DOCSLIB.ORG

Sleeping Beauty Screen Identifies RREB1 and Other Genetic Drivers in Human B-Cell Lymphoma

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sleeping Beauty Screen Identifies RREB1 and Other Genetic Drivers in Human B-Cell Lymphoma Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Sleeping Beauty Screen Identifies RREB1 and Other Genetic Drivers in Human B-cell Lymphoma Eric P. Rahrmann1,2, Natalie K. Wolf1, George M. Otto2, Lynn Heltemes-Harris2,3,5, Laura B. Ramsey5, Jingmin Shu2, Rebecca S. LaRue2, Michael A. Linden2,4, Susan K. Rathe2, Timothy K. Starr2,6, Michael A. Farrar2,3,5, Branden S. Moriarity2,7,8, David A. Largaespada1,2,7,8 1Department of Genetics, Cell Biology, and Development; University of Minnesota, Minneapolis, Minnesota; 2Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455 USA; 3Lab Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota; 4Division of Hematopathology, Department of Laboratory Medicine and pathology, University of Minnesota, Minneapolis 55455 USA; 5Center for Immunology, University of Minnesota, Minneapolis, Minnesota 55455 USA; 6 Department of Ob-Gyn & Women’s Health, University of Minnesota, Minneapolis, Minnesota 55455 USA; 7Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455 USA; 8Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 USA Running title: Driver Genes Identified in DLBCL Using an SB Screen Keywords: DLBCL, Sleeping Beauty, RREB1, KRAS Corresponding Author: Eric P. Rahrmann, PhD Cancer Research UK Cambridge Institute Li Ka Shing Center Robinson Way Cambridge CB2 0RE T: 01223730854 [email protected] Disclosure of conflicts of interest: D.A. Largaespada has ownership interest in Immusoft, Inc., NeoClone Biotechnologies International, Discovery Genomics, Inc., and B-MoGen Biotechnologies Inc. He is also a consultant/Advisory Board member of Discovery Genomics, Inc. and NeoClone Biotechnologies International. B.S. Moriarity has ownership interest (including patents) in B- MoGen Biotechnologies Inc. Text word count: 5719 Abstract word count: 177 Figure/Table count: 7 figures Reference count: 50 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. KEY POINTS 1. Targeted mutagenesis to Cnp-Cre positive cells caused lymphomagenesis and identified multiple, recurrently altered genes and signaling pathways in human DLBCL. 2. Functionally validated Rreb1 as a driver of human B-cell lymphoma that influenced KRAS expression. 2 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the most common non-Hodgkin lymphomas distinguishable by unique mutations, chromosomal rearrangements and gene expression patterns. Here it is demonstrated that early B cell progenitors express 2',3'-Cyclic-nucleotide 3' phosphodiesterase (CNP) and that when targeted with Sleeping Beauty (SB) mutagenesis, Trp53R270H mutation or Pten loss gave rise to highly-penetrant lymphoid diseases, predominantly FL and DLBCL. In efforts to identify genetic drivers and signaling pathways that are functionally important in lymphomagenesis, SB transposon insertions were analyzed from splenomegaly specimens of SB-mutagenized mice (n=23) and SB-mutagenized mice on a Trp53R270H background (n=7) and identified 48 and 12 sites with statistically recurrent transposon insertion events, respectively. Comparison to human data sets revealed novel and known driver genes for B cell development, disease and signaling pathways: PI3K-AKT-mTOR, MAPK, NF-κB and BCR. Lastly, functional data indicates that modulating Ras responsive element binding protein 1 (RREB1) expression in human DLBCL cell lines in vitro alters KRAS expression, signaling, and proliferation; thus, suggesting that this proto-oncogene is a common mechanism of RAS-MAPK hyperactivation in human DLBCL. Implications A forward genetic screen identified new genetic drivers of human B-cell lymphoma and uncovered a RAS/MAPK activating mechanism not previously appreciated in human lymphoid disease. Overall, these data support targeting the RAS/MAPK pathway as a viable therapeutic target in a subset of human DLBCL patients. 3 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Introduction B cell malignancies comprise a large family of diseases ranging from highly curable Hodgkin’s lymphoma to the more diverse non-Hodgkin lymphoma subtypes including indolent follicular lymphoma (FL) and the aggressive, genetically heterogeneous Diffuse Large B Cell Lymphoma (DLBCL)1. Molecular profiling of B cell malignancies has identified defining genetics features for many of the subtypes leading to new therapeutic targets and increased survival-rates for some diseases1. DLBCL, which occur predominantly in older adults, diagnosis and treatment has greatly been impacted by the genetic profiling efforts. DLBCL is categorized into two unique molecular subtypes based on gene expression profiling: activated B cell-like (ABC) and germinal center B cell-like (GCB)1. Transcriptomic and genomic analyses identified recurrent genomic aberrations and signaling pathway alterations unique to each subtype and common to both2,3. Mutations in genes altering B cell receptor (BCR) signaling and NF-B activation (e.g. CD79A, MALT1, MYD88) are more