Mediated Topoisomerase II&Beta
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Transcription-Induced DNA Double Strand Breaks: Both Oncogenic Force and Potential Therapeutic Target?
Published OnlineFirst March 8, 2011; DOI: 10.1158/1078-0432.CCR-10-2044 Clinical Cancer Molecular Pathways Research Transcription-Induced DNA Double Strand Breaks: Both Oncogenic Force and Potential Therapeutic Target? Michael C. Haffner, Angelo M. De Marzo, Alan K. Meeker, William G. Nelson, and Srinivasan Yegnasubramanian Abstract An emerging model of transcriptional activation suggests that induction of transcriptional programs, for instance by stimulating prostate or breast cells with androgens or estrogens, respectively, involves the formation of DNA damage, including DNA double strand breaks (DSB), recruitment of DSB repair proteins, and movement of newly activated genes to transcription hubs. The DSB can be mediated by the class II topoisomerase TOP2B, which is recruited with the androgen receptor and estrogen receptor to regulatory sites on target genes and is apparently required for efficient transcriptional activation of these genes. These DSBs are recognized by the DNA repair machinery triggering the recruitment of repair proteins such as poly(ADP-ribose) polymerase 1 (PARP1), ATM, and DNA-dependent protein kinase (DNA-PK). If illegitimately repaired, such DSBs can seed the formation of genomic rearrangements like the TMPRSS2- ERG fusion oncogene in prostate cancer. Here, we hypothesize that these transcription-induced, TOP2B- mediated DSBs can also be exploited therapeutically and propose that, in hormone-dependent tumors like breast and prostate cancers, a hormone-cycling therapy, in combination with topoisomerase II poisons or inhibitors of the DNA repair components PARP1 and DNA-PK, could overwhelm cancer cells with transcription-associated DSBs. Such strategies may find particular utility in cancers, like prostate cancer, which show low proliferation rates, in which other chemotherapeutic strategies that target rapidly proliferating cells have had limited success. -
Targeting Topoisomerase I in the Era of Precision Medicine Anish Thomas and Yves Pommier
Published OnlineFirst June 21, 2019; DOI: 10.1158/1078-0432.CCR-19-1089 Review Clinical Cancer Research Targeting Topoisomerase I in the Era of Precision Medicine Anish Thomas and Yves Pommier Abstract Irinotecan and topotecan have been widely used as including the indenoisoquinolines LMP400 (indotecan), anticancer drugs for the past 20 years. Because of their LMP776 (indimitecan), and LMP744, and on tumor- selectivity as topoisomerase I (TOP1) inhibitors that trap targeted delivery TOP1 inhibitors using liposome, PEGyla- TOP1 cleavage complexes, camptothecins are also widely tion, and antibody–drug conjugates. We also address how used to elucidate the DNA repair pathways associated with tumor-specific determinants such as homologous recombi- DNA–protein cross-links and replication stress. This review nation defects (HRD and BRCAness) and Schlafen 11 summarizes the basic molecular mechanisms of action (SLFN11) expression can be used to guide clinical appli- of TOP1 inhibitors, their current use, and limitations cation of TOP1 inhibitors in combination with DNA dam- as anticancer agents. We introduce new therapeutic strate- age response inhibitors including PARP, ATR, CHEK1, and gies based on novel TOP1 inhibitor chemical scaffolds ATM inhibitors. Introduction DNA structures such as plectonemes, guanosine quartets, R-loops, and DNA breaks (reviewed in ref. 1). Humans encodes six topoisomerases, TOP1, TOP1MT, TOP2a, TOP2b, TOP3a, and TOP3b (1) to pack and unpack the approx- imately 2 meters of DNA that needs to be contained in the nucleus Anticancer TOP1 Inhibitors Trap TOP1CCs whose diameter (6 mm) is approximately 3 million times smaller. as Interfacial Inhibitors Moreover, the genome is organized in chromosome loops and the separation of the two strands of DNA during transcription and The plant alkaloid camptothecin and its clinical derivatives, replication generate torsional stress and supercoils that are topotecan and irinotecan (Fig. -
Single-Nuclei RNA-Seq on Human Retinal Tissue Provides Improved Transcriptome Profiling
