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CD44 As a Hematopoietic Stem Cell Marker

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CD44 as a Hematopoietic stem cell marker Zur Erlangung des akademischen Grades eines DOKTORS DER NATURWISSENSCHAFTEN (Dr. rer. nat.) Fakultät für Chemie und Biowissenschaften Karlsruher Institut für Technologie (KIT) – Universitätsbereich vorgelegte DISSERTATION Von Rahul Singh aus Indien 2011 Dekan: Prof. Dr. Stefan Bräse Referent: Prof. Dr. Margot Zöller Korreferent: Prof. Dr. Andrew Cato Tag der mündlichen Prüfung: 15.04.2011 i “Never give up on what you want to do. A person with real big dreams is more powerful than all the facts” To my loving parents and my family…. ii Table of Contents Abbreviations………………………………………………………………………........1 Zusammenfassung……………………………………………………………………...4 1: Introduction………………………………………………………………………….6 1. Stem cells and Hematopoietic stem cells…………………………………..6 1.1 Definition of stem cells………………………………………………………...6 1.2 Hematopoietic stem cells and Hematopoiesis………………………………8 1.2.1 Hematopoietic stem cells……………………………………………...….8 1.2.2 Hematopoiesis………………………………………………………..…..10 1.3 Characterization of HSC…………………………………………………..…13 1.4 The importance of the HSC niche………………………………………..…15 1.5 The clinical demand on HSC…………………………………………….….17 1.6 Sources of HSC……………………………………………………………....18 1.6.1 Bone marrow & Mobilized peripheral blood…………………………...18 1.6.2 Umbilical cord blood……………………………………………………..18 1.6 3 Embryonic stem cells………………………………………………….…19 2. CD44 molecule………………………………………………………………....20 2.1 Structure ……………………………………………………………………....20 2.2 Hyaluron binding, amino terminal domain ………………………………….22 2.3 Stem structure………………………………………………………………….22 2.4 Transmembrane and cytoplasmic domain……………………………...…..23 2.5 CD44 functions…………………………………………………………......….25 2.5.1 Cell adhesion and migration……………………………………………..25 2.5.2 Interaction with the cytoskeleton……………………………...………...26 2.5.3 Interaction with cytokines, chemokines and enzymes………………...28 2.5.4 CD44 as a co-receptor and signalling……………………………...…...29 2.6 CD44 in hematopoietic stem cells……………………………………..…….35 3. AIM…………………………………………………………………………….......36 2: Materials and methods………………………………………………………........37 2.1 Materials………………………………………………………………….….....37 2.1.1 Animals……………………………………………………………….…..37 iii 2.1.2 Bacterial strain………………………………………………………….…37 2.1.3 Cell lines………………………………………………………..…….…...37 2.1.4 Primers………………………………………………………...…………..38 2.1.5 Primary antibodies…………………………………………………….....38 2.1.6 Secondary antibodies…………………………………………………....41 2.1.7 Inhibitors and enzymes……………………………………………….....42 2.1.8 Instruments…………………………………………………………….....42 2.1.9 Miscellaneous ……………………………………………………………44 2.1.10 Chemicals…………………………………………………………….....45 2.1.11 Buffers and solutions…………………………………………………..48 2.2 Methods…………………………………………………………………….…..49 2.2.1 Molecular Biology……………………………………………………....49 2.2.1.1 Chemical competent cells………………………………………….....49 2.2.1.2 Transformation………………………………………………………....49 2.2.1.3 Mini-prep…………………………………………………………….….49 2.2.1.4 Enzymatic restriction digestion……………………………….………50 2.2.1.5 Midi-prep……………………………………………………….……….50 2.2.1.6 RNA preparation, cDNA synthesis and amplification………….…..50 2.2.1.7 DNA gel electrophoresis………………………………………….…...51 2.2.2 Protein chemistry………………………………………………….……52 2.2.2.1 Antibody purification……………………………………………….…..52 2.2.2.2 Column preparation……………………………………………….…...52 2.2.2.3 Purification of the CD44 recombinant soluble molecule……….…..53 2.2.2.4 Biorad assay………………………………………………………....…53 2.2.2.5 Pull down assay …………………………………………………….….53 2.2.2.6 SDS-PAGE………………………………………………………….…..54 2.2.2.7 Immunoprecipitation …………………………………………….