Final Exam: Introduction to Bioinformatics and Genomics DUE: Thursday June 23Rd at 4:00 Pm
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Plag1 and Plagl2 Are Oncogenes That Induce Acute Myeloid Leukemia in Cooperation with Cbfb-MYH11
University of Massachusetts Medical School eScholarship@UMMS Open Access Articles Open Access Publications by UMMS Authors 2004-12-09 Plag1 and Plagl2 are oncogenes that induce acute myeloid leukemia in cooperation with Cbfb-MYH11 Sean F. Landrette University of Massachusetts Medical School Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/oapubs Part of the Genetics and Genomics Commons, and the Neuroscience and Neurobiology Commons Repository Citation Landrette SF, Kuo Y, Hensen K, Barjesteh van Waalwijk van Doorn-Khosrovani S, Perrat PN, Van de Ven WJ, Delwel R, Castilla LH. (2004). Plag1 and Plagl2 are oncogenes that induce acute myeloid leukemia in cooperation with Cbfb-MYH11. Open Access Articles. https://doi.org/10.1182/blood-2004-09-3630. Retrieved from https://escholarship.umassmed.edu/oapubs/277 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in Open Access Articles by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. From www.bloodjournal.org at UNIV OF MASSACHUSETTS on April 3, 2008. For personal use only. 2005 105: 2900-2907 Prepublished online Dec 7, 2004; doi:10.1182/blood-2004-09-3630 Plag1 and Plagl2 are oncogenes that induce acute myeloid leukemia in cooperation with Cbfb-MYH11 Sean F. Landrette, Ya-Huei Kuo, Karen Hensen, Sahar Barjesteh van Waalwijk van Doorn-Khosrovani, Paola N. Perrat, Wim J. M. Van de Ven, Ruud Delwel and Lucio H. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Noncanonical Role of Transferrin Receptor 1 Is Essential for Intestinal Homeostasis
Noncanonical role of transferrin receptor 1 is essential for intestinal homeostasis Alan C. Chena, Adriana Donovanb, Renee Ned-Sykesc, and Nancy C. Andrewsa,d,1 aDepartment of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27705; bDivision of Pharmacology and Preclinical Biology, Scholar Rock, Cambridge, MA 02142; cDivision of Laboratory Systems, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA 30333; and dDepartment of Pediatrics, Duke University School of Medicine, Durham, NC 27705 Contributed by Nancy C. Andrews, August 4, 2015 (sent for review June 16, 2015; reviewed by Jerry Kaplan and Ramesh A. Shivdasani) Transferrin receptor 1 (Tfr1) facilitates cellular iron uptake through Surprisingly, the mice showed marked induction of genes asso- receptor-mediated endocytosis of iron-loaded transferrin. It is ex- ciated with epithelial–mesenchymal transition in IECs, suggest- pressed in the intestinal epithelium but not involved in dietary iron ing that Tfr1 normally acts to suppress this cell fate change. absorption. To investigate its role, we inactivated the Tfr1 gene There was also abnormal accumulation of lipids, similar to mice selectively in murine intestinal epithelial cells. The mutant mice had lacking transcription factor Plagl2, and increased expression of severe disruption of the epithelial barrier and early death. There stem cell markers. was impaired proliferation of intestinal epithelial cell progenitors, aberrant lipid handling, increased mRNA expression of stem cell Results markers, and striking induction of many genes associated with Conditional Deletion of Tfr1 in IECs. We developed Tfr1fl/fl mice epithelial-to-mesenchymal transition. Administration of parenteral carrying loxP sites flanking Tfr1 exons 3–6(Fig. -
The DNA Sequence and Comparative Analysis of Human Chromosome 20
articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M. -
Overexpressed PLAGL2 Transcriptionally Activates Wnt6 and Promotes Cancer Development in Colorectal Cancer
