Medical Corps, Thessaloniki, Greece Division of Surgical Anatomy, Laboratory of Anatomy, Medical School, Democritus University of E.
    [Show full text]
  • An Evaluation of Cancer Subtypes and Glioma Stem Cell Characterisation Unifying Tumour Transcriptomic Features with Cell Line Expression and Chromatin Accessibility
    An evaluation of cancer subtypes and glioma stem cell characterisation Unifying tumour transcriptomic features with cell line expression and chromatin accessibility Ewan Roderick Johnstone EMBL-EBI, Darwin College University of Cambridge This dissertation is submitted for the degree of Doctor of Philosophy Darwin College December 2016 Dedicated to Klaudyna. Declaration • I hereby declare that except where specific reference is made to the work of others, the contents of this dissertation are original and have not been submitted in whole or in part for consideration for any other degree or qualification in this, or any other university. • This dissertation is my own work and contains nothing which is the outcome of work done in collaboration with others, except as specified in the text and Acknowledge- ments. • This dissertation is typeset in LATEX using one-and-a-half spacing, contains fewer than 60,000 words including appendices, footnotes, tables and equations and has fewer than 150 figures. Ewan Roderick Johnstone December 2016 Acknowledgements This work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC, Ref:1112564) and supported by the European Molecular Biology Laboratory (EMBL) and its outstation, the European Bioinformatics Institute (EBI). I have many people to thank for assistance in preparing this thesis. First and foremost I must thank my supervisor, Paul Bertone for his support and willingness to take me on as a student. My thanks are also extended to present and past members of the Bertone group, particularly Pär Engström and Remco Loos who have provided a great deal of guidance over the course of my studentship.
    [Show full text]
  • MAL Antibody / Myelin and Lymphocyte Protein (RQ6195)
    MAL Antibody / Myelin and lymphocyte protein (RQ6195) Catalog No. Formulation Size RQ6195 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Affinity purified Buffer Lyophilized from 1X PBS with 2% Trehalose and 0.0125% sodium azide UniProt P21145 Applications Western blot : 1-2ug/ml Limitations This MAL antibody is available for research use only. Western blot testing of human 1) Jurkat, 2) Raji and 3) HL60 cell lysate with MAL antibody. Predicted molecular weight ~17 kDa. Description Myelin and lymphocyte protein is a protein that in humans is encoded by the MAL gene. The protein encoded by this gene is a highly hydrophobic integral membrane protein belonging to the MAL family of proteolipids. The protein has been localized to the endoplasmic reticulum of T-cells and is a candidate linker protein in T-cell signal transduction. In addition, this proteolipid is localized in compact myelin of cells in the nervous system and has been implicated in myelin biogenesis and/or function. The protein plays a role in the formation, stabilization and maintenance of glycosphingolipid-enriched membrane microdomains. Down-regulation of this gene has been associated with a variety of human epithelial malignancies. Alternative splicing produces four transcript variants which vary from each other by the presence or absence of alternatively spliced exons 2 and 3. Application Notes Optimal dilution of the MAL antibody should be determined by the researcher. Immunogen Amino acids HAVFSLIRWKSS from the human protein were used as the immunogen for the MAL antibody.
    [Show full text]