ARTICLE https://doi.org/10.1038/s41467-019-12917-9 OPEN Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling Qingnan Liang 1,2,3,9, Rachayata Dharmat1,2,8,9, Leah Owen4, Akbar Shakoor4, Yumei Li1, Sangbae Kim1, Albert Vitale4, Ivana Kim4, Denise Morgan4,5, Shaoheng Liang 6, Nathaniel Wu1, Ken Chen 6, Margaret M. DeAngelis4,5,7* & Rui Chen1,2,3* Single-cell RNA-seq is a powerful tool in decoding the heterogeneity in complex tissues by 1234567890():,; generating transcriptomic profiles of the individual cell. Here, we report a single-nuclei RNA- seq (snRNA-seq) transcriptomic study on human retinal tissue, which is composed of mul- tiple cell types with distinct functions. Six samples from three healthy donors are profiled and high-quality RNA-seq data is obtained for 5873 single nuclei. All major retinal cell types are observed and marker genes for each cell type are identified. The gene expression of the macular and peripheral retina is compared to each other at cell-type level. Furthermore, our dataset shows an improved power for prioritizing genes associated with human retinal dis- eases compared to both mouse single-cell RNA-seq and human bulk RNA-seq results. In conclusion, we demonstrate that obtaining single cell transcriptomes from human frozen tissues can provide insight missed by either human bulk RNA-seq or animal models. 1 HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. 2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston 77030 TX, USA. 3 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. -
The Ski Oncoprotein Interacts with Skip, the Human Homolog of Drosophila Bx42
Oncogene (1998) 16, 1579 ± 1586 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 The Ski oncoprotein interacts with Skip, the human homolog of Drosophila Bx42 Richard Dahl, Bushra Wani and Michael J Hayman Department of Microbiology, State University of New York, Stony Brook, New York 11794, USA The v-Ski avian retroviral oncogene is postulated to act Little is known about how Ski functions. Both the as a transcription factor. Since protein ± protein interac- cellular and the viral genes share transforming and tions have been shown to play an important role in the muscle inducing ability. Ski localizes to the nucleus and transcription process, we attempted to identify Ski is observed to associate with chromatin (Barkas et al., protein partners with the yeast two-hybrid system. Using 1986; Sutrave et al., 1990a). Because of its nuclear v-Ski sequence as bait, the human gene skip (Ski localization and its ability to induce expression of Interacting Protein) was identi®ed as encoding a protein muscle speci®c genes in quail cells (Colmenares and which interacts with both the cellular and viral forms of Stavnezer, 1989), Ski has been assumed to be a Ski in the two-hybrid system. Skip is highly homologous transcription factor. Consistent with this assumption, to the Drosophila melanogaster protein Bx42 which is c-Ski has been shown to bind DNA in vitro with the found associated with chromatin in transcriptionally help of an unknown protein factor (Nagase et al., active pus of salivary glands. The Ski-Skip interaction 1990), and has been recently shown to enhance MyoD is potentially important in Ski's transforming activity dependent transactivation of a myosin light chain since Skip was demonstrated to interact with a highly enhancer linked reporter gene in muscle cells (Engert conserved region of Ski required for transforming et al., 1995). -
Identifying Novel Actionable Targets in Colon Cancer
biomedicines Review Identifying Novel Actionable Targets in Colon Cancer Maria Grazia Cerrito and Emanuela Grassilli * Department of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy; [email protected] * Correspondence: [email protected] Abstract: Colorectal cancer is the fourth cause of death from cancer worldwide, mainly due to the high incidence of drug-resistance toward classic chemotherapeutic and newly targeted drugs. In the last decade or so, the development of novel high-throughput approaches, both genome-wide and chemical, allowed the identification of novel actionable targets and the development of the relative specific inhibitors to be used either to re-sensitize drug-resistant tumors (in combination with chemotherapy) or to be synthetic lethal for tumors with specific oncogenic mutations. Finally, high- throughput screening using FDA-approved libraries of “known” drugs uncovered new therapeutic applications of drugs (used alone or in combination) that have been in the clinic for