PAX3-FOXO1 Candidate Interactors
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Single Nucleotide Variants in Metastasis-Related Genes Are
View metadata, citation and similar papers at core.ac.uk brought to you by CORE HHS Public Access provided by CDC Stacks Author manuscript Author ManuscriptAuthor Manuscript Author Mol Carcinog Manuscript Author . Author manuscript; Manuscript Author available in PMC 2018 March 01. Published in final edited form as: Mol Carcinog. 2017 March ; 56(3): 1000–1009. doi:10.1002/mc.22565. Single nucleotide variants in metastasis-related genes are associated with breast cancer risk, by lymph node involvement and estrogen receptor status, in women with European and African ancestry Michelle R. Roberts1,2,3, Lara E. Sucheston-Campbell4, Gary R. Zirpoli5, Michael Higgins6, Jo L. Freudenheim3, Elisa V. Bandera7, Christine B. Ambrosone2, and Song Yao2 1Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 2Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 3Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY 4Division of Pharmacy Practice and Science, The Ohio State University, Columbus, OH 5Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 7Rutgers Cancer Institute of New Jersey, New Brunswick, NJ Abstract Background—Single nucleotide polymorphisms (SNPs) in pathways influencing lymph node (LN) metastasis and estrogen receptor (ER) status in breast cancer may partially explain inter- patient variability in prognosis. We examined 154 SNPs in 12 metastasis-related genes for associations with breast cancer risk, stratified by LN and ER status, in European-American (EA) and African-American (AA) women. Methods—2,671 women enrolled in the Women’s Circle of Health Study were genotyped. -
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. -
Understanding Molecular Functions of the SMC5/6 Complex
G C A T T A C G G C A T genes Review Scaffolding for Repair: Understanding Molecular Functions of the SMC5/6 Complex Mariana Diaz 1,2 and Ales Pecinka 1,* ID 1 Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelu˚ 31, 77900 Olomouc-Holice, Czech Republic 2 Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829 Cologne, Germany; [email protected] * Correspondence: [email protected]; Tel.: +420-585-238-709 Received: 15 November 2017; Accepted: 4 January 2018; Published: 12 January 2018 Abstract: Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex. SMC5/6 complex was originally identified based on the sensitivity of its mutants to genotoxic stress but there is increasing number of studies demonstrating its roles in the control of DNA replication, sister chromatid resolution and genomic location-dependent promotion or suppression of homologous recombination. Some of these functions appear to be due to a very dynamic interaction with cohesin or other repair complexes. Studies in Arabidopsis indicate that, besides its canonical function in repair of damaged DNA, the SMC5/6 complex plays important roles in regulating plant development, abiotic stress responses, suppression of autoimmune responses and sexual reproduction. -
The Smc5-6 Protein Complex in Human Cells
Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex Article (Accepted Version) Taylor, Elaine M, Copsey, Alice C, Hudson, Jessica J, Vidot, Susanne and Lehmann, Alan R (2008) Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex. Molecular and Cellular Biology, 28 (4). pp. 1197-1206. ISSN 0270-7306 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/id/eprint/1806/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the URL above for details on accessing the published version. Copyright and reuse: Sussex Research Online is a digital repository of the research output of the University. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. -
Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer Stephen Shang1, Jiekun Yang1, Amir A
Published OnlineFirst July 29, 2019; DOI: 10.1158/0008-5472.CAN-19-0215 Cancer Genome and Epigenome Research Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer Stephen Shang1, Jiekun Yang1, Amir A. Jazaeri2, Alexander James Duval1, Turan Tufan1, Natasha Lopes Fischer1, Mouadh Benamar1,3, Fadila Guessous3, Inyoung Lee1, Robert M. Campbell4, Philip J. Ebert4, Tarek Abbas1,3, Charles N. Landen5, Analisa Difeo6, Peter C. Scacheri6, and Mazhar Adli1 Abstract Chemoresistance is driven by unique regulatory net- tance, our findings identified SOX9 as a critical SE-regulated works in the genome that are distinct from those necessary transcription factor that plays a critical role in acquiring for cancer development. Here, we investigate the contri- and maintaining the chemoresistant state in ovarian cancer. bution of enhancer elements to cisplatin resistance in The approach and findings presented here suggest that ovarian cancers. Epigenome profiling of multiple cellular integrative analysis of epigenome and transcriptional pro- models of chemoresistance identified unique sets of distal grams could identify targetable key drivers of chemoresis- enhancers, super-enhancers (SE), and their gene targets tance in cancers. that coordinate and maintain the transcriptional program of the platinum-resistant state in ovarian cancer. Pharma- Significance: Integrative genome-wide epigenomic and cologic inhibition of distal enhancers through small- transcriptomic analyses of platinum-sensitive and -resistant molecule epigenetic inhibitors suppressed the expression ovarian lines identify key distal regulatory regions and of their target genes and restored cisplatin sensitivity in vitro associated master regulator transcription factors that can be and in vivo. In addition to known drivers of chemoresis- targeted by small-molecule epigenetic inhibitors. -