common in ABC DLBCL while mutations in genes altering histone modifications and B cell homing (e.g. EZH2, CREBBP, MLL2) are more common in GCB DLBC4-6. Mutations in TP53, immunosurveillance genes (e.g. B2M, CD58), epigenetic modifiers (e.g. CREBBP) and MYC copy number alteration (CNA) gains occur in both subtypes2. Whole genome and exome sequencing efforts have identified over 300 recurrently mutated genes in primary DLBCL samples3,5,7,8. However, there is still limited knowledge on functional impact of many of these mutations and genetic alterations on disease initiation and progression; genetically engineered mouse models (GEMMs) provide a platform to begin evaluating these putative targets. The Sleeping Beauty (SB) somatic cell mutagenesis system has successfully identified genetic drivers of various cancers including hepatic, intestinal, pancreatic, osteosarcoma and T-cell9-14. We previously reported the identification of novel genetic drivers of peripheral 4 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. nerve-related cancers targeting SB-mutagenesis to 2’,3’-Cyclic-nucelotide 3’- phosphodiesterase (Cnp) expressing cells in mice in the context of EGFR overexpression with Trp53R270H mutation12. Mutagenesis alone or in the context of only Trp53R270H mutation was inefficient at developing peripheral nervous system tumors12. We describe here how these animals developed highly penetrant (65%) lymphoid disease (FL and DLBCL). Analysis of SB-induced lymphomas identified 59 common insertion sites (CIS), of which several were associated with signaling pathways altered in human DLBCL formation: PI3K- AKT-mTOR, NF-B and BCR signaling. We also identified several novel proto-oncogenes and tumor suppressor genes (TSGs) for B cell lymphoma e.g. Rreb1 and Ambra1, respectively. Furthermore, we described new roles for Rreb1, a MAPK pathway effector, in DLBCL maintenance and its impact on Kras expression, revealing an unknown mechanism for RAS activation in DLBCL. Materials and Methods Transgenic animals. Three transgenes were used to induce SB mutagenesis: Conditionally expressed SB (R26SB11LSL)15, Cnp promoter driven cre-recombinase (Cnp-Cre)16 and oncogenic transposon concatemer (T2/Onc15). Cnp-Cre;R26SB11LSL;T2/Onc15 (SB- mutagenized) mice undergo insertional mutagenesis in Cnp+ cells. Genotyping PCR was performed on phenol-chloroform extracted mouse-tail DNA10,16,17. Conditionally expressed Pten (Ptenf/f) and Trp53 (Trp53R270H) allele mice were utilized17,18. B6.129(Cg)- Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J reporter mice (Jackson Labs) were utilized for lineage tracing studies. All mice were bred and cared for under the guidelines of the University of Minnesota Animal Care and Use Committee. 5 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 24, 2018; DOI: 10.1158/1541-7786.MCR-18-0582 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. V(D)J PCR. 100ng of DNA from control and SB-mutagenized spleens underwent PCR to assess V(D)J clonality for VHJ558/JH3, VHQ52/JH3, VH7183/JH3, and DHL/JH3 recombination19. PCR for Actb served as the loading control. Flow cytometry. Single cell suspensions from bone marrow (femur and tibia), spleen and
Load more

Recommended publications
  • Directed Proximity-Dependent Biotin Labelling in Zebrafish
    TOOLS AND RESOURCES In vivo proteomic mapping through GFP- directed proximity-dependent biotin labelling in zebrafish Zherui Xiong1, Harriet P Lo1, Kerrie-Ann McMahon1, Nick Martel1, Alun Jones1, Michelle M Hill2, Robert G Parton1,3*, Thomas E Hall1* 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; 2QIMR Berghofer Medical Research Institute, Herston, Australia; 3Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia Abstract Protein interaction networks are crucial for complex cellular processes. However, the elucidation of protein interactions occurring within highly specialised cells and tissues is challenging. Here, we describe the development, and application, of a new method for proximity- dependent biotin labelling in whole zebrafish. Using a conditionally stabilised GFP-binding nanobody to target a biotin ligase to GFP-labelled proteins of interest, we show tissue-specific proteomic profiling using existing GFP-tagged transgenic zebrafish lines. We demonstrate the applicability of this approach, termed BLITZ (Biotin Labelling In Tagged Zebrafish), in diverse cell types such as neurons and vascular endothelial cells. We applied this methodology to identify interactors of caveolar coat protein, cavins, in skeletal muscle. Using this system, we defined specific interaction networks within in vivo muscle cells for the closely related but functionally distinct Cavin4 and Cavin1 proteins. *For correspondence: Introduction [email protected] (RGP); [email protected] (TEH) The understanding of the biological functions of a protein requires detailed knowledge of the mole- cules with which it interacts. However, robust elucidation of interacting proteins, including not only Competing interests: The strong direct protein-protein interactions, but also weak, transient or indirect interactions is challeng- authors declare that no ing.
