Species Specific Differences in Use of ANP32 Proteins by Influenza a Virus
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ANP32A and ANP32B Are Key Factors in the Rev Dependent CRM1 Pathway
bioRxiv preprint doi: https://doi.org/10.1101/559096; this version posted February 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 1 ANP32A and ANP32B are key factors in the Rev dependent CRM1 pathway 2 for nuclear export of HIV-1 unspliced mRNA 3 Yujie Wang1, Haili Zhang1, Lei Na 1, Cheng Du1, Zhenyu Zhang1, Yong-Hui Zheng1,2, Xiaojun Wang1* 4 1State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese 5 Academy of Agricultural Sciences, Harbin 150069, China 6 2Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 7 USA. 8 * Address correspondence to Xiaojun Wang, [email protected]. 9 10 11 12 13 14 15 16 17 18 19 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/559096; this version posted February 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 22 Abstract 23 The nuclear export receptor CRM1 is an important regulator involved in the shuttling of various cellular 24 and viral RNAs between the nucleus and the cytoplasm. HIV-1 Rev interacts with CRM1 in the late phase of 25 HIV-1 replication to promote nuclear export of unspliced and single spliced HIV-1 transcripts. However, the 26 knowledge of cellular factors that are involved in the CRM1-dependent viral RNA nuclear export remains 27 inadequate. Here, we identified that ANP32A and ANP32B mediate the export of unspliced or partially spliced 28 viral mRNA via interacting with Rev and CRM1. -
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. -
Fine Mapping Studies of Quantitative Trait Loci for Baseline Platelet Count in Mice and Humans
Fine mapping studies of quantitative trait loci for baseline platelet count in mice and humans A thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy Melody C Caramins December 2010 University of New South Wales ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date …………………………………………….............. This thesis is dedicated to my father. Dad, thanks for the genes – and the environment! ACKNOWLEDGEMENTS “Nothing can come out of nothing, any more than a thing can go back to nothing.” - Marcus Aurelius Antoninus A PhD thesis is never the work of one person in isolation from the world at large. I would like to thank the following people, without whom this work would not have existed. Thank you firstly, to all my teachers, of which there have been many. Undoubtedly, the greatest debt is owed to my supervisor, Dr Michael Buckley. -
A. Cellular Senescence
Generation of antisense RNAs at convergent gene loci in cells undergoing senescence Maharshi Krishna Deb To cite this version: Maharshi Krishna Deb. Generation of antisense RNAs at convergent gene loci in cells undergo- ing senescence. Human genetics. Université Paul Sabatier - Toulouse III, 2016. English. NNT : 2016TOU30274. tel-03209213 HAL Id: tel-03209213 https://tel.archives-ouvertes.fr/tel-03209213 Submitted on 27 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 5)µ4& &OWVFEFMPCUFOUJPOEV %0$503"5%&-6/*7&34*5²%&506-064& %ÏMJWSÏQBS Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) 1SÏTFOUÏFFUTPVUFOVFQBS DEB Maharshi Krishna -F mercredi 30 mars 2016 5Jtre : Generation of antisense RNAs at convergent gene loci in cells undergoing senescence École doctorale et discipline ou spécialité : ED BSB : Génétique moléculaire 6OJUÏEFSFDIFSDIF CNRS-UMR5088; LBCMCP %JSFDUFVS T EFʾÒTF Dr. TROUCHE Didier Co-Directeur/trice(s) de Thèse : Dr. NICOLAS Estelle 3BQQPSUFVST Prof. GILSON Eric, Dr. LIBRI Domenico, Dr. VERDEL Andre "VUSF T NFNCSF T EVKVSZ Prof. GLEIZES Pierre Emmanuel, President of Jury Dr. TROUCHE Didier, Thesis Supervisor This thesis is dedicated to any patients who may get cured with treatments manifesting from this work. -
Supplementary Data
SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche). -
GENOME EDITING in AFRICA’S AGRICULTURE 2021 an EARLY TAKE-OFF TABLE of CONTENTS Abbreviations and Acronyms 3
