Cdc42 and the Guanine Nucleotide Exchange Factors Ect2 and Trio Mediate Fn14-Induced Migration and Invasion of Glioblastoma Cells

Total Page:16

File Type:pdf, Size:1020Kb

Cdc42 and the Guanine Nucleotide Exchange Factors Ect2 and Trio Mediate Fn14-Induced Migration and Invasion of Glioblastoma Cells Published OnlineFirst May 9, 2012; DOI: 10.1158/1541-7786.MCR-11-0616 Molecular Cancer Signaling and Regulation Research Cdc42 and the Guanine Nucleotide Exchange Factors Ect2 and Trio Mediate Fn14-Induced Migration and Invasion of Glioblastoma Cells Shannon P. Fortin1,2, Matthew J. Ennis1, Cassie A. Schumacher3, Cassandra R. Zylstra-Diegel3, Bart O. Williams3, Julianna T.D. Ross1, Jeffrey A. Winkles4, Joseph C. Loftus5, Marc H. Symons6, and Nhan L. Tran1 Abstract Malignant glioblastomas are characterized by their ability to infiltrate into normal brain. We previously reported that binding of the multifunctional cytokine TNF-like weak inducer of apoptosis (TWEAK) to its receptor fibroblast growth factor–inducible 14 (Fn14) induces glioblastoma cell invasion via Rac1 activation. Here, we show that Cdc42 plays an essential role in Fn14-mediated activation of Rac1. TWEAK-treated glioma cells display an increased activation of Cdc42, and depletion of Cdc42 using siRNA abolishes TWEAK-induced Rac1 activation and abrogates glioma cell migration and invasion. In contrast, Rac1 depletion does not affect Cdc42 activation by Fn14, showing that Cdc42 mediates TWEAK-stimulated Rac1 activation. Furthermore, we identified two guanine nucleotide exchange factors (GEF), Ect2 and Trio, involved in TWEAK-induced activation of Cdc42 and Rac1, respectively. Depletion of Ect2 abrogates both TWEAK-induced Cdc42 and Rac1 activation, as well as subsequent TWEAK-Fn14–directed glioma cell migration and invasion. In contrast, Trio depletion inhibits TWEAK-induced Rac1 activation but not TWEAK-induced Cdc42 activation. Finally, inappropriate expression of Fn14 or Ect2 in mouse astrocytes in vivo using an RCAS vector system for glial-specific gene transfer in G-tva transgenic mice induces astrocyte migration within the brain, corroborating the in vitro importance of the TWEAK-Fn14 signaling cascade in glioblastoma invasion. Our results suggest that the TWEAK-Fn14 signaling axis stimulates glioma cell migration and invasion through two GEF-GTPase signaling units, Ect2-Cdc42 and Trio-Rac1. Components of the Fn14-Rho GEF-Rho GTPase signaling pathway present innovative drug targets for glioma therapy. Mol Cancer Res; 10(7); 958–68. Ó2012 AACR. Introduction therapeutic strategies, the mechanisms of which are complex Glioblastomas are the most malignant and common and remain to be fully characterized (2). primary brain tumor in adults. Glioblastomas are highly Glioma cell invasion requires adhesion to extracellular infiltrative, leading to a poorly defined tumor mass. As a matrix, subsequent degradation, and remodeling of this result, complete resection of the tumor is not feasible matrix, as well as signaling initiated by promigratory growth factors, and Rho GTPase–mediated organization and remo- without compromising neurologic function, and despite fi adjuvant chemo- and radiation therapy, the 5-year survival deling of the actin cytoskeleton (3). Speci cally, the Rho rate is just under 10% (1). The invasive nature of glioblas- GTPase family members RhoA, Rac1, and Cdc42 are key toma correlates to an increased resistance to current regulators of cell migration and have been implicated in the formation of stress fibers, induction of lamellipodia, and filopodia protrusion (4). The regulation of Rho GTPase Authors' Affiliations: 1Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix; 2Cancer Biology Graduate Inter- activation is mediated by 3 classes of proteins: guanine disciplinary Program, University of Arizona, Tucson, Arizona; 3Van Andel nucleotide exchange factors (GEF), which are responsible for Research Institute, Grand Rapids, Michigan; 