Evaluating the Effects of Fasting Conditions in Combination with Temozolomide for the Treatment of Glioblastoma Multiforme

Total Page:16

File Type:pdf, Size:1020Kb

Evaluating the Effects of Fasting Conditions in Combination with Temozolomide for the Treatment of Glioblastoma Multiforme Northern Michigan University NMU Commons All NMU Master's Theses Student Works 7-2020 EVALUATING THE EFFECTS OF FASTING CONDITIONS IN COMBINATION WITH TEMOZOLOMIDE FOR THE TREATMENT OF GLIOBLASTOMA MULTIFORME Joseph Duffy [email protected] Follow this and additional works at: https://commons.nmu.edu/theses Part of the Cancer Biology Commons Recommended Citation Duffy, Joseph, "EVALUATING THE EFFECTS OF FASTING CONDITIONS IN COMBINATION WITH TEMOZOLOMIDE FOR THE TREATMENT OF GLIOBLASTOMA MULTIFORME" (2020). All NMU Master's Theses. 638. https://commons.nmu.edu/theses/638 This Open Access is brought to you for free and open access by the Student Works at NMU Commons. It has been accepted for inclusion in All NMU Master's Theses by an authorized administrator of NMU Commons. For more information, please contact [email protected],[email protected]. EVALUATING THE EFFECTS OF FASTING CONDITIONS IN COMBINATION WITH TEMOZOLOMIDE FOR THE TREATMENT OF GLIOBLASTOMA MULTIFORME By Joseph T. Duffy THESIS Submitted to Northern Michigan University In partial fulfillment of the requirements For the degree of MASTER OF SCIENCE Office of Graduate Education and Research June 2020 i Dr. Robert Winn Dr. Richard Rovin Dr. Amber LaCrosse ABSTRACT EVALUATING THE EFFECTS OF FASTING CONDITIONS IN COMBINATION WITH TEMOZOLOMIDE FOR THE TREATMENT OF GLIOBLASTOMA MULTIFORME By Joseph Duffy Glioblastoma multiforme (GBM) is the most aggressive type of glioma and most lethal of adult brain tumors. The standard of care for GBM is maximal surgical resection followed by adjuvant treatment with the chemotherapeutic agent temozolomide (TMZ) and radiotherapy. The presence of TMZ-resistant cells in GBM that can reverse the TMZ induced cytotoxic lesions by expressing MGMT contribute to therapy resistance. A common trait of cancer is an altered carbohydrate metabolism. Known as the Warburg effect, cancer cells will preferentially oxidize glucose to lactate in glycolysis. This less effective pathway of ATP production per mole of glucose means cancer cells must uptake significantly greater amounts of glucose to sustain physiological needs. One method that directly targets the bioavailability of glucose is fasting. Fasting lowers systemic glucose levels, lowers anabolic hormone levels (insulin and IGF-1), and elevates ketone bodies like ß-hydroxybutyrate (ß-HB). This study sought to evaluate the effects of fasting in combination with TMZ on viability of GBM cell lines LN229 and T98G, and normal astroglial cell line SVG p12. The data from showed that glucose restricted media significantly enhanced the cytotoxic effects of TMZ in LN229 and T98G cells, while having no effect in SVG p12 cells. ß-HB in combination with TMZ potentiated the cytotoxicity of TMZ in LN229 and T98G cells, while reducing the cytotoxicity of TMZ in SVG p12 cells. Western blot analysis for MGMT determined T98G cells were the only cell line to express MGMT. Both glucose restricted media and ß-HB supplemented media in combination with TMZ significantly decreased the expression of MGMT levels in T98G cells. Together, this initial evidence suggests fasting may be a useful method to selectively increase cytotoxicity of TMZ in GBM cells, while protecting normal cells. Future research is needed to further assess the potential of fasting as an adjuvant therapy in the treatment of GBM. iii Copyright by Joseph T. Duffy 2020 iv This thesis is dedicated to all those who have been affected by Cancer, especially those who are suffering or have suffered from Glioblastoma Multiforme, and those who work tirelessly to advance the field of oncology. On a personal level, I would like to dedicate this thesis to Joe Duffy, Judy Duffy, Joyce Duffy, Robert Duffy, and Tommy McGuire. You continue to motivate me on this quest to understand the nature of cancer. v ACKNOWLEDGMENTS The work presented in this thesis would not have been possible without the help of the Upper Michigan Brain Tumor Center, graduate research assistantship, summer fellowship, and Excellence in Education grant. I would like to thank my research advisor, Dr. Robert Winn, and my committee members, Dr. Richard Rovin and Dr. Amber LaCrosse, for their support and guidance throughout graduate school. I would also like to thank the other members of the Upper Michigan Brain Tumor Center for their various contributions, especially, Dr. Matt Jennings and Dr. Paul Mann for their guidance in cell and molecular work, and Dr. Sonia Geschwindt, Dr. Sheetal Acharya, John Paul Velasco, Dan Raymond, Allison Riehl, Kyle Flickinger, and Nick Shortreed for their assistance throughout my research project. Finally, I would like to thank Northern Michigan University for giving me a second chance at life, and for believing in me during a time when I did not believe in myself. For that I am forever in grateful. vi TABLE OF CONTENTS List of Figures.....