….....54 2.2.2.8 Western blotting………………………………………………….……..55 2.2.2.9 Silver staining …………………………………………………….….…55 2.2.3 Cell biology………………………………………………………….…...55 2.2.3.1 Cell culture………………………………………………………...........55 iv 2.2.3.2 Magnetic beads separation…………………………………………..56 2.2.3.3 Flow cytometry………………………………………………………...57 2.2.3.4 Apoptosis assay…………………………………………………….…58 2.2.3.5 Proliferation assay…………………………………………………….58 2.2.3.6 Phosphatase assay…………………………………………………...58 2.2.3.7 Sucrose gradient centrifugation …………………………………….59 2.2.3.8 Cytosol, nuclei and mitochondrial preparation……………………..59 2.2.3.9 Transfection of adherent cells ……………………………………….59 2.2.4 Animal Experiment ………………………………………………….…60 2.2.4.1 Long term bone marrow culture (LTBMC)…………………………..60 2.2.4.2 Reconstitution and tumor cell injection……………………………...60 2.2.5 Statistical analysis……………………………………………………..60 3: Results………………………………………………………………………………..61 Part-I The importance of CD44 in the crosstalk between HSC and bone marrow stroma………………………………………………61 1. CD44 expression, associating molecules & ligands on HSC & niche cells………………………………………………………………….61 1.1 CD44 expression on BMC and LTBMC stroma cells…………………..61 1.1.1 RT-PCR profiling on BMC subpopulations…………………………....65 1.1.2 Adhesion molecule profile on BMC & LTBMC stroma ………….......67 1.1.3 Cytokines & cytokine/chemokine receptor expression on BMC & LTBMC stroma………………………………………………...68 1.2 CD44 associating molecules in HSC & LTBMC stroma cells………....69 1.2.1 CD44 co-expression with stem cells, progenitor cells and leukocyte markers on BMC/HSC & LTBMC stroma……………….…69 1.2.2 CD44 co-expression with cytokine/chemokine receptor on BMC/HSC and LTBMC stroma………………………………………....72 1.2.3 CD44 co-expression with adhesion molecules on BMC/HSC and LTBMC stroma………………………………………………………74 1.2.4 CD44 associating molecules on BM, HSC & LTBMC stroma……….76 1.3 Potential ligands on HSC and stroma cells for CD44 and CD44v…….78 v 1.3.1 Generation of soluble recombinant CD44s & CD44v7…………….…78 1.3.2 Pulldown assay…………………………………………………………...80 1.4 Functional consequences of HSC CD44 interaction with LTBMC stroma………………………………………………………………82 1.4.1 Role of HSC CD44 interaction in the maintenance of quiescence……………………………………………………………..82 1.4.2 Role of HSC CD44 interaction in the apoptosis resistance……….83 Part-II The importance of CD44 in the crosstalk between leukemia and the bone marrow stroma…………………………………………...86 2.1 Anti-panCD44 interferes with hematopoiesis and thymoma growth...86 2.2 Anti-CD44 promotes thymoma cell apoptosis…………………………89 2.3 Apoptosis induction, loss of mitochondrial membrane polarization and caspase-9 activation…………………………………………….…...91 2.4 Anti-CD44 induces ERK inhibition through PP2A………………….....94 2.5 ERK1/2 inhibition promotes apoptosis and caspase-9 cleavage…....98 4: Discussion……………………………………………………………….…………..101 4.1 CD44 expression in HSC and bone marrow stroma cells……….….....101 4.2 CD44 associating molecule in HSC and bone marrow stroma cells....102 4.3 Functional consequences of HSC CD44 interaction with bone marrow stroma cells………………………………………………….…….102 4.4 CD44 activities in leukemic cells……………………………...………...103 4.5 T lymphoma cells are less CD44-dependent than hematopoietic progenitors…………………………………………………………………….....104 4.6 A CD44 antibody blockade promotes death receptor-independent leukemic T cell apoptosis…………………………………………………..…..104 4.7 Anti-CD44-promoted apoptosis proceeds via CD44 redistribution and PP2A association…………………………………………………………….…105 4.8 CD44-associated PP2A promotes mitochondrial membrane de- stabilization via ERK1/2 dephosphorylation………………………………....105 5: Summary………………………………………………………………………….….107 6: References……………………………………………………………………….