DOCSLIB.ORG

Characterization of CAMTA1 and Nkx2.2 in the Context of Glioblastoma Cancer Stem Cell Biology

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterization of CAMTA1 and Nkx2.2 in the Context of Glioblastoma Cancer Stem Cell Biology Characterization of CAMTA1 and Nkx2.2 in the context of glioblastoma cancer stem cell biology Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Ludwig Wankerl aus Regensburg im Jahr 2015 II Das Promotionsgesuch wurde eingereicht am: 03. Juli 2015 Die Arbeit wurde angeleitet von: Prof. Dr. rer. nat. Gunter Meister Unterschrift: III Our greatest weakness lies in giving up. The most certain way to succeed is always to try just one more time. Thomas A. Edison IV V Abstract Glioblastoma multiforme (glioblastoma) is the most malignant type of tumor in the human brain. For glioblastomas and several other cancer types, the existence of so called "cancer stem cells" was described. Cancer stem cells are characterized by stem cell-like traits such as the capacity of self-renewal and differentiation. Moreover, there is evidence that these cells contribute to cancer recurrence after therapy. Several molecular-pathological factors are crucial for the emergence of glioblastomas in general and for glioblastoma cancer stem cells in particular. For example, certain microRNAs (miRNAs) such as the miRNA pair miR-9/9* are specifically enriched in glioblastoma cancer stem cells. This miRNA pair acts as oncogene for glioblastomas by repressing the tumor suppressor Calmodulin-binding transcription activator 1 (CAMTA1). In this thesis, the upstream and downstream pathways of the CAMTA1 transcription factor were investigated in terms of their relevance in cancer biology. Therefore, siRNAs and antibodies against CAMTA1 were generated and established. Beyond that, a potential interaction partner of CAMTA1, Nkx2.2, was identified. Nkx2.2 is an important transcription factor for neural development and is also a potential tumor suppressor for glioblastomas. The tumor-suppressive effect of Nkx2.2 reported previously was further confirmed by this thesis. In this regard, it was shown that an overexpression of Nkx2.2 affected glioblastoma cancer stem cells negatively and impaired the proliferation of glioma cells. Additionally, a positive correlation between Nkx2.2 expression and survival of glioma patients was revealed. Furthermore, it was hypothesized that Nkx2.2 and CAMTA1 act in concert to stimulate the transcription of NPPA, which encodes for the precursor of the natriuretic VI – Abstract peptide (ANP). This activation was thought to be the main mechanism for these two transcription factors to cause their tumor-suppressive effects. Consistently, it was shown that an overexpression of Nkx2.2 elevated the NPPA mRNA levels and that Nkx2.2 can strongly induce the NPPA promoter. Nkx2.2 was further characterized in terms of additional interaction partners and a potential regulation by miRNAs. The findings of this thesis allow to postulate a model which describes a possible regulatory network important for understanding glioblastomas, in particular the formation and traits of glioblastoma cancer stem cells. This will advance therapy strategies that "tackle" these persistent cells. VII Zusammenfassung Glioblastoma multiforme (Glioblastom) ist eine Tumorform, die im Gehirn auftritt und unter den Gehirntumoren den höchsten Grad an Malignität aufweist. Für Glioblastome und diverse andere Krebsarten wurde die Existenz von sog. "Krebs-Stammzellen" nachgewiesen. Krebs-Stammzellen zeichnen sich durch ähnliche Charakteristika aus wie Stammzellen von normalem, gesundem Gewebe, d.h. sie sind fähig, sich zu differenzieren und selbst zu erneuern. Verschiedene molekular-pathologische Faktoren tragen zur Entstehung von Glioblastomen bzw. deren Krebs-Stammzellen bei. So sind beispielsweise bestimmte mikroRNAs (miRNAs) wie das bifunktionelle miRNA-Paar miR-9/9* vermehrt in diesen Krebs-Stammzellen exprimiert. Dieses spezielle miRNA-Paar reprimiert den Tumorsuppressor Calmodulin-binding transcription activator 1 (CAMTA1) und wirkt dadurch onkogen für Glioblastome. In dieser Arbeit sollte das zelluläre Netzwerk von CAMTA1, durch welches die tumor- suppressive Wirkung hervorgerufen wird, näher untersucht werden. Dazu wurden siRNAs und Antikörper gegen CAMTA1 generiert und auf ihre Funktionalität überprüft. Darüber hinaus konnte der Transkriptionsfaktor Nkx2.2 als ein potentieller Interaktionspartner von CAMTA1 identifiziert werden. Nkx2.2 spielt bei der Entwicklung des zentralen Nervensystems eine wichtige Rolle und gilt ebenfalls als potentieller Tumorsuppressor für Glioblastome. Diese tumor-suppressive Wirkung von Nkx2.2 wurde in einer früheren Studie gezeigt und konnte durch diese Arbeit bestätigt werden: Eine Überexpression von Nkx2.2 beeinflusste Glioblastom-Krebs-Stammzellen negativ und verminderte deutlich