…………………………………………………………………………………………(v) List of Abbreviations.……………………………………………………………………………………….…...(vi) Introduction…………………………………………………………………………………………………1 Chapter One: Literature Review.…………………………………………………………………………...5 Introduction………………………………………………………………………………………...5 Temozolomide: Mechanism of action, DNA repair mechanisms, and cellular resistance......................................................................................................................…………….5 The Warburg Effect in Cancer and Its Role in GBM…………………………………………...…8 Fasting: Systemic Changes and Role in Cancer Therapy……………………………………...…10 Conclusion……………………………………………………………………………………..…16 Chapter Two: Aims and Goals………………………………………………………………………….…17 Chapter Three: Culture and Maintenance of Cell Lines.………………………………………………….19 Chapter Four: Analyzing Cytotoxicity of Glucose Restricted Media in Combination with Temozolomide in GBM Cells……………………………………………………………………………..21 Introduction….................................................................................................................................21 Methods and Materials…................................................................................................................21 Results.........................................................................................................................................…25 Discussion...................................................................................................................................…31 Chapter Five: Analyzing Cytotoxicity of Glucose Restricted Media in Combination with Temozolomide in Administered Without DMSO in GBM and Human Astroglial Cells.......…………….33 Introduction……………………………………………………………………………………….33 Methods and Materials……………………………………………………………………………33 Results…………………………………………………………………………………………….37 Discussion………………………………………………………………………………………...42 Chapter Six: Analyzing Cytotoxicity of Glucose Restricted Media Supplemented with ß-Hydroxybutyrate in Combination with Temozolomide in GBM and Human Astroglial Cells…........…47 Introduction……………………………………………………………………………………….47 Methods and Materials……………………………………………………………………………48 vii Results…………………………………………………………………………………………….51 Discussion………………………………………………………………………………………...63 Chapter Seven: Analyzing the Effects of Glucose Restricted Media and ß-Hydroxybutyrate in Combination with Temozolomide on MGMT expression in GBM and Human Astroglial Cells..…….67 Introduction……………………………………………………………………………………….67 Methods and Materials……………………………………………………………………………68 Results…………………………………………………………………………………………….72 Discussion………………………………………………………………………………………...75 Chapter 8: Summary and Conclusions…………………………………………………………………….78 References…………………………………………………………………………………………………83 viii LIST OF FIGURES Figure 1. Temozolomide (TMZ) mechanism of action and cellular repair mechanism...……………….....7 Figure 2. Systemic changes induced by fasting...........................................................................................11 Figure 3. Morphology of adherent LN229, T98G, and SVG p12 cells…………………………………...20 Figure 4. Temozolomide (TMZ) dilution scheme.......................................................................................24 Figure 5. CellTiter-Glo 2.0 Assay principal................................................................................................24 Figure 6. DMSO is cytotoxic to GBM cells.................................................................................................28 Figure 7. Glucose restriction sensitizes LN229 GBM cells to temozolomide treatment.............................29 Figure 8. Glucose restriction sensitizes T98G GBM cells to temozolomide treatment. .............................30 Figure 9. Temozolomide (TMZ) dilution scheme.......................................................................................36 Figure 10. CellQuanti-Blue™ Assay principal...........................................................................................36 Figure 11. Glucose restriction sensitizes LN229 GBM cells to temozolomide treatment...........................39 Figure 12. Glucose restriction sensitizes T98G GBM cells to temozolomide treatment.............................40 Figure 13. Glucose restriction has no effect on SVG p12 normal astrocyte sensitivity to temozolomide treatment...........................................................................................................................45 Figure 14. Differential stress response (DSR) between normal cells and LN229 cells in response to fasting conditions..................................................................................................................51 Figure