4University of Maryland School of Medicine, Baltimore, Maryland; 5Mayo Clinic, Scottsdale, Ari- activating Rho GTPases to their GTP-bound state; GTPase- zona; and 6Center for Oncology and Cell Biology, The Feinstein Institute for activating proteins (GAP), which enact phosphate bond Medical Research at North Shore-LIJ, Manhasset, New York hydrolysis thus inactivating Rho GTPases to a GDP-bound Corresponding Authors: Nhan L. Tran, The Translational Genomics state; and GDP dissociation inhibitors (GDI) which bind to Research Institute, 445 N Fifth Street, Suite 400, Phoenix, AZ 85004. and stabilize Rho GTPases in their inactive GDP-bound form Phone: 602-343-8771; Fax: 602-343-8717; E-mail: [email protected]; and Marc H. Symons, The Feinstein Institute, 350 Community Dr., Manhasset, (5). To date, 22 Rho GTPases and 80 Rho GEFs belonging NY 11030. Phone: 516-562-1193; Fax: 516-562-1022; E-mail: to either the Dbl or DOCK families have been identified (6). [email protected] Previous studies have shown that the fibroblast growth doi: 10.1158/1541-7786.MCR-11-0616 factor inducible–14 (Fn14) receptor can signal to induce Ó2012 American Association for Cancer Research. Rac1 activation (7). Fn14 is a transmembrane receptor 958 Mol Cancer Res; 10(7) July 2012 Downloaded from mcr.aacrjournals.org on September 28, 2021. © 2012 American Association for Cancer Research. Published OnlineFirst May 9, 2012; DOI: 10.1158/1541-7786.MCR-11-0616 Ect2 and Trio Regulate Fn14-Induced Glioblastoma Invasion belonging to the TNF receptor superfamily (TNFRSF) and Antibodies, reagents, and Western blot analysis serves as the receptor for the multifunctional cytokine A monoclonal Cdc42 antibody was purchased from Santa TWEAK (8). The Fn14 cytoplasmic tail lacks a death Cruz Biotechnology. Anti-myc was purchased from Cell domain but contains TNFR-associated factor (TRAF) bind- Signaling Technologies. A polyclonal Ect2 antibody and a ing sites specific for TRAF1, 2, 3, and 5 (9). Fn14 expression monoclonal antibody to tubulin were purchased from Milli- is minimal to absent in normal brain tissue but correlates pore. Human recombinant TWEAK was purchased from with tumor grade in glioblastoma (10). Activation of Fn14 PeproTech, and laminin from human placenta was obtained by TWEAK promotes glioma cell migration, invasion, and from Sigma. Lipofectamine 2000 was purchased from survival (7, 10, 11). The TWEAK-Fn14 signaling axis Invitrogen. mediates glioma migration and invasion via the Rac1 For immunoblotting, cells were lysed in 2Â SDS sample GTPase and fosters a self-promoting feedback loop whereby buffer (0.25 mol/L Tris-HCl, pH 6.8, 10% SDS, 25% Rac1-mediated TWEAK-Fn14 signaling induces Fn14 gene glycerol) containing 10 mg/mL aprotinin, 10 mg/mL leu- expression via the NF-kB pathway (7). While Rac1 is peptin, 20 mmol/L NaF, 2 mmol/L sodium orthovanadate, ubiquitously expressed among tissue types (12, 13), the and 1 mmol/L phenylmethylsulfonylfluoride. Protein con- levels of Rac1 protein expression in astrocytomas directly centrations were determined using the BCA Assay (Pierce) correlate with tumor grade in tissue microarray analysis. with BSA as a standard. Thirty micrograms of total cellular Furthermore, in glioblastoma, but not in lower grade astro- protein was loaded per lane and separated by SDS-PAGE. cytomas, prominent plasma membrane staining of Rac1 is After transfer at 4C, the nitrocellulose (Invitrogen) was observed. These observations indicate that Rac1 is consti- blocked with either 5% nonfat milk or 5% BSA in TBS, pH tutively active in glioblastomas, underlining the importance 8.0, containing 0.1% Tween-20 (TBST) before addition of of Rac1 in these tumors (14). To date, 5 GEFs that can primary antibodies and followed with peroxidase-conjugated activate Rac1 (Ect2, Vav3, Trio, SWAP-70, and Dock180- anti-mouse IgG or anti-rabbit IgG. Protein bands were ELMO1) have been shown to contribute to the invasive detected using