decades for treating non-cancerous diseases (re-positioning or re-purposing approach). Thus, several novel actionable targets have been identified and some of them are already being tested in clinical trials, indicating that high-throughput approaches, especially those involving drug re-positioning, may lead in a near future to significant improvement of the therapy for colon cancer patients, especially in the context of a personalized approach, i.e., in defined subgroups of patients whose tumors carry certain mutations. Keywords: colon cancer; drug resistance; target therapy; high-throughput screen; si/sh-RNA screen; CRISPR/Cas9 knockout screen; drug re-purposing; drug re-positioning Citation: Cerrito, M.G.; Grassilli, E. -
Mutations in SKI in Shprintzen–Goldberg Syndrome Lead to Attenuated TGF-B Responses Through SKI Stabilization
RESEARCH ARTICLE Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-b responses through SKI stabilization Ilaria Gori1, Roger George2, Andrew G Purkiss2, Stephanie Strohbuecker3, Rebecca A Randall1, Roksana Ogrodowicz2, Virginie Carmignac4, Laurence Faivre4, Dhira Joshi5, Svend Kjær2, Caroline S Hill1* 1Developmental Signalling Laboratory, The Francis Crick Institute, London, United Kingdom; 2Structural Biology Facility, The Francis Crick Institute, London, United Kingdom; 3Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, United Kingdom; 4INSERM - Universite´ de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France; 5Peptide Chemistry Facility, The Francis Crick Institute, London, United Kingdom Abstract Shprintzen–Goldberg syndrome (SGS) is a multisystemic connective tissue disorder, with considerable clinical overlap with Marfan and Loeys–Dietz syndromes. These syndromes have commonly been associated with enhanced TGF-b signaling. In SGS patients, heterozygous point mutations have been mapped to the transcriptional co-repressor SKI, which is a negative regulator of TGF-b signaling that is rapidly degraded upon ligand stimulation. The molecular consequences of these mutations, however, are not understood. Here we use a combination of structural biology, genome editing, and biochemistry to show that SGS mutations in SKI abolish its binding to phosphorylated SMAD2 and SMAD3. This results in stabilization of SKI and consequently attenuation of TGF-b responses, both in knockin cells expressing an SGS mutation and in fibroblasts from SGS patients. Thus, we reveal that SGS is associated with an attenuation of TGF-b- *For correspondence: induced transcriptional responses, and not enhancement, which has important implications for [email protected] other Marfan-related syndromes. Competing interests: The authors declare that no competing interests exist. -
The New Melanoma: a Novel Model for Disease Progression
DISS. ETH NO. 17606 The new melanoma: A novel model for disease progression A dissertation submitted to SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZÜRICH for the degree of DOCTOR OF SCIENCES presented by Natalie Schlegel Master of Science, Otago University (New Zealand) born on January 20th 1976 citizen of Zürich (ZH) accepted on the recommendation of Professor Sabine Werner, examinor Professor Reinhard Dummer, co-examinor Professor Josef Jiricny, co-examinor 2008 22 Table of Contents Abstract ...................................................................................................................................... 6 Résumé....................................................................................................................................... 8 Abbreviations ........................................................................................................................... 10 1. Introduction ...................................................................................................................... 13 1.1 Definition ................................................................................................................. 14 1.2 Clinical features........................................................................................................ 14 1.3 Pathological features and staging............................................................................. 16 1.3.2 Clark’s level of invasion and Breslow’s thickness........................................... 16 1.3.3 TNM staging ................................................................................................... -