Recommended publications
  • Thesis Template
    Functional and Structural Characterization Reveals Novel FBXW7 Biology by Tonny Chao Huang A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Medical Biophysics University of Toronto © Copyright by Tonny Chao Huang 2018 Functional and Structural Characterization Reveals Novel FBXW7 Biology Tonny Chao Huang Master of Science Department of Medical Biophysics University of Toronto 2018 Abstract This thesis aims to examine aspects of FBXW7 biology, a protein that is frequently mutated in a variety of cancers. The first part of this thesis describes the characterization of FBXW7 isoform and mutant substrate profiles using a proximity-dependent biotinylation assay. Isoform-specific substrates were validated, revealing the involvement of FBXW7 in the regulation of several protein complexes. Characterization of FBXW7 mutants also revealed site- and residue-specific consequences on the binding of substrates and, surprisingly, possible neo-substrates. In the second part of this thesis, we utilize high-throughput peptide binding assays and statistical modelling to discover novel features of the FBXW7-binding phosphodegron. In contrast to the canonical motif, a possible preference of FBXW7 for arginine residues at the +4 position was discovered. I then attempted to validate this feature in vivo and in vitro on a novel substrate discovered through BioID. ii Acknowledgments The past three years in the Department of Medical Biophysics have defied expectations. I not only had the opportunity to conduct my own independent research, but also to work with distinguished collaborators and to explore exciting complementary fields. I experienced the freedom to guide my own academic development, as well as to pursue my extracurricular interests.
    [Show full text]
  • Supplemental Information to Mammadova-Bach Et Al., “Laminin Α1 Orchestrates VEGFA Functions in the Ecosystem of Colorectal Carcinogenesis”
    Supplemental information to Mammadova-Bach et al., “Laminin α1 orchestrates VEGFA functions in the ecosystem of colorectal carcinogenesis” Supplemental material and methods Cloning of the villin-LMα1 vector The plasmid pBS-villin-promoter containing the 3.5 Kb of the murine villin promoter, the first non coding exon, 5.5 kb of the first intron and 15 nucleotides of the second villin exon, was generated by S. Robine (Institut Curie, Paris, France). The EcoRI site in the multi cloning site was destroyed by fill in ligation with T4 polymerase according to the manufacturer`s instructions (New England Biolabs, Ozyme, Saint Quentin en Yvelines, France). Site directed mutagenesis (GeneEditor in vitro Site-Directed Mutagenesis system, Promega, Charbonnières-les-Bains, France) was then used to introduce a BsiWI site before the start codon of the villin coding sequence using the 5’ phosphorylated primer: 5’CCTTCTCCTCTAGGCTCGCGTACGATGACGTCGGACTTGCGG3’. A double strand annealed oligonucleotide, 5’GGCCGGACGCGTGAATTCGTCGACGC3’ and 5’GGCCGCGTCGACGAATTCACGC GTCC3’ containing restriction site for MluI, EcoRI and SalI were inserted in the NotI site (present in the multi cloning site), generating the plasmid pBS-villin-promoter-MES. The SV40 polyA region of the pEGFP plasmid (Clontech, Ozyme, Saint Quentin Yvelines, France) was amplified by PCR using primers 5’GGCGCCTCTAGATCATAATCAGCCATA3’ and 5’GGCGCCCTTAAGATACATTGATGAGTT3’ before subcloning into the pGEMTeasy vector (Promega, Charbonnières-les-Bains, France). After EcoRI digestion, the SV40 polyA fragment was purified with the NucleoSpin Extract II kit (Machery-Nagel, Hoerdt, France) and then subcloned into the EcoRI site of the plasmid pBS-villin-promoter-MES. Site directed mutagenesis was used to introduce a BsiWI site (5’ phosphorylated AGCGCAGGGAGCGGCGGCCGTACGATGCGCGGCAGCGGCACG3’) before the initiation codon and a MluI site (5’ phosphorylated 1 CCCGGGCCTGAGCCCTAAACGCGTGCCAGCCTCTGCCCTTGG3’) after the stop codon in the full length cDNA coding for the mouse LMα1 in the pCIS vector (kindly provided by P.