die Proliferation von Glioma-Zellen. Zudem konnte VIII – Zusammenfassung ein Zusammenhang zwischen einer erhöhter Nkx2.2-Expression und einer höheren Überlebensrate von Patienten mit Gliomen festgestellt werden. In dieser Arbeit wurde die Hypothese aufgestellt, dass CAMTA1 und Nkx2.2 miteinander interagieren, um die Transkription des Gens NPPA zu steigern. NPPA kodiert für den Vorläufer des atrialen natriuretischen Peptids (ANP). Die Aktivierung des NPPA-Gens stellt vermutlich einen zentralen Mechanismus dar, über den die beiden Transkriptionsfaktoren CAMTA1 und Nkx2.2 ihre tumor-suppressive Wirkung vermitteln. Es konnte gezeigt werden, dass eine Überexpression von Nkx2.2 tatsächlich zu einer Erhöhung der NPPA-Expression führte und dass Nkx2.2 in der Lage ist, den Promotor dieses Gens zu aktivieren. Ferner wurde untersucht, ob für Nkx2.2 weitere potentielle Interaktionspartner identifiziert werden können und ob Nkx2.2 durch miRNAs reguliert wird. Mit den in dieser Arbeit erbrachten Ergebnissen lässt sich ein Modell entwerfen, wie die Entstehung von Glioblastoma multiforme und dessen Krebsstam-Zellen durch einen Regulationsmechanismus potentiell unterdrückt wird. Dieses Modell kann dazu beitragen, die molekularen Mechanismen für die Entstehung von Glioblastomen, insbesondere von deren Krebs-Stammzellen, besser zu verstehen. Dadurch lassen sich möglicherweise neue Therapieansätze entwickeln. IX Contents Abstract .......................................................................................................................... V Zusammenfassung ....................................................................................................... VII Contents .......................................................................................................................IX List of Figures ............................................................................................................ XIV List of Tables ............................................................................................................. XVI List of Abbreviations ................................................................................................ XVII 1. Introduction ................................................................................................................ 1 1.1. Cancer stem cells .................................................................................................. 1 1.2. Glioblastoma multiforme ........................................................................................ 3 1.3. The role of microRNAs in glioblastoma biology .................................................. 7 1.3.1. miRNA biogenesis and miRNA-directed transcript regulation .................... 7 1.3.2. Several miRNAs are important for glioblastoma progression and glioblastoma cancer stem cell maintenance ............................................................. 8 1.4. The Calmodulin-binding transcription activator 1 is a tumor suppressor for glioblastomas ............................................................................................................. 11 1.4.1. The CAMTA family of transcription factors: Protein organization ............ 11 1.4.2. Function of CAMTA proteins from plants to mammals ............................ 14 1.4.3. CAMTA1 acts as tumor suppressor in neural tumors ................................. 16 1.5. Nkx2.2: A glioblastoma tumor suppressor candidate ......................................... 19 X – Contents 1.5.1. The Nkx protein family: Transcription factors essential for development ... 19 1.5.2. Nkx2.2 is important for neural development and a potential tumor suppressor protein .................................................................................................. 21 1.6. Aims and working model for this thesis ............................................................. 24 2. Results ....................................................................................................................... 27 2.1. Characterization of CAMTA1 ........................................................................... 27 2.1.1. Establishing of efficient CAMTA1 knockdown strategies .......................... 27 2.1.2. Polyclonal antibodies against CAMTA1 ..................................................... 29 2.1.3. Localization of CAMTA1 ........................................................................... 37 2.1.4. A potential CAMTA1 interaction partner: Nkx2.2 .................................... 44 2.2. Characterization of Nkx2.2 ................................................................................ 50 2.2.1. Nuclear localization of Nkx2.2 .................................................................... 50 2.2.2. Nkx2.2 interaction partners ........................................................................