The Role of Sumoylation of DNA Topoisomerase Iiα C-Terminal Domain in the Regulation of Mitotic Kinases In
SUMOylation at the centromere: The role of SUMOylation of DNA topoisomerase IIα C-terminal domain in the regulation of mitotic kinases in cell cycle progression. By Makoto Michael Yoshida Submitted to the graduate degree program in the Department of Molecular Biosciences and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________________ Chairperson: Yoshiaki Azuma, Ph.D. ________________________________________ Roberto De Guzman, Ph.D. ________________________________________ Kristi Neufeld, Ph.D. _________________________________________ Berl Oakley, Ph.D. _________________________________________ Blake Peterson, Ph.D. Date Defended: July 12, 2016 The Dissertation Committee for Makoto Michael Yoshida certifies that this is the approved version of the following dissertation: SUMOylation at the centromere: The role of SUMOylation of DNA topoisomerase IIα C-terminal domain in the regulation of mitotic kinases in cell cycle progression. ________________________________________ Chairperson: Yoshiaki Azuma, Ph.D. Date approved: July 12, 2016 ii ABSTRACT In many model systems, SUMOylation is required for proper mitosis; in particular, chromosome segregation during anaphase. It was previously shown that interruption of SUMOylation through the addition of the dominant negative E2 SUMO conjugating enzyme Ubc9 in mitosis causes abnormal chromosome segregation in Xenopus laevis egg extract (XEE) cell-free assays, and DNA topoisomerase IIα (TOP2A) was identified as a substrate for SUMOylation at the mitotic centromeres. TOP2A is SUMOylated at K660 and multiple sites in the C-terminal domain (CTD). We sought to understand the role of TOP2A SUMOylation at the mitotic centromeres by identifying specific binding proteins for SUMOylated TOP2A CTD. Through affinity isolation, we have identified Haspin, a histone H3 threonine 3 (H3T3) kinase, as a SUMOylated TOP2A CTD binding protein. -
The Role of Drosophila Bx42/SKIP in Cell Cycle
The Role of Drosophila Bx42/SKIP in Cell Cycle D i s s e r t a t i o n zur Erlangung des akademischen Grades d o c t o r r e r u m n a t u r a l i u m (Dr. rer. nat.) im Fach Biologie eingereicht an der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin von Diplom-Biologin Shaza Dehne Präsidentin der Humboldt-Universität zu Berlin Prof. Dr.-Ing. Dr. Sabine Kunst Dekanin/Dekan der Lebenswissenschaftlichen Fakultät Prof. Dr. Richard Lucius Gutachter/innen: 1. Prof. Dr. Harald Saumweber 2. Prof. Dr. Christian Schmitz-Linneweber 3. Prof. Dr. Achim Leutz Tag der mündlichen Prüfung: 30.11.2016 Contents Abstract Abstrakt 1 Introduction .................................................................. 10 1.1 Bx42: Identification, protein structure and function .................................................. 11 1.2 Bx42/SNW/SKIP is an essential protein family, conserved in evolution and involved in several biological processes ............................................................................................ 13 1.2.1 Involvement of Bx42/SNW/SKIP in signaling pathways ................................ 16 1.2.1.1 Involvement in nuclear receptor pathways ................................................ 16 1.2.1.2 Involvement in the Notch signaling pathway ............................................ 17 1.2.1.3 Involvement in the TGF-ß/Dpp signal pathway ........................................ 19 1.2.2 Involvement of Bx42/SNW/SKIP in RNA splicing ......................................... 20 1.2.3 Bx42/SNW/SKIP protein family and cell cycle regulation .............................. 22 1.2.3.1 Short overview on cell cycle regulation. ................................................... 22 1.2.3.2 Evidence for Bx42/SNW/SKIP contribution to cell cycle regulation ....... 24 1.3 Drosophila eye imaginal disc: a model to study proliferation and cell cycle regulation during development. -
(Cxxc5) a Thesis Submitted to the Graduate
STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE CXXC-TYPE ZINC FINGER PROTEIN 5 (CXXC5) A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES OF MIDDLE EAST TECHNICAL UNIVERSITY BY GAMZE AYAZ ŞEN IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOLOGY NOVEMBER 2018 Approval of the thesis: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE CXXC-TYPE ZINC FINGER PROTEIN 5 (CXXC5) submitted by GAMZE AYAZ ŞEN in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Department, Middle East Technical University by, Prof. Dr. Halil Kalıpçılar Dean, Graduate School of Natural and Applied Sciences Prof. Dr. Orhan Adalı Head of Department, Biological Sciences Prof. Dr. Mesut Muyan Supervisor, Biological Sciences Dept., METU Examining Committee Members: Prof. Dr. A. Elif Erson Bensan Biological Sciences Dept., METU Prof. Dr. Mesut Muyan Biological Sciences Dept., METU Asst. Prof. Dr. Murat Alper Cevher Molecular Biology and Genetics Dept., Bilkent University Assoc. Prof. Dr. Nurcan Tunçbağ Informatics Institute, METU Asst. Prof. Dr. Onur Çizmecioğlu Molecular Biology and Genetics Dept., Bilkent University Date: 16.11.2018 I hereby declare that all information in this document has been obtained and presented in accordance with academic rules and ethical conduct. I also declare that, as required by these rules and conduct, I have fully cited and referenced all material and results that are not original to this work. Name, Last name: Gamze Ayaz Şen Signature: iv To All Women Who Pursue Their Dreams In Science v ABSTRACT STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE CXXC-TYPE ZINC FINGER PROTEIN 5 (CXXC5) Ayaz Şen, Gamze Ph.D., Biology Department Supervisor: Prof. -
GAK and PRKCD Are Positive Regulators of PRKN-Independent
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.05.369496; this version posted November 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 GAK and PRKCD are positive regulators of PRKN-independent 2 mitophagy 3 Michael J. Munson1,2*, Benan J. Mathai1,2, Laura Trachsel1,2, Matthew Yoke Wui Ng1,2, Laura 4 Rodriguez de la Ballina1,2, Sebastian W. Schultz2,3, Yahyah Aman4, Alf H. Lystad1,2, Sakshi 5 Singh1,2, Sachin Singh 2,3, Jørgen Wesche2,3, Evandro F. Fang4, Anne Simonsen1,2* 6 1Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo 7 2Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway. 8 3Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway 9 4Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway 10 11 Keywords: GAK, Cyclin G Associated Kinase, PRKCD, Protein Kinase C Delta, Mitophagy, DFP, 12 DMOG, PRKN 13 14 *Corresponding Authors: 15 [email protected] 16 [email protected] 17 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.05.369496; this version posted November 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. -
Differential Expression of Multiple Disease-Related Protein Groups
brain sciences Article Differential Expression of Multiple Disease-Related Protein Groups Induced by Valproic Acid in Human SH-SY5Y Neuroblastoma Cells 1,2, 1, 1 1 Tsung-Ming Hu y, Hsiang-Sheng Chung y, Lieh-Yung Ping , Shih-Hsin Hsu , Hsin-Yao Tsai 1, Shaw-Ji Chen 3,4 and Min-Chih Cheng 1,* 1 Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; [email protected] (T.-M.H.); [email protected] (H.-S.C.); [email protected] (L.-Y.P.); fi[email protected] (S.-H.H.); [email protected] (H.-Y.T.) 2 Department of Future Studies and LOHAS Industry, Fo Guang University, Jiaosi, Yilan County 26247, Taiwan 3 Department of Psychiatry, Mackay Medical College, New Taipei City 25245, Taiwan; [email protected] 4 Department of Psychiatry, Taitung Mackay Memorial Hospital, Taitung County 95064, Taiwan * Correspondence: [email protected]; Tel.: +886-3888-3141 (ext. 475) These authors contributed equally to this work. y Received: 10 July 2020; Accepted: 8 August 2020; Published: 12 August 2020 Abstract: Valproic acid (VPA) is a multifunctional medication used for the treatment of epilepsy, mania associated with bipolar disorder, and migraine. The pharmacological effects of VPA involve a variety of neurotransmitter and cell signaling systems, but the molecular mechanisms underlying its clinical efficacy is to date largely unknown. In this study, we used the isobaric tags for relative and absolute quantitation shotgun proteomic analysis to screen differentially expressed proteins in VPA-treated SH-SY5Y cells. We identified changes in the expression levels of multiple proteins involved in Alzheimer’s disease, Parkinson’s disease, chromatin remodeling, controlling gene expression via the vitamin D receptor, ribosome biogenesis, ubiquitin-mediated proteolysis, and the mitochondrial oxidative phosphorylation and electron transport chain.