SuperSignal West Dura Chemiluminescent behavior of glioblastoma (14–16). Four of these GEFs have Substrate (Thermo Scientific) with a UVP BioSpectrum 500 been shown to be overexpressed in glioblastoma versus non- Imaging System. neoplastic brain (Ect2, Vav3, Trio, and SWAP-70; refs. 14, 16), and expression of Dock180 is higher in the Preparation of recombinant adenoviruses and infection tumor rim than in the tumor core. Adenoviruses expressing myc-tagged Fn14 wild-type pro- In this study, we describe a role for TWEAK-Fn14 tein and the cytoplasmic domain truncation mutant myc- signaling through a multi-GEF, multi-Rho GTPase sig- Fn14tCT protein were previously described (7). Cells were naling pathway that includes Ect2, Trio, Cdc42, and infected at matched multiplicity of infections ranging from 5 Rac1. We show that Rac1 activation via TWEAK-Fn14 to 20. For adenoviral infection, 1.5 Â 105 cells were plated signaling is dependent upon Cdc42 function. We also into a 6-well plate and cultured for 24 hours before infection. report that Ect2 mediates Cdc42 activation, whereas Trio mediates Rac1 activation following TWEAK stimu- Immunoprecipitation, Rac and Cdc42 activity assays, lation. Depletion of Ect2, Trio, or Cdc42 by siRNA and nucleotide-free GEF pulldowns oligonucleotides suppresses TWEAK-Fn14–induced Rac1 For immunoprecipitation, cells were lysed on ice for activation and subsequently glioma cell migration and 10 minutes in a buffer containing 10 mmol/L Tris- invasion. Finally, we show that the inappropriate expres- HCl (pH 7.4), 0.5% Nonidet P-40, 150 mmol/L NaCl, sion of either Fn14 or Ect2 in the astrocyte population of 1 mmol/L phenylmethylsulfonylfluoride, 1 mmol/L EDTA, glial fibrillary acidic protein (GFAP)-tva transgenic mice 2 mmol/L sodium orthovanadate, 10 mg/mL aprotinin, and induces astrocyte cell motility and proliferation, suggest- 10 mg/mL leupeptin (Sigma). Equivalent amounts of protein
Recommended publications
  • Cytoplasmic Expression of Epithelial Cell Transforming Sequence 2 in Lung Adenocarcinoma and Its Implications for Malignant Progression
    Laboratory Investigation (2019) 99:551–567 https://doi.org/10.1038/s41374-018-0142-4 ARTICLE Cytoplasmic expression of epithelial cell transforming sequence 2 in lung adenocarcinoma and its implications for malignant progression 1 2 3 1 2 2 Zeinab Kosibaty ● Yoshihiko Murata ● Yuko Minami ● Tomoko Dai ● Junko Kano ● Ryota Matsuoka ● 2 2 Noriyuki Nakano ● Masayuki Noguchi Received: 8 March 2018 / Revised: 14 August 2018 / Accepted: 20 August 2018 / Published online: 12 December 2018 © United States & Canadian Academy of Pathology 2018 Abstract Epithelial cell transforming sequence 2 (ECT2), a guanine nucleotide exchange factor, is predominantly localized in the nucleus of non-transformed cells and functions to regulate cytokinesis. ECT2 is also localized in the cytoplasm of cancer cells. Aberrant cytoplasmic expression of ECT2 is thought to drive tumor growth and invasion. In this study, we investigated the cytoplasmic expression of ECT2 and its prognostic and biological significance in lung adenocarcinoma. Western blotting of cellular fractions from the nucleus and cytoplasm was performed to determine the subcellular localization of ECT2 in lung adenocarcinoma cell lines. The cytoplasmic expression of ECT2 in 167 lung fi 1234567890();,: 1234567890();,: adenocarcinomas was evaluated by immunohistochemistry and its clinical signi cance was examined using Kaplan–Meier curves and Cox regression analysis. Scraping cytology specimens of 13 fresh lung adenocarcinomas were used to assess the subcellular localization of ECT2 and its phosphorylation at Thr790 (P-ECT2(T790)). We found that ECT2 was localized in both the nucleus and cytoplasm of lung adenocarcinoma cell lines and tumor tissues. Cytoplasmic expression of ECT2 was detected by immunohistochemistry in 83 (50%) of the lung adenocarcinomas, and was found to increase during cancer progression.