Load more

Recommended publications
  • Proteomic Identification of the Transcription Factors Ikaros And
    European School of Molecular Medicine (SEMM) University of Milan and University of Naples “Federico II” PhD degree in Systems Medicine (curriculum in Molecular Oncology) Settore disciplinare: BIO/11 Proteomic identification of the transcription factors Ikaros and Aiolos as new Myc interactors on chromatin Chiara Veronica Locarno Matricola: R10755 Center for Genomic Science IIT@SEMM, Milan Supervisor: Bruno Amati, PhD IEO, Milan Added Supervisor: Arianna Sabò, PhD IEO, Milan Academic year 2017-2018 Table of contents List of abbreviations ........................................................................................................... 4 List of figures ....................................................................................................................... 8 List of tables ....................................................................................................................... 11 Abstract .............................................................................................................................. 12 1. INTRODUCTION ......................................................................................................... 13 1.1 Myc ........................................................................................................................................ 13 1.1.1 Myc discovery and structure ........................................................................................... 13 1.1.2. Role of Myc in physiological and pathological conditions ...........................................
    [Show full text]
  • TASOR Is a Pseudo-PARP That Directs HUSH Complex Assembly and Epigenetic Transposon Control
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.974832; this version posted March 11, 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. TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control Christopher H. Douse1,‡, Iva A. Tchasovnikarova2,‡, Richard T. Timms2,‡, Anna V. Protasio2, Marta Seczynska2, Daniil M. Prigozhin1, Anna Albecka1,2, Jane Wagstaff3, James C. Williamson2, Stefan M.V. Freund3, Paul J. Lehner2*, Yorgo Modis1,2* 1 Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK 2 Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK 3 Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK Current addresses: Department of Experimental Medical Science, Lund University, Sölvegatan 19, Lund, Sweden (C.H.D.); The Gurdon Institute, Tennis Court Road, Cambridge, UK (I.A.T.); Department of Pathology, Tennis Court Road, Cambridge, UK (A.V.P.); Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (D.M.P.) ‡These authors contributed equally *co-corresponding authors Keywords: Transcriptional repression; epigenetic silencing; antiretroviral response; genome stability; histone H3 lysine 9 methylation (H3K9me3); transposable element (TE); long interspersed nuclear element-1 (LINE-1); poly-ADP ribose polymerase (PARP); RNA-binding protein; RNA-induced transcriptional silencing; CUT&RUN; CUT&Tag; genome profiling 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.974832; this version posted March 11, 2020.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • 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
    [Show full text]
  • Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
    Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A.