    [Show full text]
  • 1A Multiple Sclerosis Treatment
    The Pharmacogenomics Journal (2012) 12, 134–146 & 2012 Macmillan Publishers Limited. All rights reserved 1470-269X/12 www.nature.com/tpj ORIGINAL ARTICLE Network analysis of transcriptional regulation in response to intramuscular interferon-b-1a multiple sclerosis treatment M Hecker1,2, RH Goertsches2,3, Interferon-b (IFN-b) is one of the major drugs for multiple sclerosis (MS) 3 2 treatment. The purpose of this study was to characterize the transcriptional C Fatum , D Koczan , effects induced by intramuscular IFN-b-1a therapy in patients with relapsing– 2 1 H-J Thiesen , R Guthke remitting form of MS. By using Affymetrix DNA microarrays, we obtained and UK Zettl3 genome-wide expression profiles of peripheral blood mononuclear cells of 24 MS patients within the first 4 weeks of IFN-b administration. We identified 1Leibniz Institute for Natural Product Research 121 genes that were significantly up- or downregulated compared with and Infection Biology—Hans-Knoell-Institute, baseline, with stronger changed expression at 1 week after start of therapy. Jena, Germany; 2University of Rostock, Institute of Immunology, Rostock, Germany and Eleven transcription factor-binding sites (TFBS) are overrepresented in the 3University of Rostock, Department of Neurology, regulatory regions of these genes, including those of IFN regulatory factors Rostock, Germany and NF-kB. We then applied TFBS-integrating least angle regression, a novel integrative algorithm for deriving gene regulatory networks from gene Correspondence: M Hecker, Leibniz Institute for Natural Product expression data and TFBS information, to reconstruct the underlying network Research and Infection Biology—Hans-Knoell- of molecular interactions. An NF-kB-centered sub-network of genes was Institute, Beutenbergstr.
    [Show full text]
  • PROTEOME of the HUMAN CHROMOSOME 18: GENE-CENTRIC IDENTIFICATION of TRANSCRIPTS, PROTEINS and PEPTIDES Addendum to the Roadmap
    PROTEOME OF THE HUMAN CHROMOSOME 18: GENE-CENTRIC IDENTIFICATION OF TRANSCRIPTS, PROTEINS AND PEPTIDES Addendum to the Roadmap: HEALTH ASPECTS 1. PROTEOMICS MEETS MEDICINE At its very beginning, one of the goals of human proteomics became a disease biomarker discovery. Many works compared diseased and normal tissues and liquids to get diagnostic profiles by many proteomics methods. Of them, some cancer proteome profiling studies were considered too optimistic in terms of clinical applicability due to incorrect experimental design [Petricoin], thereby conferring the negative expectations from proteomics in translational medicine [Diamantidis, Nature]. The interlaboratory reproducibility of proteomics pipelines also was considered as a shortage in some papers, e.g. in the works of Bell et al [2009] who tested the proteome MS methods with 20-protein standard sample. These difficulties at the early stage of proteomics were partly caused by the fact that many attempts were mostly directed to the technique adjustment rather than to the clinically relevant result. However, the recent advances in mass-spectrometry including the use of MRM to quantify peptides of proteome [Anderson Hunter 2006] made the community to have a view of cautious optimism on the problem of translation to medicine [Nilsson 2010]. A reproducibility problem stated in [Bell 2009] was shown to be mainly caused by the bioinformatics misinterpretation whereas the MS itself worked properly. The readiness of MRM-based platforms to the clinical use is illustrated by the attempt to pass FDA with the mock application which describes MS-based quantitation test for 10 proteins [Regnier FE 2010]. In its current state, the test has not got a clearance.