Cytokine-Enhanced Cytolytic Activity of Exosomes from NK Cells
Cancer Gene Therapy https://doi.org/10.1038/s41417-021-00352-2 ARTICLE Cytokine-enhanced cytolytic activity of exosomes from NK Cells 1 1 2 3 2 3 Yutaka Enomoto ● Peng Li ● Lisa M. Jenkins ● Dimitrios Anastasakis ● Gaelyn C. Lyons ● Markus Hafner ● Warren J. Leonard 1 Received: 4 February 2021 / Revised: 9 May 2021 / Accepted: 18 May 2021 This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. This article is published with open access Abstract Natural killer (NK) cells play key roles in immune surveillance against tumors and viral infection. NK cells distinguish abnormal cells from healthy cells by cell–cell interaction with cell surface proteins and then attack target cells via multiple mechanisms. In addition, extracellular vesicles (EVs) derived from NK cells (NK-EVs), including exosomes, possess cytotoxic capacity against tumor cells, but their characteristics and regulation by cytokines remain unknown. Here, we report that EVs derived from human NK-92 cells stimulated with IL-15 + IL-21 show enhanced cytotoxic capacity against tumor cells. Major cytolytic granules, granzyme B and granzyme H, are enriched by IL-15 + IL-21 stimulation in NK-EVs; however, knockout experiments reveal those cytolytic granules are independent of enhanced cytotoxic capacity. To find out the key molecules, mass spectrometry analyses were 1234567890();,: 1234567890();,: performed with different cytokine conditions, no cytokine, IL-15, IL-21, or IL-15 + IL-21. We then found that CD226 (DNAM-1) on NK-EVs is enriched by IL-15 + IL-21 stimulation and that blocking antibodies against CD226 reduced the cytolytic activity of NK-EVs. -
Loss of ISWI Atpase SMARCA5 (SNF2H) in Acute Myeloid Leukemia Cells Inhibits Proliferation and Chromatid Cohesion
International Journal of Molecular Sciences Article Loss of ISWI ATPase SMARCA5 (SNF2H) in Acute Myeloid Leukemia Cells Inhibits Proliferation and Chromatid Cohesion 1, 1, 1 2,3,4 1 Tomas Zikmund y , Helena Paszekova y , Juraj Kokavec , Paul Kerbs , Shefali Thakur , Tereza Turkova 1, Petra Tauchmanova 1, Philipp A. Greif 2,3,4 and Tomas Stopka 1,* 1 Biocev, 1st Medical Faculty, Charles University, 25250 Vestec, Czech Republic; [email protected] (T.Z.); [email protected] (H.P.); [email protected] (J.K.); [email protected] (S.T.); [email protected] (T.T.); [email protected] (P.T.) 2 Department of Medicine III, University Hospital, LMU Munich, D-80539 Munich, Germany; [email protected] (P.K.); [email protected] (P.A.G.) 3 German Cancer Consortium (DKTK), partner site Munich, D-80336 Munich, Germany 4 German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany * Correspondence: [email protected]; Tel.: +420-32587-3001 These authors contributed equally. y Received: 26 February 2020; Accepted: 16 March 2020; Published: 18 March 2020 Abstract: ISWI chromatin remodeling ATPase SMARCA5 (SNF2H) is a well-known factor for its role in regulation of DNA access via nucleosome sliding and assembly. SMARCA5 transcriptionally inhibits the myeloid master regulator PU.1. Upregulation of SMARCA5 was previously observed in CD34+ hematopoietic progenitors of acute myeloid leukemia (AML) patients. Since high levels of SMARCA5 are necessary for intensive cell proliferation and cell cycle progression of developing hematopoietic stem and progenitor cells in mice, we reasoned that removal of SMARCA5 enzymatic activity could affect the cycling or undifferentiated state of leukemic progenitor-like clones. -
Integrative Genomics Discoveries and Development at the Center for Applied Genomics at CHOP
The Children’s Hospital of Philadelphia Integrative Genomics Discoveries and Development at The Center for Applied Genomics at CHOP Novel Genome-based Therapeutic Approaches Hakon Hakonarson, MD, PhD, Professor of Pediatrics CHOP’s Endowed Chair in Genetic Research Director, Center for Applied Genomics The Children’s Hospital of Philadelphia University of Pennsylvania, School of Medicine Duke Center for Applied Genomics and Precision Medicine 2019 Genomic and Precision Medicine Forum Nov 07, 2019 Genomics in the 21st Century Disclosures Dr. Hakonarson and CHOP own stock in Aevi Genomic Medicine Inc. developing anti-LIGHT therapy for IBD. Dr. Hakonarson is an inventor of technology involving therapeutic development of ADHD, GLA and HCCAA Novel Therapeutic Stem Cell/Gene Editing Approaches § iPS and stem cell therapy shows early promise § Gene therapy for LCA (RPE65) at CHOP via AAV § Targeted T cell therapy for cancer (UPENN/CHOP) § CRISPR-cas9 gene editing § Single cell sequencing The Center for Applied Genomics (CAG) at CHOP u Founded in June 2006 u Staff of 70 u Over 100 active disease projects with CHOP/Penn collaborators u TARGET: Genotype 100,000 children u ~450k GWAS samples >130k kids u IC - participation in future studies >85% u Database u Electronic Health Records u extensive information on each child u >1.2 million visits per year to Population Genomics Research CHOP Recruitment of CHOP/PENN HealthCare Network Patients u High-level of automation ADHD, Autism, Diabetes, IBD, Autoimmunity, Asthma/Atopy, Cancer, RDs - all high priority -