…..109 Acknowledgements………………………………………………………………..…..127 Curriculum vitae………………………………………………………….…………….128 vi Figures Part I Figure 1A Expression of stem cells, progenitors and mature leukocyte marker in BMC/HSC……………………………………………………….…62 Figure 1B Expression of stem cells, progenitors and mature leukocyte marker in LTBMC- stroma…………………………………………………...63 Figure 1C Expression of CD44 and CD44v in BMC sub populations…………….…63 Figure 1D Expression of CD44 and CD44v in LTBMC-stroma and S17 cells……...64 Figure 1E RT-PCR for BM and LTBMC-Stroma…………………………………….…65 Figure 1F RT-PCR of separated BMC subpopulations…………………………….…66 Figure 1G Integrin expression profile on BMC, HSC and LTBMC-stroma cell……..67 Figure 1H Expression of cell adhesion molecule and selectins on BMC, HSC and LTBMC-stroma cell…………………………………………….….67 Figure 1I cytokines and cytokines receptors expression on BMC, HSC and LTBMC-stroma cells……………………………………………………….….68 Figure 2A CD44 co-expression with stem cells, progenitors and mature leukocyte markers on BMC……………………………………………….....70 Figure 2B CD44 co-expression with stem cells, progenitors and mature leukocyte markers on LTBMC-stroma…………………………………..….71 Figure 2C CD44 co-expression with cytokine/chemokine receptors on BMC………72 Figure 2D CD44 co-expression with cytokine/chemokine receptors on LTBMC-stroma………………………………………………………………..73 Figure 2E CD44 co-expression with adhesion molecules on BMC………………….74 Figure 2F CD44 co-expression with adhesion molecules on LTBMC-stroma cells..75 Figure 2G CD44 associating molecules on BMC……………………………………...76 Figure 2H CD44 associating molecules on BMC, subpopulations and LTBMC-stroma………………………………………………………………..77 Figure 2I CD44 associating molecules on LTBMC-stroma…………………………...77 Figure 3A Confirmation of cDNA of soluble CD44s and soluble CD44v7…………..79 Figure 3B Expression of sCD44s and sCD44v7 in transfected cells……………..…79 Figure 3C sCD44v7 binding proteins…………………………………………………....80 vii Figure 3D sCD44s binding proteins………………………………………………….…..81 Figure 4A comparison of BMC Vs HSC quiescence……………………………….…..83 Figure 4B Comparative analysis of the apoptosis resistance of HSC Vs BMC…......84 Figure 4C Comparative analysis of apoptosis resistance of CD44+ BMC and HSC……………………………………………………………………..….84 Figure 4D The impact of a
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    Cell. Mol. Life Sci. DOI 10.1007/s00018-007-6417-3 Cellular and Molecular Life Sciences Birkhuser Verlag, Basel, 2007 Review Hearing molecules: contributions from genetic deafness M.D. Eisena and D.K. Ryugoa,b Departments of aOtolaryngology-Head and Neck Surgery and bNeuroscience, Center for Hearing and Balance, Traylor 510, 720 Rutland Avenue, Baltimore, Maryland 21205 (USA), Fax: +4106144748, e-mail: [email protected] Received 20 September 2006; received after revision 24 October 2006; accepted 5 December 2006 Abstract. Considerable progress has been made over decade that address the function of the proteins the past decade identifying many genes associated implicated in genetic deafness and to place them in the with deafness. With the identification of these heredi- context of basic molecular mechanisms in hearing. tary deafness genes and the proteins they encode, The first part of this review highlights structural and molecular elements of basic hearing mechanisms functional features of the cochlea and auditory nerve. emerge. As functional studies of these molecular This background will provide a context for the second elements become available, we can put together the part, which addresses the molecular mechanisms pieces of the puzzle and begin to reach an under- underlying cochlear function as elucidated by genetic standing of the molecular mechanisms of hearing. The causes of deafness. goal of this review is to discuss studies over the past Keywords. Genetic deafness, auditory, cochlea, hearing, hair cell. Introduction auditory processing, whereas sensorineural’ hearing loss refers to malfunction of the electrochemical arm. Normal mammalian auditory function relies on two Conductive hearing loss typically results from middle broad categories of function – mechanical and electro- ear pathology – tympanic membrane perforation, chemical.