    [Show full text]
  • The Role of Integrins in Enterovirus Infections and in Metastasis of Cancer
    TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS _____________________________________________________________________ SARJA – SER. D OSA– TOM. 908 MEDICA - ODONTOLOGICA THE ROLE OF INTEGRINS IN ENTEROVIRUS INFECTIONS AND IN METASTASIS OF CANCER by Åse Karttunen TURUN YLIOPISTO UNIVERSITY OF TURKU Turku 2010 TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS _____________________________________________________________________ SARJA – SER. D OSA– TOM. 908 MEDICA - ODONTOLOGICA THE ROLE OF INTEGRINS IN ENTEROVIRUS INFECTIONS AND IN METASTASIS OF CANCER by Åse Karttunen TURUN YLIOPISTO UNIVERSITY OF TURKU Turku 2010 From the Department of Virology, University of Turku, Turku, the Department of Virology, Haartman Institute, the Helsinki Biomedical Graduate School, University of Helsinki, Helsinki, and the Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku, Finland. Supervised by Professor Timo Hyypiä Department of Virology University of Turku Turku, Finland Reviewed by Professor Klaus Hedman Haartman Institute Department of Virology University of Helsinki Helsinki, Finland and Docent Arno Hänninen Department of Medical Microbiology and Immunology University of Turku Turku, Finland Opponent Professori Ari Hinkkanen A. I. Virtanen-instituutti Bioteknologia ja molekulaarinen lääketiede Itä-Suomen yliopisto Kuopio, Finland ISBN 978-951-29-4313-5 (PRINT) ISBN 978-951-29-4314-2 (PDF) ISSN 03559483 Helsinki University Printing House Helsinki 2010 To my Family ABSTRACT Åse Karttunen THE ROLE OF INTEGRINS IN ENTEROVIRUS INFECTIONS AND IN METASTASIS OF CANCER The Department of Virology, University of Turku, Turku, the Department of Virology, Haartman Institute, and the Helsinki Biomedical Graduate School, University of Helsinki, Helsinki, and the Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku, Finland. Annales Universitatis Turkuensis, Medica-Odontologica, Yliopistopaino, Helsinki, 2010. Integrins are a family of transmembrane glycoproteins, composed of two different subunits (α and β).
    [Show full text]
  • TGIF1 Antibody (Center A160) Purified Rabbit Polyclonal Antibody (Pab) Catalog # Ap12062c
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 TGIF1 Antibody (Center A160) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP12062c Specification TGIF1 Antibody (Center A160) - Product Information Application WB,E Primary Accession Q15583 Other Accession Q90655, NP_733796.2, NP_003235.1 Reactivity Human Predicted Chicken Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Calculated MW 43013 Antigen Region 145-174 Western blot analysis of TGIF1 (arrow) using TGIF1 Antibody (Center A160) - Additional rabbit polyclonal TGIF1 Antibody (Center Information A160) (Cat. #AP12062c). 293 cell lysates (2 ug/lane) either nontransfected (Lane 1) or Gene ID 7050 transiently transfected (Lane 2) with the TGIF1 gene. Other Names Homeobox protein TGIF1, 5'-TG-3'-interacting factor 1, TGIF1, TGIF TGIF1 Antibody (Center A160) - Background Target/Specificity This TGIF1 antibody is generated from The protein encoded by this gene is a member rabbits immunized with a KLH conjugated of the synthetic peptide between 145-174 amino three-amino acid loop extension (TALE) acids from the Central region of human superclass of atypical TGIF1. homeodomains. TALE homeobox proteins are highly conserved Dilution transcription regulators. This particular WB~~1:1000 homeodomain binds to a previously characterized retinoid X receptor Format responsive element Purified polyclonal antibody supplied in PBS from the cellular retinol-binding protein II with 0.09% (W/V) sodium azide. This promoter. In addition antibody is prepared by Saturated to its role in inhibiting 9-cis-retinoic Ammonium Sulfate (SAS) precipitation acid-dependent RXR alpha followed by dialysis against PBS. transcription activation of the retinoic acid Storage responsive element, Maintain refrigerated at 2-8°C for up to 2 the protein is an active transcriptional weeks.