    [Show full text]
  • Cell Division Symmetry Control and Cancer Stem Cells
    AIMS Molecular Science, 7(2): 82–98. DOI: 10.3934/molsci.2020006 Received: 15 February 2020 Accepted: 26 April 2020 Published: 06 May 2020 http://www.aimspress.com/journal/Molecular Review Cell division symmetry control and cancer stem cells Sreemita Majumdar and Song-Tao Liu* Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA * Correspondence: Email: [email protected]; Tel: +14195307853. Table S1. Genes encoding polarity and fate-determinant proteins involved in asymmetric cell division. C. elegans1 D. melanogaster 1 Mammals1 Description2 Associated with/ Interactors 3 Cellular Localization (mammalian cell)4 Serine/threonine protein microtubule-associated protein cell membrane, peripheral and lateral, par-1 par-1 MARK1/2/3/4 kinase MAPT/TAU cytoplasm, dendrite RING, Lipid binding par-2 - - domain PDZ for membrane, cell junction, adherens junction, cell cortex, par-3 baz PARD3 Oligomerization domain at actin, PARD6 endomembrane system, NTD Continued on next page 2 C. elegans1 D. melanogaster 1 Mammals1 Description2 Associated with/ Interactors 3 Cellular Localization (mammalian cell)4 Serine/threonine-protein nucleus, mitochondria, cytoplasm, par-4 Lkb1 STK11/LKB1 STRAD complex kinase membrane 14-3-3 domain binding par-5 14-3-3 YWHAB phosphoserine/ adapter to many proteins cytoplasm phosphothreonine motif cell membrane, centriolar satellite, actin par-6 par-6 PARD6A/B/G PB1, CRIB, PDZ PARD3 cytoskeleton,centrosome, cytoplasm ,ruffles PARD3, and a PARD6 protein PB1, AGC-Kinase (PARD6A, PARD6B or PARD6G) pkc-3 aPKC PRKCI/Z domain, DAG binding, cytoplasm, nucleus, membrane and a GTPase protein (CDC42 or Zinc finger domain RAC1), LLGL1,ECT2 LRR and PDZ protein Cadherin, Scrib-APC-beta-catenin nucleoplasm, basolateral plasma membrane, let-413 scrib SCRIB family.
    [Show full text]
  • The Rac Gtpase in Cancer: from Old Concepts to New Paradigms Marcelo G
    Published OnlineFirst August 14, 2017; DOI: 10.1158/0008-5472.CAN-17-1456 Cancer Review Research The Rac GTPase in Cancer: From Old Concepts to New Paradigms Marcelo G. Kazanietz1 and Maria J. Caloca2 Abstract Rho family GTPases are critical regulators of cellular func- mislocalization of Rac signaling components. The unexpected tions that play important roles in cancer progression. Aberrant pro-oncogenic functions of Rac GTPase-activating proteins also activity of Rho small G-proteins, particularly Rac1 and their challenged the dogma that these negative Rac regulators solely regulators, is a hallmark of cancer and contributes to the act as tumor suppressors. The potential contribution of Rac tumorigenic and metastatic phenotypes of cancer cells. This hyperactivation to resistance to anticancer agents, including review examines the multiple mechanisms leading to Rac1 targeted therapies, as well as to the suppression of antitumor hyperactivation, particularly focusing on emerging paradigms immune response, highlights the critical need to develop ther- that involve gain-of-function mutations in Rac and guanine apeutic strategies to target the Rac pathway in a clinical setting. nucleotide exchange factors, defects in Rac1 degradation, and Cancer Res; 77(20); 5445–51. Ó2017 AACR. Introduction directed toward targeting Rho-regulated pathways for battling cancer. Exactly 25 years ago, two seminal papers by Alan Hall and Nearly all Rho GTPases act as molecular switches that cycle colleagues illuminated us with one of the most influential dis- between GDP-bound (inactive) and GTP-bound (active) forms. coveries in cancer signaling: the association of Ras-related small Activation is promoted by guanine nucleotide exchange factors GTPases of the Rho family with actin cytoskeleton reorganization (GEF) responsible for GDP dissociation, a process that normally (1, 2).