ONCOLOGY REPORTS 41: 875-884, 2019 Overexpressed PLAGL2 transcriptionally activates Wnt6 and promotes cancer development in colorectal cancer NANPENG LI*, DAOJIANG LI*, YUHENG DU, CHEN SU, CHUNXING YANG, CHANGWEI LIN, XIAORONG LI and GUI HU Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China Received May 12, 2018; Accepted November 28, 2018 DOI: 10.3892/or.2018.6914 Abstract. Researchers hold the view that PLAGL2 is overex- most common tumors worldwide. The incidence rate is ranked pressed in many malignancies and that it can promote tumor third among cancers (1). The number of deaths attributed to proliferation, migration, invasion and self-renewal; however, there colorectal cancer each year still reaches 610,000 (2), ranking it is no evidence revealing a relationship between PLAGL2 and second in malignant tumors (1). colorectal cancer (CRC). In the present study, genes that are over- Polymorphic adenoma‑like protein 2 (PLAGL2) is a zinc finger expressed in CRC were screened using the COSMIC database protein of the PLAG gene family with 7 C2H2 zinc finger domains and GEPIA database and the expression of PLAGL2 in carcinoma on the N-terminus (3-5). This structure is highly conserved, can tissues and pericarcinomatous tissues was detected by RT-qPCR bind DNA and enables the transcription factor PLAGL2 to acti- and western blot assays. A Cell Counting Kit-8 assay, a cell cycle vate the transcription of specific genes (6). PLAGL2 is closely analysis experiment and a xenograft model were used to explore related to the development of malignant tumors. -
Atlas Journal
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 5, Sep-Oct 2008 Previous Issue / Next Issue Genes XAF1 (XIAP associated factor-1) (17p13.2). Stéphanie Plenchette, Wai Gin Fong, Robert G Korneluk. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 668-673. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/XAF1ID44095ch17p13.html WWP1 (WW domain containing E3 ubiquitin protein ligase 1) (8q21.3). Ceshi Chen. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 674-680. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/WWP1ID42993ch8q21.html TSPAN1 (tetraspanin 1) (1p34.1). David Murray, Peter Doran. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 681-683. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TSPAN1ID44178ch1p34.html TCL1B (T-cell leukemia/lymphoma 1B) (14q32.13). Herbert Eradat, Michael A Teitell. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 684-686. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TCL1BID354ch14q32.html PVRL4 (poliovirus receptor-related 4) (1q23.3). Marc Lopez. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 687-690. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/PVRL4ID44141ch1q23.html PTTG1IP (pituitary tumor-transforming 1 interacting protein) (21q22.3). Vicki Smith, Chris McCabe. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 691-694. -
Unexplored Regulatory Sequences of Divergently Paired GLA And
EXPERIMENTAL AND THERAPEUTIC MEDICINE 21: 154, 2021 Unexplored regulatory sequences of divergently paired GLA and HNRNPH2 loci pertinent to Fabry disease in human kidney and skin cells: Presence of an active bidirectional promoter MOHAMMED A. IBRAHIM AL‑OBAIDE, IBTISAM I. AL‑OBAIDI and TETYANA L. VASYLYEVA Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA Received June 9, 2020; Accepted December 1, 2020 DOI: 10.3892/etm.2020.9586 Abstract. Fabry disease (FD) is a rare hereditary disorder suggested that the expression of the divergent paired loci, GLA characterized by a wide range of symptoms caused by a and HNRNPH2, were controlled by BDP. Mutations in BDP variety of mutations in the galactosidase α (GLA) gene. The may also serve a role in FD and may explain clinical disease heterogeneous nuclear ribonucleoprotein (HNRNPH2) gene is diversity. divergently paired with GLA on chromosome X and is thought to be implicated in FD. However, insufficient information is Introduction available on the regulatory mechanisms associated with the expression of HNRNPH2 and the GLA loci. Therefore, the Fabry disease (FD; OMIM 301500) is an X‑linked inherited current study performed bioinformatics analyses to assess error lysosomal storage disorder, caused by mutations in the the GLA and HNRNPH2 loci and investigate the regulatory galactosidase α (GLA) gene that encodes the α‑galactosidase A mechanisms involved in the expression of each gene. The enzyme (α‑GAL A) (1‑6). Patients with α‑GAL A deficien‑ regulatory mechanisms underlying GLA and HNRNPH2 were cies exhibit a harmful accumulation of globotriaosylceramide revealed. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