    [Show full text]
  • Centre for Arab Genomic Studies a Division of Sheikh Hamdan Award for Medical Sciences
    Centre for Arab Genomic Studies A Division of Sheikh Hamdan Award for Medical Sciences The Catalogue for Transmission Genetics in Arabs CTGA Database Transforming Growth Factor-Beta-Induced Factor Alternative Names Mutations in the TGIF1 gene have been associated TGIF with Holoprosencephaly 4 (HPE4), an autosomal TGIF1 dominant neurological condition. TGFB-Induced Factor TG-Interacting Factor Molecular Genetics Record Category The TGIF1 gene is located on the short arm of Gene locus chromosome 18. It spans a length of 48.3 kb of DNA and its coding sequence is spread across 12 WHO-ICD exons. The gene encodes a 43 kDa protein product N/A to gene loci comprised of 401 amino acids. Four distinct isoforms of the TGIF1 protein exist due to Incidence per 100,000 Live Births alternatively spliced transcript variants. The gene is N/A to gene loci expressed in various tissues, including the liver, lung, thymus, bone marrow and brain. OMIM Number Heterozygous mutations in the TGIF1 gene 602630 associated with HPE4 include deletions, missense variants and premature truncations that impair its Mode of Inheritance function. N/A to gene loci Epidemiology in the Arab World Gene Map Locus Saudi Arabia 18p11.31 Monies et al. (2017) reported the genomic landscape of Saudi Arabia based on the findings of Description 1000 diagnostic panels and exomes. One patient, an Retinoid X receptors (RXRs) are nuclear receptors 11-year-old male, suffered from that function as transcriptional activators. In hemimegalencephaly, developmental delay and response to retinoids, they bind to specific cis- ADHD. He also had abnormal pigmentation all acting RXR responsive promoter elements of the over his body.
    [Show full text]
  • VU Research Portal
    VU Research Portal Genetic architecture and behavioral analysis of attention and impulsivity Loos, M. 2012 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Loos, M. (2012). Genetic architecture and behavioral analysis of attention and impulsivity. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 28. Sep. 2021 Chapter 5 Independent genetic loci for sensorimotor gating and attentional performance in BXD recombinant inbred strains Maarten Loos, Jorn Staal, Tommy Pattij, Neuro-BSIK Mouse Phenomics consortium, August B. Smit, Sabine Spijker Genes Brain and Behavior, In Press 87 88 Sensorimotor gating and attention Abstract A startle reflex in response to an intense acoustic stimulus is inhibited when a barely detectable pulse precedes the startle stimulus by 30 – 500 ms.
    [Show full text]
  • Use of Signals of Positive and Negative Selection to Distinguish Cancer
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.133199; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Use of signals of positive and negative selection to distinguish cancer 2 genes and passenger genes 3 4 5 László Bányai1, Mária Trexler1, Krisztina Kerekes1, Orsolya Csuka2 & László Patthy*1 6 7 1Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary 8 2 Department of Pathogenetics, National Institute of Oncology, Budapest, Hungary. 9 10 [email protected] 11 [email protected] 12 [email protected] 13 [email protected] 14 [email protected] 15 16 * Correspondence: [email protected]; Tel.: +36-1382-6751 17 18 19 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.133199; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 22 Abstract 23 Background 24 A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. 25 Most of the approaches aimed to achieve this goal focused on genes that are positively selected 26 for mutations that drive carcinogenesis and neglected the role of negative selection.
    [Show full text]
  • Use of Signals of Positive and Negative Selection to Distinguish Cancer
    RESEARCH ARTICLE Use of signals of positive and negative selection to distinguish cancer genes and passenger genes La´ szlo´ Ba´ nyai1, Maria Trexler1, Krisztina Kerekes1, Orsolya Csuka2, La´ szlo´ Patthy1* 1Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; 2Department of Pathogenetics, National Institute of Oncology, Budapest, Hungary Abstract A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. We have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations, oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells. Introduction *For correspondence: Genetic, epigenetic, transcriptomic, and proteomic changes driving [email protected] carcinogenesis In the last two decades, the rapid advance in genomics, epigenomics, transcriptomics, and proteo- Competing interests: The mics permitted an insight into the molecular basis of carcinogenesis. These studies have confirmed authors declare that no that tumors evolve from normal tissues by acquiring a series of genetic, epigenetic, transcriptomic, competing interests exist.