GENOME EDITING IN AFRICA’S AGRICULTURE 2021 AN EARLY TAKE-OFF TABLE OF CONTENTS Abbreviations and Acronyms 3 1. Introduction 4 1.1 Milestones in Plant Breeding 5 1.2 How CRISPR genome editing works in agriculture 6 2 . Genome editing projects and experts in eastern Africa 7 2.1 Kenya 8 2.2 Ethiopia 14 2.3 Uganda 15 3 . Gene editing projects and experts in southern Africa 17 3.1 South Africa 18 4. Gene editing projects and experts in West Africa 19 4.1 Nigeria 20 5. Gene editing projects and experts in Central Africa 21 5.1 Cameroon 22 6. Gene editing projects and experts in North Africa 23 6.1 Egypt 24 7. Conclusion 25 8. CRISPR genome editing: inside a crop breeder’s toolkit 26 9. Regulatory Approaches for Genome Edited Products in Various Countries 27 10. Communicating about Genome Editing in Africa 28 2 ABBREVIATIONS AND ACRONYMS CRISPR Clustered Regularly Interspaced Short Palindromic Repeats DNA Deoxyribonucleic acid GM Genetically Modified GMO Genetically Modified Organism HDR Homology Directed Repair ISAAA International Service for the Acquisition of Agri-biotech Applications NHEJ Non Homologous End Joining PCR Polymerase Chain Reaction RNA Ribonucleic Acid LGS1 Low germination stimulant 1 3 1.0 INTRODUCTION Genome editing (also referred to as gene editing) comprises a arm is provided with the CRISPR-Cas9 cassette, homology-directed group of technologies that give scientists the ability to change an repair (HDR) will occur, otherwise the cell will employ non- organism’s DNA. These technologies allow addition, removal or homologous end joining (NHEJ) to create small indels at the cut site alteration of genetic material at particular locations in the genome. -
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 -
Identification of Differentially Methylated Cpg
biomedicines Article Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars Mansour A. Alghamdi 1,2 , Hilary J. Wallace 3,4 , Phillip E. Melton 5,6 , Eric K. Moses 5,6, Andrew Stevenson 4 , Laith N. Al-Eitan 7,8 , Suzanne Rea 9, Janine M. Duke 4, 10 11 4,9,12 4, , Patricia L. Danielsen , Cecilia M. Prêle , Fiona M. Wood and Mark W. Fear * y 1 Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia; [email protected] 2 Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia 3 School of Medicine, The University of Notre Dame Australia, Fremantle 6959, Australia; [email protected] 4 Burn Injury Research Unit, School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth 6009, Australia; andrew@fionawoodfoundation.com (A.S.); [email protected] (J.M.D.); fi[email protected] (F.M.W.) 5 Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, The University of Western Australia, Perth 6009, Australia; [email protected] (P.E.M.); [email protected] (E.K.M.) 6 School of Pharmacy and Biomedical Sciences, Faculty of Health Science, Curtin University, Perth 6102, Australia 7 Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; [email protected] 8 Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, -
ANP32B Deficiency Impairs Proliferation and Suppresses Tumor Progression by Regulating AKT Phosphorylation
Citation: Cell Death and Disease (2016) 7, e2082; doi:10.1038/cddis.2016.8 OPEN & 2016 Macmillan Publishers Limited All rights reserved 2041-4889/16 www.nature.com/cddis ANP32B deficiency impairs proliferation and suppresses tumor progression by regulating AKT phosphorylation S Yang1,6, L Zhou2,6, PT Reilly3, S-M Shen1,PHe1, X-N Zhu1, C-X Li1, L-S Wang4, TW Mak5, G-Q Chen*,1 and Y Yu*,1 The acidic leucine-rich nuclear phosphoprotein 32B (ANP32B) is reported to impact normal development, with Anp32b-knockout mice exhibiting smaller size and premature aging. However, its cellular and molecular mechanisms, especially its potential roles in tumorigenesis, remain largely unclear. Here, we utilize 'knockout' models, RNAi silencing and clinical cohorts to more closely investigate the role of this enigmatic factor in cell proliferation and cancer phenotypes. We report that, compared with Anp32b wild- type (Anp32b+/+) littermates, a broad panel of tissues in Anp32b-deficient (Anp32b− / −) mice are demonstrated hypoplasia. Anp32b− / − mouse embryo fibroblast cell has a slower proliferation, even after oncogenic immortalization. ANP32B knockdown also significantly inhibits in vitro and in vivo growth of cancer cells by inducing G1 arrest. In line with this, ANP32B protein has higher expression in malignant tissues than adjacent normal tissues from a cohort of breast cancer patients, and its expression level positively correlates with their histopathological grades. Moreover, ANP32B deficiency downregulates AKT phosphorylation, which involves its regulating effect on cell growth. Collectively, our findings suggest that ANP32B is an oncogene and a potential therapeutic target for breast cancer treatment. Cell Death and Disease (2016) 7, e2082; doi:10.1038/cddis.2016.8; published online 4 February 2016 The acidic leucine-rich nuclear phosphoprotein 32 kDa lethality and reduced body weight,22–25 indicating a greater (ANP32) protein family are characterized by a N-terminal importance of Anp32b in normal development. -
Nuclear PTEN Safeguards Pre-Mrna Splicing to Link Golgi Apparatus for Its Tumor Suppressive Role