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 -
The Genome of Schmidtea Mediterranea and the Evolution Of
OPEN ArtICLE doi:10.1038/nature25473 The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms Markus Alexander Grohme1*, Siegfried Schloissnig2*, Andrei Rozanski1, Martin Pippel2, George Robert Young3, Sylke Winkler1, Holger Brandl1, Ian Henry1, Andreas Dahl4, Sean Powell2, Michael Hiller1,5, Eugene Myers1 & Jochen Christian Rink1 The planarian Schmidtea mediterranea is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of S. mediterranea, using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads. The S. mediterranea genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms. Rapid regeneration from tiny pieces of tissue makes planarians a prime De novo long read assembly of the planarian genome model system for regeneration. Abundant adult pluripotent stem cells, In preparation for genome sequencing, we inbred the sexual strain termed neoblasts, power regeneration and the continuous turnover of S. mediterranea (Fig. 1a) for more than 17 successive sib- mating of all cell types1–3, and transplantation of a single neoblast can rescue generations in the hope of decreasing heterozygosity. We also developed a lethally irradiated animal4. Planarians therefore also constitute a a new DNA isolation protocol that meets the purity and high molecular prime model system for stem cell pluripotency and its evolutionary weight requirements of PacBio long-read sequencing12 (Extended Data underpinnings5. -
Proteomic Analysis of the Mammalian Nuclear Pore Complex
JCBArticle Proteomic analysis of the mammalian nuclear pore complex Janet M. Cronshaw,1 Andrew N. Krutchinsky,2 Wenzhu Zhang,2 Brian T. Chait,2 and Michael J. Matunis1 1Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205 2Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, New York, NY 10021 s the sole site of nucleocytoplasmic transport, the these proteins were classified as nucleoporins, and a further nuclear pore complex (NPC) has a vital cellular 18 were classified as NPC-associated proteins. Among the 29 Arole. Nonetheless, much remains to be learned about nucleoporins were six previously undiscovered nucleoporins many fundamental aspects of NPC function. To further and a novel family of WD repeat nucleoporins. One of understand the structure and function of the mammalian these WD repeat nucleoporins is ALADIN, the gene mutated NPC, we have completed a proteomic analysis to identify in triple-A (or Allgrove) syndrome. Our analysis defines the and classify all of its protein components. We used mass proteome of the mammalian NPC for the first time and spectrometry to identify all proteins present in a biochemically paves the way for a more detailed characterization of NPC purified NPC fraction. Based on previous characterization, structure and function. sequence homology, and subcellular localization, 29 of Introduction Nucleocytoplasmic transport is mediated by nuclear pore A proteomic analysis revealed that the yeast NPC is com- complexes (NPCs)* (Allen et al., 2000) which span the nuclear posed of 29 nucleoporins (Rout et al., 2000). To date, 24 envelope (NE) lumen, inserting into pores formed by the nucleoporins have been identified in mammals, with up to 25 fusion of inner and outer nuclear membranes. -
The 3D Enhancer Network of the Developing T Cell Genome Is Controlled by 2 SATB1
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.09.451769; this version posted July 9, 2021. 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 4.0 International license. 1 The 3D enhancer network of the developing T cell genome is controlled by 2 SATB1 3 4 Tomas Zelenka1,2, Antonios Klonizakis1, Despina Tsoukatou2, Sören Franzenburg3, Petros Tzerpos1,4, 5 Dionysios-Alexandros Papamatheakis1,2, Ioannis-Rafail Tzonevrakis1, Christoforos Nikolaou1,2,5, 6 Dariusz Plewczynski6, Charalampos Spilianakis1,2,# 7 8 1 Department of Biology, University of Crete, Heraklion, Crete, Greece 9 2 Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, 10 Heraklion, Crete, Greece 11 3 University Hospital Schleswig Holstein, Kiel, Germany 12 4 Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 13 Debrecen, HU-4032 Hungary (current address) 14 5 Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming," 16672 Vari, 15 Greece (current address) 16 6 Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information 17 Science, Warsaw University of Technology, Warsaw, Poland; Laboratory of Functional and Structural 18 Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland 19 # Corresponding author, email: [email protected] 20 21 Tomas Zelenka 22 ORCID: 0000-0003-2753-9754 23 Researcher ID: F-2402-2015 24 25 Charalampos Spilianakis 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.09.451769; this version posted July 9, 2021.