    [Show full text]
  • Whole-Genome Sequencing for Optimized Patient Management Matthew N
    Whole-Genome Sequencing for Optimized Patient Management Matthew N. Bainbridge et al. Sci Transl Med 3, 87re3 (2011); DOI: 10.1126/scitranslmed.3002243 Editor's Summary Guiding Treatment with Genomics Whole-genome sequencing of DNA from patients with different diseases is proving useful for identifying new disease-causing mutations, but can it help physicians make better decisions about treatment options for these patients? A new study by Bainbridge and colleagues suggests that it can. Bainbridge et al. sequenced the complete genomes of a male and female fraternal twin pair, who had been diagnosed 9 years earlier with the movement disorder dopa (3,4-dihydroxyphenylalanine)−responsive dystonia (DRD). This complex disorder is difficult to diagnose and may be mistaken for other movement disorders involving loss of the neurotransmitter dopamine. The standard treatment for DRD is to replace dopamine by providing a dopamine precursor called l-dopa, the drug that is also used to treat the common movement disorder Parkinson disease. When the twins were diagnosed with DRD, they seemed to fit the classic description of DRD and were given l-dopa, which did help to alleviate many of their symptoms. When Bainbridge and colleagues analyzed the full genome sequences of the twins, they were surprised to discover no mutations in the two genes most commonly mutated in DRD. Instead, they pinpointed a mutation in the SPR gene encoding sepiapterin reductase, which synthesizes a cofactor needed for the action of enzymes that make not only dopamine but also the neurotransmitter serotonin. This finding suggested to the authors that supplementing the twin's current l-dopa treatment with a serotonin precursor, 5-hydroxytryptophan, might provide further improvement in their symptoms.
    [Show full text]
  • Bioinformatics Analysis for the Identification of Differentially Expressed Genes and Related Signaling Pathways in H
    Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells Dingyu Chen*, Chao Li, Yan Zhao, Jianjiang Zhou, Qinrong Wang and Yuan Xie* Key Laboratory of Endemic and Ethnic Diseases , Ministry of Education, Guizhou Medical University, Guiyang, China * These authors contributed equally to this work. ABSTRACT Aim. Helicobacter pylori cytotoxin-associated protein A (CagA) is an important vir- ulence factor known to induce gastric cancer development. However, the cause and the underlying molecular events of CagA induction remain unclear. Here, we applied integrated bioinformatics to identify the key genes involved in the process of CagA- induced gastric epithelial cell inflammation and can ceration to comprehend the potential molecular mechanisms involved. Materials and Methods. AGS cells were transected with pcDNA3.1 and pcDNA3.1::CagA for 24 h. The transfected cells were subjected to transcriptome sequencing to obtain the expressed genes. Differentially expressed genes (DEG) with adjusted P value < 0.05, | logFC |> 2 were screened, and the R package was applied for gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The differential gene protein–protein interaction (PPI) network was constructed using the STRING Cytoscape application, which conducted visual analysis to create the key function networks and identify the key genes. Next, the Submitted 20 August 2020 Kaplan–Meier plotter survival analysis tool was employed to analyze the survival of the Accepted 11 March 2021 key genes derived from the PPI network. Further analysis of the key gene expressions Published 15 April 2021 in gastric cancer and normal tissues were performed based on The Cancer Genome Corresponding author Atlas (TCGA) database and RT-qPCR verification.