ARTICLE DOI: 10.1038/s41467-018-04760-1 OPEN Nuclear PTEN safeguards pre-mRNA splicing to link Golgi apparatus for its tumor suppressive role Shao-Ming Shen1, Yan Ji2, Cheng Zhang1, Shuang-Shu Dong2, Shuo Yang1, Zhong Xiong1, Meng-Kai Ge1, Yun Yu1, Li Xia1, Meng Guo1, Jin-Ke Cheng3, Jun-Ling Liu1,3, Jian-Xiu Yu1,3 & Guo-Qiang Chen1 Dysregulation of pre-mRNA alternative splicing (AS) is closely associated with cancers. However, the relationships between the AS and classic oncogenes/tumor suppressors are 1234567890():,; largely unknown. Here we show that the deletion of tumor suppressor PTEN alters pre-mRNA splicing in a phosphatase-independent manner, and identify 262 PTEN-regulated AS events in 293T cells by RNA sequencing, which are associated with significant worse outcome of cancer patients. Based on these findings, we report that nuclear PTEN interacts with the splicing machinery, spliceosome, to regulate its assembly and pre-mRNA splicing. We also identify a new exon 2b in GOLGA2 transcript and the exon exclusion contributes to PTEN knockdown-induced tumorigenesis by promoting dramatic Golgi extension and secretion, and PTEN depletion significantly sensitizes cancer cells to secretion inhibitors brefeldin A and golgicide A. Our results suggest that Golgi secretion inhibitors alone or in combination with PI3K/Akt kinase inhibitors may be therapeutically useful for PTEN-deficient cancers. 1 Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China. 2 Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and SJTU-SM, Shanghai 200025, China. -
Open Full Page
Published OnlineFirst February 10, 2017; DOI: 10.1158/2159-8290.CD-16-1045 RESEARCH ARTICLE Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer Hannah Carter 1 , 2 , 3 , 4 , Rachel Marty 5 , Matan Hofree 6 , Andrew M. Gross 5 , James Jensen 5 , Kathleen M. Fisch1,2,3,7 , Xingyu Wu 2 , Christopher DeBoever 5 , Eric L. Van Nostrand 4,8 , Yan Song 4,8 , Emily Wheeler 4,8 , Jason F. Kreisberg 1,3 , Scott M. Lippman 2 , Gene W. Yeo 4,8 , J. Silvio Gutkind 2 , 3 , and Trey Ideker 1 , 2 , 3 , 4 , 5,6 Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2017 American Association for Cancer Research. Published OnlineFirst February 10, 2017; DOI: 10.1158/2159-8290.CD-16-1045 ABSTRACT Recent studies have characterized the extensive somatic alterations that arise dur- ing cancer. However, the somatic evolution of a tumor may be signifi cantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal and systematically validate 412 genetic interactions between germline polymorphisms and major somatic events, including tumor formation in specifi c tissues and alteration of specifi c cancer genes. Among germline–somatic interactions, we found germline variants in RBFOX1 that increased incidence of SF3B1 somatic mutation by 8-fold via functional alterations in RNA splicing. Similarly, 19p13.3 variants were associated with a 4-fold increased likelihood of somatic mutations in PTEN. In support of this associ- ation, we found that PTEN knockdown sensitizes the MTOR pathway to high expression of the 19p13.3 gene GNA11 . -
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Published OnlineFirst September 12, 2018; DOI: 10.1158/2159-8290.CD-17-1018 RESEARCH ARTICLE Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network Manon Eckhardt 1 , 2 , 3 , Wei Zhang 4 , Andrew M. Gross 4 , John Von Dollen 1 , 3 , Jeffrey R. Johnson 1 , 2 , 3 , Kathleen E. Franks-Skiba1 , 3 , Danielle L. Swaney 1 , 2 , 3 , 5 , Tasha L. Johnson 3 , Gwendolyn M. Jang 1 , 3 , Priya S. Shah1 , 3 , Toni M. Brand 6 , Jacques Archambault 7 , Jason F. Kreisberg 4 , 5 , Jennifer R. Grandis 5 , 6 , Trey Ideker4 , 5 , and Nevan J. Krogan 1 , 2 , 3 , 5 ABSTRACT We have mapped a global network of virus–host protein interactions by purifi cation of the complete set of human papillomavirus (HPV) proteins in multiple cell lines followed by mass spectrometry analysis. Integration of this map with tumor genome atlases shows that the virus targets human proteins frequently mutated in HPV − but not HPV + cancers, providing a unique opportunity to identify novel oncogenic events phenocopied by HPV infection. For example, we fi nd that the NRF2 transcriptional pathway, which protects against oxidative stress, is activated by interaction of the NRF2 regulator KEAP1 with the viral protein E1. We also demonstrate that the L2 HPV protein physically interacts with the RNF20/40 histone ubiquitination complex and promotes tumor cell inva- sion in an RNF20/40-dependent manner. This combined proteomic and genetic approach provides a systematic means to study the cellular mechanisms hijacked by virally induced cancers. SIGNIFICANCE : In this study, we created a protein–protein interaction network between HPV and human proteins.