    [Show full text]
  • Profiling Cytotoxic Micrornas in Pediatric and Adult Glioblastoma
    Oncogene https://doi.org/10.1038/s41388-020-1360-y ARTICLE Profiling cytotoxic microRNAs in pediatric and adult glioblastoma cells by high-content screening, identification, and validation of miR-1300 1 1 2 2 1 1 1 1,3 1 M. Boissinot ● H. King ● M. Adams ● J. Higgins ● G. Shaw ● T. A. Ward ● L. P. Steele ● D. Tams ● R. Morton ● 4 4 5 1,6 7 8 9 2,7 E. Polson ● B. da Silva ● A. Droop ● J. L. Hayes ● H. Martin ● P. Laslo ● E. Morrison ● D. C. Tomlinson ● 4 2,10 1,11 1,12 H. Wurdak ● J. Bond ● S. E. Lawler ● S. C. Short Received: 29 November 2019 / Revised: 20 May 2020 / Accepted: 5 June 2020 © The Author(s) 2020. This article is published with open access Abstract MicroRNAs play an important role in the regulation of mRNA translation and have therapeutic potential in cancer and other diseases. To profile the landscape of microRNAs with significant cytotoxicity in the context of glioblastoma (GBM), we performed a high-throughput screen in adult and pediatric GBM cells using a synthetic oligonucleotide library representing all known human microRNAs. Bioinformatics analysis was used to refine this list and the top seven microRNAs were validated in a 1234567890();,: 1234567890();,: larger panel of GBM cells using state-of-the-art in vitro assays. The cytotoxic effect of our most relevant candidate was assessed in a preclinical model. Our screen identified ~100 significantly cytotoxic microRNAs with 70% concordance between cell lines. MicroRNA-1300 (miR-1300) was the most potent and robust candidate. We observed a striking binucleated phenotype in miR- 1300 transfected cells due to cytokinesis failure followed by apoptosis.
    [Show full text]
  • Identification of Biomarkers in Colon Cancer Based on Bioinformatic Analysis
    4895 Original Article Identification of biomarkers in colon cancer based on bioinformatic analysis Ying Zhu1#^, Leitao Sun2#^, Jieru Yu3, Yuying Xiang1^, Minhe Shen2^, Harpreet S. Wasan4^, Shanming Ruan2^, Shengliang Qiu2^ 1The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China; 2Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China; 3College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China; 4Department of Cancer Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK Contributions: (I) Conception and design: Y Zhu, L Sun; (II) Administrative support: M Shen, S Ruan, S Qiu; (III) Provision of study materials or patients: Z Ying, L Sun; (IV) Collection and assembly of data: J Yu, Y Xiang; (V) Data analysis and interpretation: Ying Zhu, Leitao Sun, Harpreet S. Wasan, S Qiu, S Ruan; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Shengliang Qiu. Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Shangcheng, Hangzhou 310006, China. Email: [email protected]; Shanming Ruan. Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Shangcheng, Hangzhou 310006, China. Email: shanmingruan@ zcmu.edu.cn. Background: Colon cancer is one of the most common cancers in the world. Targeting biomarkers is helpful for the diagnosis and treatment of colon cancer. This study aimed to identify biomarkers in colon cancer, in addition to those that have already been reported, using microarray datasets and bioinformatics analysis.