393LN V 393P 344SQ V 393P Probe Set Entrez Gene
393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393 -
Pleomorphic Adenoma Gene 1 Is Needed for Timely Zygotic Genome Activation and Early
bioRxiv preprint doi: https://doi.org/10.1101/305375; this version posted December 13, 2018. 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 Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early 2 Embryo Development 3 Elo Madissoon,1,9 Anastasios Damdimopoulos,2,9 Shintaro Katayama,1,9 Kaarel Krjutškov,3,4 4 Elisabet Einarsdottir,1,4 Katariina Mamia,5 Bert De Groef,6 Outi Hovatta,5 Juha Kere,1,7,8,* and 5 Pauliina Damdimopoulou1,5,* 6 7 1Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186 Stockholm, Sweden 8 2Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, 9 Karolinska Institutet, SE-14186 Stockholm, Sweden 10 3Competence Centre on Health Technologies, 50410 Tartu, Estonia 11 4Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of 12 Genetics, 00014 Helsinki, Finland 13 5Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186 14 Stockholm, Sweden 15 6Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, 16 Victoria, 3086, Australia 17 7Research Programs Unit, Molecular Neurology, University of Helsinki, and Folkhälsan Institute 18 of Genetics, 00014 Helsinki, Finland 19 8School of Basic and Medical Biosciences, King’s College London, Guy’s Hospital, London 20 WC2R 2LS, UK 21 9These authors contributed equally. 22 *Correspondence: [email protected] and [email protected] 23 1 bioRxiv preprint doi: https://doi.org/10.1101/305375; this version posted December 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
S41598-019-44882-0 1
www.nature.com/scientificreports OPEN Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Received: 21 March 2019 Accepted: 22 May 2019 Development Published: xx xx xxxx Elo Madissoon 1, Anastasios Damdimopoulos2, Shintaro Katayama1, Kaarel Krjutškov3,4, Elisabet Einarsdottir1,4, Katariina Mamia5, Bert De Groef 6, Outi Hovatta5, Juha Kere 1,7,8 & Pauliina Damdimopoulou1,5 Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is needed for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent signifcantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a signifcant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 afects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes. -
Functional Characterization of POFUT1 Variants Associated with Colorectal Cancer
cancers Article Functional Characterization of POFUT1 Variants Associated with Colorectal Cancer Marlène Deschuyter 1, Florian Pennarubia 1,2, Emilie Pinault 1,3 ,Sébastien Legardinier 1 and Abderrahman Maftah 1,* 1 PEIRENE, EA 7500, Glycosylation and Cell Differentiation, Faculty of Sciences and Technology, University of Limoges, F-87060 Limoges, France; [email protected] (M.D.); fl[email protected] (F.P.); [email protected] (E.P.); [email protected] (S.L.) 2 Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA 3 BISCEm US042 INSERM—UMS 2015 CNRS, Mass Spectrometry Platform, Faculty of Medicine and Pharmacy, University of Limoges, F-87025 Limoges, France * Correspondence: [email protected]; Tel.: +33-5554-57684; Fax: +33-5554-57653 Received: 6 May 2020; Accepted: 28 May 2020; Published: 31 May 2020 Abstract: Background: Protein O-fucosyltransferase 1 (POFUT1) overexpression, which is observed in many cancers such as colorectal cancer (CRC), leads to a NOTCH signaling dysregulation associated with the tumoral process. In rare CRC cases, with no POFUT1 overexpression, seven missense mutations were found in human POFUT1. Methods: Recombinant secreted forms of human WT POFUT1 and its seven mutated counterparts were produced and purified. Their O-fucosyltransferase activities were assayed in vitro using a chemo-enzymatic approach with azido-labeled GDP-fucose as a donor substrate and NOTCH1 EGF-LD26, produced in E. coli periplasm, as a relevant acceptor substrate. Targeted mass spectrometry (MS) was carried out to quantify the O-fucosyltransferase ability of all POFUT1 proteins. Findings: MS analyses showed a significantly higher O-fucosyltransferase activity of six POFUT1 variants (R43H, Y73C, T115A, I343V, D348N, and R364W) compared to WT POFUT1.