    [Show full text]
  • Strand Breaks for P53 Exon 6 and 8 Among Different Time Course of Folate Depletion Or Repletion in the Rectosigmoid Mucosa
    SUPPLEMENTAL FIGURE COLON p53 EXONIC STRAND BREAKS DURING FOLATE DEPLETION-REPLETION INTERVENTION Supplemental Figure Legend Strand breaks for p53 exon 6 and 8 among different time course of folate depletion or repletion in the rectosigmoid mucosa. The input of DNA was controlled by GAPDH. The data is shown as ΔCt after normalized to GAPDH. The higher ΔCt the more strand breaks. The P value is shown in the figure. SUPPLEMENT S1 Genes that were significantly UPREGULATED after folate intervention (by unadjusted paired t-test), list is sorted by P value Gene Symbol Nucleotide P VALUE Description OLFM4 NM_006418 0.0000 Homo sapiens differentially expressed in hematopoietic lineages (GW112) mRNA. FMR1NB NM_152578 0.0000 Homo sapiens hypothetical protein FLJ25736 (FLJ25736) mRNA. IFI6 NM_002038 0.0001 Homo sapiens interferon alpha-inducible protein (clone IFI-6-16) (G1P3) transcript variant 1 mRNA. Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15 GALNTL5 NM_145292 0.0001 (GALNT15) mRNA. STIM2 NM_020860 0.0001 Homo sapiens stromal interaction molecule 2 (STIM2) mRNA. ZNF645 NM_152577 0.0002 Homo sapiens hypothetical protein FLJ25735 (FLJ25735) mRNA. ATP12A NM_001676 0.0002 Homo sapiens ATPase H+/K+ transporting nongastric alpha polypeptide (ATP12A) mRNA. U1SNRNPBP NM_007020 0.0003 Homo sapiens U1-snRNP binding protein homolog (U1SNRNPBP) transcript variant 1 mRNA. RNF125 NM_017831 0.0004 Homo sapiens ring finger protein 125 (RNF125) mRNA. FMNL1 NM_005892 0.0004 Homo sapiens formin-like (FMNL) mRNA. ISG15 NM_005101 0.0005 Homo sapiens interferon alpha-inducible protein (clone IFI-15K) (G1P2) mRNA. SLC6A14 NM_007231 0.0005 Homo sapiens solute carrier family 6 (neurotransmitter transporter) member 14 (SLC6A14) mRNA.
    [Show full text]
  • Noncoding Rnas As Novel Pancreatic Cancer Targets
    NONCODING RNAS AS NOVEL PANCREATIC CANCER TARGETS by Amy Makler A Thesis Submitted to the Faculty of The Charles E. Schmidt College of Science In Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL August 2018 Copyright 2018 by Amy Makler ii ACKNOWLEDGEMENTS I would first like to thank Dr. Narayanan for his continuous support, constant encouragement, and his gentle, but sometimes critical, guidance throughout the past two years of my master’s education. His faith in my abilities and his belief in my future success ensured I continue down this path of research. Working in Dr. Narayanan’s lab has truly been an unforgettable experience as well as a critical step in my future endeavors. I would also like to extend my gratitude to my committee members, Dr. Binninger and Dr. Jia, for their support and suggestions regarding my thesis. Their recommendations added a fresh perspective that enriched our initial hypothesis. They have been indispensable as members of my committee, and I thank them for their contributions. My parents have been integral to my successes in life and their support throughout my education has been crucial. They taught me to push through difficulties and encouraged me to pursue my interests. Thank you, mom and dad! I would like to thank my boyfriend, Joshua Disatham, for his assistance in ensuring my writing maintained a logical progression and flow as well as his unwavering support. He was my rock when the stress grew unbearable and his encouraging words kept me pushing along.