    [Show full text]
  • Novel Variants in Established Hypopituitarism Genes Expands Our Knowledge of Phenotypic Spectrum
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 May 2021 doi:10.20944/preprints202105.0521.v1 Novel variants in established hypopituitarism genes expands our knowledge of phenotypic spectrum Marilena Nakaguma 1, Nathalia Ferreira1, Anna Flavia Benedetti1,2,, Mariana Madi1, Juliana M Silva1, Sally A Camper3, Jun Li3, Qianyi Ma3, Asye B Ozel3, Qing Fang3, Amanda de Moraes Narcizo2, Laís Cavalca Cardoso2, Luciana Ribeiro Montenegro1,2, Mariana Ferreira de Assis Funari1,2, Mirian Yumie Nishi1,2,Berenice B Mendonca1,2, Ivo J P Arnhold1, Alex A L Jorge4, Luciani R Carvalho1. 1 Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil 2Laboratorio de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR. 3 Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA 4 Genetic Endocrinology Unit (LIM25), Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil Abstract We report four allelic variants (3 novel) in three genes previously established as causal for hypopituitarism or related disorders. A novel homozygous variant in the growth hormone gene, GH1 c.171delT (p. Phe 57Leufs * 43), was found in a male patient with severe isolated growth hormone deficiency (IGHD) born to consanguineous parents. A SOX3 allelic variant (p.Met304Ile) was found in a male patient with IGHD and hypoplastic anterior pituitary. YASARA, a tool to evaluate protein stability, suggests that p.Met304Ile destabilizes the SOX3 protein (ΔΔG = 2.49 kcal/mol).
    [Show full text]
  • Transcription Factors
    Flexi® ORF Clone www.promega.co.jp/flexiclone/ Transcription Factors 1216個 (2012/4/1 現在) 遺伝子シンボル 説明 FXC_PID 価格 FHC_PID 価格 AATF apoptosis antagonizing transcription factor FXC01868 ¥40,000 FHC01868 ¥50,000 ABT1 activator of basal transcription 1 FXC02664 ¥40,000 FHC02664 ¥50,000 AEBP2 AE binding protein 2, transcript variant 2 FXC30523M ¥90,000 FHC30523M ¥100,000 AFF1 AF4/FMR2 family, member 1 FXC01899 ¥40,000 FHC01899 ¥50,000 AFF4 AF4/FMR2 family, member 4 FXC07632M ¥50,000 FHC07632 ¥50,000 AHR aryl hydrocarbon receptor FXC01249 ¥40,000 FHC01249 ¥50,000 AHRR aryl-hydrocarbon receptor repressor FXC00775 ¥40,000 FHC00775 ¥50,000 ALX1 ALX homeobox 1 FXC24829M ¥50,000 FHC24829 ¥50,000 ALX4 ALX homeobox 4 FXC01180 ¥40,000 FHC01180 ¥50,000 ANP32A acidic (leucine-rich) nuclear phosphoprotein 32 family, FXC02366 ¥40,000 FHC02366 ¥50,000 Androgen receptor (Dihydrotestosterone receptor)(Nuclear AR FXC11949M ¥50,000 FHC11949 ¥50,000 receptor subfamily 3 group C member 4) Androgen receptor (Dihydrotestosterone receptor)(Nuclear AR FXC11950M ¥50,000 FHC11950 ¥50,000 receptor subfamily 3 group C member 4) AR androgen receptor FXC11031M ¥50,000 FHC11031 ¥50,000 ARID1B AT rich interactive domain 1B (SWI1-like) FXC11963M ¥140,000 FHC11963M ¥150,000 ARID3A AT rich interactive domain 3A (BRIGHT-like) FXC11107M ¥50,000 FHC11107 ¥50,000 ARID5B AT rich interactive domain 5B (MRF1-like) FXC11014 ¥40,000 FHC11014 ¥50,000 ARNT aryl hydrocarbon receptor nuclear translocator FXC01533 ¥40,000 FHC01533 ¥50,000 ARNT2 aryl-hydrocarbon receptor nuclear translocator 2
    [Show full text]