    [Show full text]
  • Rho Guanine Nucleotide Exchange Factors: Regulators of Rho Gtpase Activity in Development and Disease
    Oncogene (2014) 33, 4021–4035 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc REVIEW Rho guanine nucleotide exchange factors: regulators of Rho GTPase activity in development and disease DR Cook1, KL Rossman2,3 and CJ Der1,2,3 The aberrant activity of Ras homologous (Rho) family small GTPases (20 human members) has been implicated in cancer and other human diseases. However, in contrast to the direct mutational activation of Ras found in cancer and developmental disorders, Rho GTPases are activated most commonly in disease by indirect mechanisms. One prevalent mechanism involves aberrant Rho activation via the deregulated expression and/or activity of Rho family guanine nucleotide exchange factors (RhoGEFs). RhoGEFs promote formation of the active GTP-bound state of Rho GTPases. The largest family of RhoGEFs is comprised of the Dbl family RhoGEFs with 70 human members. The multitude of RhoGEFs that activate a single Rho GTPase reflects the very specific role of each RhoGEF in controlling distinct signaling mechanisms involved in Rho activation. In this review, we summarize the role of Dbl RhoGEFs in development and disease, with a focus on Ect2 (epithelial cell transforming squence 2), Tiam1 (T-cell lymphoma invasion and metastasis 1), Vav and P-Rex1/2 (PtdIns(3,4,5)P3 (phosphatidylinositol (3,4,5)-triphosphate)-dependent Rac exchanger). Oncogene (2014) 33, 4021–4035; doi:10.1038/onc.2013.362; published online 16 September 2013 Keywords: Rac1; RhoA; Cdc42; guanine nucleotide exchange factors; cancer;
    [Show full text]
  • Novel Potential ALL Low-Risk Markers Revealed by Gene
    Leukemia (2003) 17, 1891–1900 & 2003 Nature Publishing Group All rights reserved 0887-6924/03 $25.00 www.nature.com/leu BIO-TECHNICAL METHODS (BTS) Novel potential ALL low-risk markers revealed by gene expression profiling with new high-throughput SSH–CCS–PCR J Qiu1,5, P Gunaratne2,5, LE Peterson3, D Khurana2, N Walsham2, H Loulseged2, RJ Karni1, E Roussel4, RA Gibbs2, JF Margolin1,6 and MC Gingras1,6 1Texas Children’s Cancer Center and Department of Pediatrics; 2Human Genome Sequencing Center, Department of Molecular and Human Genetics; 3Department of Internal Medicine; 1,2,3 are all departments of Baylor College of Medicine, Baylor College of Medicine, Houston, TX, USA; and 4BioTher Corporation, Houston, TX, USA The current systems of risk grouping in pediatric acute t(1;19), BCR-ABL t(9;22), and MLL-AF4 t(4;11).1 These chromo- lymphoblastic leukemia (ALL) fail to predict therapeutic suc- somal modifications and other clinical findings such as age and cess in 10–35% of patients. To identify better predictive markers of clinical behavior in ALL, we have developed an integrated initial white blood cell count (WBC) define pediatric ALL approach for gene expression profiling that couples suppres- subgroups and are used as diagnostic and prognostic markers to sion subtractive hybridization, concatenated cDNA sequencing, assign specific risk-adjusted therapies. For instance, 1.0 to 9.9- and reverse transcriptase real-time quantitative PCR. Using this year-old patients with none of the determinant chromosomal approach, a total of 600 differentially expressed genes were translocation (NDCT) mentioned above but with a WBC higher identified between t(4;11) ALL and pre-B ALL with no determi- than 50 000 cells/ml are associated with higher risk group.2 nant chromosomal translocation.
    [Show full text]
  • A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase.
    [Show full text]
  • Supplementary Information
    Osa et al Supplementary Information Clinical implications of monitoring nivolumab immunokinetics in previously treated non– small cell lung cancer patients Akio Osa, Takeshi Uenami, Shohei Koyama, Kosuke Fujimoto, Daisuke Okuzaki, Takayuki Takimoto, Haruhiko Hirata, Yukihiro Yano, Soichiro Yokota, Yuhei Kinehara, Yujiro Naito, Tomoyuki Otsuka, Masaki Kanazu, Muneyoshi Kuroyama, Masanari Hamaguchi, Taro Koba, Yu Futami, Mikako Ishijima, Yasuhiko Suga, Yuki Akazawa, Hirotomo Machiyama, Kota Iwahori, Hyota Takamatsu, Izumi Nagatomo, Yoshito Takeda, Hiroshi Kida, Esra A. Akbay, Peter S. Hammerman, Kwok-kin Wong, Glenn Dranoff, Masahide Mori, Takashi Kijima, Atsushi Kumanogoh Supplemental Figures 1 – 8 1 Osa et al Supplemental Figure 1. The frequency of nivolumab-bound T cells was maintained in patients who continued treatment. Nivolumab binding in CD8 and CD4 T cells was analyzed at two follow-up points, as indicated, in fresh peripheral blood from three representative cases from protocol 1 that continued treatment. 2 Osa et al Supplemental Figure 2. Long-term follow-up of nivolumab binding to T cells from fresh whole blood. Nivolumab binding was followed up in fresh peripheral blood from an additional case, Pt.7. 3 Osa et al Supplemental Figure 3. Long-term duration of nivolumab binding is due to sustained circulation of residual nivolumab in plasma. (A) PBMCs acquired from Pt.8 and 9 at pretreatment (pre PBMCs) and after a single dose (post 1 PBMCs) were cultured in regular medium without nivolumab (top and middle). Pre PBMCs were also incubated with 10 µg/ml nivolumab in vitro before the cultures were started (bottom). Nivolumab binding status was monitored at the indicated time points.