    [Show full text]
  • Genome-Wide Association Study of Non-Alcoholic Fatty Liver and Steatohepatitis in a Histologically-Characterised Cohort
    Journal Pre-proof Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically-characterised cohort Quentin M. Anstee, Rebecca Darlay, Simon Cockell, Marica Meroni, Olivier Govaere, Dina Tiniakos, Alastair D. Burt, Pierre Bedossa, Jeremy Palmer, Yang-Lin Liu, Guruprasad P. Aithal, Michael Allison, Hannele Yki-Järvinen, Michele Vacca, Jean- Francois Dufour, Pietro Invernizzi, Daniele Prati, Mattias Ekstedt, Stergios Kechagias, Sven Francque, Salvatore Petta, Elisabetta Bugianesi, Karine Clement, Vlad Ratziu, Jörn M. Schattenberg, Luca Valenti, Christopher P. Day, Heather J. Cordell, Ann K. Daly, , on behalf of the EPoS Consortium Investigators PII: S0168-8278(20)30213-0 DOI: https://doi.org/10.1016/j.jhep.2020.04.003 Reference: JHEPAT 7699 To appear in: Journal of Hepatology Received Date: 3 October 2019 Revised Date: 20 March 2020 Accepted Date: 2 April 2020 Please cite this article as: Anstee QM, Darlay R, Cockell S, Meroni M, Govaere O, Tiniakos D, Burt AD, Bedossa P, Palmer J, Liu YL, Aithal GP, Allison M, Yki-Järvinen H, Vacca M, Dufour JF, Invernizzi P, Prati D, Ekstedt M, Kechagias S, Francque S, Petta S, Bugianesi E, Clement K, Ratziu V, Schattenberg JM, Valenti L, Day CP, Cordell HJ, Daly AK, on behalf of the EPoS Consortium Investigators, Genome- wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically-characterised cohort, Journal of Hepatology (2020), doi: https://doi.org/10.1016/j.jhep.2020.04.003. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record.
    [Show full text]
  • Chromatin Conformation Links Distal Target Genes to CKD Loci
    BASIC RESEARCH www.jasn.org Chromatin Conformation Links Distal Target Genes to CKD Loci Maarten M. Brandt,1 Claartje A. Meddens,2,3 Laura Louzao-Martinez,4 Noortje A.M. van den Dungen,5,6 Nico R. Lansu,2,3,6 Edward E.S. Nieuwenhuis,2 Dirk J. Duncker,1 Marianne C. Verhaar,4 Jaap A. Joles,4 Michal Mokry,2,3,6 and Caroline Cheng1,4 1Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and 2Department of Pediatrics, Wilhelmina Children’s Hospital, 3Regenerative Medicine Center Utrecht, Department of Pediatrics, 4Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, 5Department of Cardiology, Division Heart and Lungs, and 6Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands ABSTRACT Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chro- mosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis.
    [Show full text]
  • Elucidation of Dna Damage Response Pathways And
    ELUCIDATION OF DNA DAMAGE RESPONSE PATHWAYS AND FUNCTIONAL EFFICIENCY OF DNA REPAIR GENES ASSOCIATED WITH REPROGRAMMED OSTEOSARCOMA CELL LINES By CHOONG PEI FENG A thesis submitted to the Department of Pre-Clinical Science, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, in partial fulfillment of the requirements for the degree of Doctor of Philosophy of Medical Sciences May 2018 ABSTRACT ELUCIDATION OF DNA DAMAGE RESPONSE PATHWAYS AND FUNCTIONAL EFFICIENCY OF DNA REPAIR GENES ASSOCIATED WITH REPROGRAMMED OSTEOSARCOMA CELL LINES Choong Pei Feng Osteosarcoma (OS) is a prevalent cancer of the bone happening mostly in children and adolescence. Alterations and mutations to genes associated with proliferation and differentiation increased the risk of OS tumourigenicity. Reprogramming of OS cell lines to a primitive phase could be used to understand the pathogenesis of OS. Furthermore, the DNA damage response (DDR) of reprogrammed cancer cells has not been well established. By using retroviral OSKM, OS cell lines were reprogrammed to pluripotency. Colonies from iG-292 and iSaos-2 showed ESC-like morphology, expressing pluripotency markers, formed embryoid body-like spheres and expressed markers from three germ layers as well as showing ability to differentiate into adipocytes and osteocytes. However, in vivo study showed teratoma formation only in reprogrammed G-292, iG-292. In the second part of this study, hierarchical clustering analysis from global gene expression profile of parental and reprogrammed OS demonstrated distinctive separation of two population. Differentially expressed genes (DEGs) ii were grouped into DNA repair, cell cycle and apoptosis pathways. Our data showed that iG-292 displayed more DEGs than iSaos-2 in all pathways.
    [Show full text]