  • Identification of Key Pathways and Genes in Dementia Via Integrated Bioinformatics Analysis

    Identification of Key Pathways and Genes in Dementia Via Integrated Bioinformatics Analysis

    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.18.440371; this version posted July 19, 2021. 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. Identification of Key Pathways and Genes in Dementia via Integrated Bioinformatics Analysis 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, Karnataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2021.04.18.440371; this version posted July 19, 2021. 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 To provide a better understanding of dementia at the molecular level, this study aimed to identify the genes and key pathways associated with dementia by using integrated bioinformatics analysis. Based on the expression profiling by high throughput sequencing dataset GSE153960 derived from the Gene Expression Omnibus (GEO), the differentially expressed genes (DEGs) between patients with dementia and healthy controls were identified. With DEGs, we performed a series of functional enrichment analyses. Then, a protein–protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network was constructed, analyzed and visualized, with which the hub genes miRNAs and TFs nodes were screened out. Finally, validation of hub genes was performed by using receiver operating characteristic curve (ROC) analysis.
  • Genetic Testing Policy Number: PG0041 ADVANTAGE | ELITE | HMO Last Review: 04/11/2021

    Genetic Testing Policy Number: PG0041 ADVANTAGE | ELITE | HMO Last Review: 04/11/2021

    Genetic Testing Policy Number: PG0041 ADVANTAGE | ELITE | HMO Last Review: 04/11/2021 INDIVIDUAL MARKETPLACE | PROMEDICA MEDICARE PLAN | PPO GUIDELINES This policy does not certify benefits or authorization of benefits, which is designated by each individual policyholder terms, conditions, exclusions and limitations contract. It does not constitute a contract or guarantee regarding coverage or reimbursement/payment. Paramount applies coding edits to all medical claims through coding logic software to evaluate the accuracy and adherence to accepted national standards. This medical policy is solely for guiding medical necessity and explaining correct procedure reporting used to assist in making coverage decisions and administering benefits. SCOPE X Professional X Facility DESCRIPTION A genetic test is the analysis of human DNA, RNA, chromosomes, proteins, or certain metabolites in order to detect alterations related to a heritable or acquired disorder. This can be accomplished by directly examining the DNA or RNA that makes up a gene (direct testing), looking at markers co-inherited with a disease-causing gene (linkage testing), assaying certain metabolites (biochemical testing), or examining the chromosomes (cytogenetic testing). Clinical genetic tests are those in which specimens are examined and results reported to the provider or patient for the purpose of diagnosis, prevention or treatment in the care of individual patients. Genetic testing is performed for a variety of intended uses: Diagnostic testing (to diagnose disease) Predictive