    [Show full text]
  • Identification of Significant Genes with Poor Prognosis in Ovarian Cancer Via Bioinformatical Analysis
    Feng et al. Journal of Ovarian Research (2019) 12:35 https://doi.org/10.1186/s13048-019-0508-2 RESEARCH Open Access Identification of significant genes with poor prognosis in ovarian cancer via bioinformatical analysis Hao Feng1†, Zhong-Yi Gu2†, Qin Li2, Qiong-Hua Liu3, Xiao-Yu Yang4* and Jun-Jie Zhang2* Abstract Ovarian cancer (OC) is the highest frequent malignant gynecologic tumor with very complicated pathogenesis. The purpose of the present academic work was to identify significant genes with poor outcome and their underlying mechanisms. Gene expression profiles of GSE36668, GSE14407 and GSE18520 were available from GEO database. There are 69 OC tissues and 26 normal tissues in the three profile datasets. Differentially expressed genes (DEGs) between OC tissues and normal ovarian (OV) tissues were picked out by GEO2R tool and Venn diagram software. Next, we made use of the Database for Annotation, Visualization and Integrated Discovery (DAVID) to analyze Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and gene ontology (GO). Then protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). There were total of 216 consistently expressed genes in the three datasets, including 110 up-regulated genes enriched in cell division, sister chromatid cohesion, mitotic nuclear division, regulation of cell cycle, protein localization to kinetochore, cell proliferation and Cell cycle, progesterone-mediated oocyte maturation and p53 signaling pathway, while 106 down-regulated genes enriched in palate development, blood coagulation, positive regulation of transcription from RNA polymerase II promoter, axonogenesis, receptor internalization, negative regulation of transcription from RNA polymerase II promoter and no significant signaling pathways.
    [Show full text]
  • Transdifferentiation of Human Mesenchymal Stem Cells
    Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone
    [Show full text]
  • Exploring the Regulation and Function of the Human Guanine Nucleotide Exchange Factor Ect2 (Epithelial Cell Transforming Protein 2) in Cytokinesis
    Exploring the regulation and function of the human guanine nucleotide exchange factor Ect2 (epithelial cell transforming protein 2) in cytokinesis Dissertation der Fakultät für Biologie der Ludwig-Maximilians-Universität München Vorgelegt von Ravindra B. Chalamalasetty Martinsried / München 2006 Dissertation eingereicht am 02, February, 2006 Tag der mündlichen Prüfung : 08, March, 2006 Erstgutachter: Prof. Dr. Erich A. Nigg Zweitgutachter: Prof.Dr. Stefan Jentsch Hiermit erkläre ich, dass ich die vorliegende Dissertation selbständig und ohne unerlaubte Hilfe angefertigt habe. Sämtliche Experimente sind von mir selbst durchgeführt worden, falls nicht explizit auf dritte verwiesen wird. Ich versichere, daß ich weder versucht habe, eine Dissertation oder Teile einer Dissertation an einer anderen Stelle einzureichen, noch eine Doktorprüfung durchzuführen. München, den 24-01-2006 Table of contents Table of contents TABLE OF CONTENTS…………………………………………...….I-IV ACKNOWLEDGEMENTS SUMMARY………………………………………………………………..1 1.0 INTRODUCTION…………………………………………………….3 1.1 Overview of the cell cycle……………………………………………..3 1.1.1 An overview of mitosis………………………………………………………..4 1.1.2 An overview of cytokinesis…………………………………………………....6 1.1.3 Regulation of M phase progression…………………………………………....6 1.2 Cytokinesis…………………………………………………………….10 1.2.1 Cytokinesis in yeasts and plants……………………………………………...10 1.3 Cytokinesis in mammalian cells……………………………………...14 1.3.1 Division site determination in mammalian cells…………………………......14 1.3.2 Models for the roles of microtubules in cleavage
    [Show full text]