    [Show full text]
  • Evidence for Differential Alternative Splicing in Blood of Young Boys With
    Stamova et al. Molecular Autism 2013, 4:30 http://www.molecularautism.com/content/4/1/30 RESEARCH Open Access Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders Boryana S Stamova1,2,5*, Yingfang Tian1,2,4, Christine W Nordahl1,3, Mark D Shen1,3, Sally Rogers1,3, David G Amaral1,3 and Frank R Sharp1,2 Abstract Background: Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume. Methods: RNA from blood was processed on whole genome exon arrays for 2-4–year-old ASD and TD boys. An ANCOVA with age and batch as covariates was used to predict DAS for ALL ASD (n=30), ASD with normal total cerebral volumes (NTCV), and ASD with large total cerebral volumes (LTCV) compared to TD controls (n=20). Results: A total of 53 genes were predicted to have DAS for ALL ASD versus TD, 169 genes for ASD_NTCV versus TD, 1 gene for ASD_LTCV versus TD, and 27 genes for ASD_LTCV versus ASD_NTCV. These differences were significant at P <0.05 after false discovery rate corrections for multiple comparisons (FDR <5% false positives). A number of the genes predicted to have DAS in ASD are known to regulate DAS (SFPQ, SRPK1, SRSF11, SRSF2IP, FUS, LSM14A). In addition, a number of genes with predicted DAS are involved in pathways implicated in previous ASD studies, such as ROS monocyte/macrophage, Natural Killer Cell, mTOR, and NGF signaling.
    [Show full text]
  • Endoglin Protein Interactome Profiling Identifies TRIM21 and Galectin-3 As
    cells Article Endoglin Protein Interactome Profiling Identifies TRIM21 and Galectin-3 as New Binding Partners 1, 1, 2, Eunate Gallardo-Vara y, Lidia Ruiz-Llorente y, Juan Casado-Vela y , 3 4 5 6, , María J. Ruiz-Rodríguez , Natalia López-Andrés , Asit K. Pattnaik , Miguel Quintanilla z * 1, , and Carmelo Bernabeu z * 1 Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain; [email protected] (E.G.-V.); [email protected] (L.R.-L.) 2 Bioengineering and Aerospace Engineering Department, Universidad Carlos III and Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Leganés, 28911 Madrid, Spain; [email protected] 3 Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; [email protected] 4 Cardiovascular Translational Research, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain; [email protected] 5 School of Veterinary Medicine and Biomedical Sciences, and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; [email protected] 6 Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC), and Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain * Correspondence: [email protected] (M.Q.); [email protected] (C.B.) These authors contributed equally to this work. y Equal senior contribution. z Received: 7 August 2019; Accepted: 7 September 2019; Published: 13 September 2019 Abstract: Endoglin is a 180-kDa glycoprotein receptor primarily expressed by the vascular endothelium and involved in cardiovascular disease and cancer.
    [Show full text]
  • S41467-020-18249-3.Pdf
    ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible.
    [Show full text]
  • CNOT2 Antibody A
    C 0 2 - t CNOT2 Antibody a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 5 5 Web: [email protected] 9 www.cellsignal.com 6 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB, IP H M R Mk Endogenous 62 Rabbit Q9NZN8 4848 Product Usage Information Application Dilution Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% glycerol. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity CNOT2 Antibody recognizes endogenous levels of total CNOT2 protein. Species Reactivity: Human, Mouse, Rat, Monkey Source / Purification Polyclonal antibodies are produced by immunizing animals with a synthetic peptide corresponding to residues near the carboxy terminus of human CNOT2 protein. Antibodies are purified by protein A and peptide affinity chromatography. Background The evolutionarily conserved CCR4-NOT (CNOT) complex regulates mRNA metabolism in eukaryotic cells (1). This regulation occurs at different levels of mRNA synthesis and degradation, including transcription initiation, elongation, deadenylation, and degradation (1). Multiple components, including CNOT1, CNOT2, CNOT3, CNOT4, CNOT6, CNOT6L, CNOT7, CNOT8, CNOT9, and CNOT10 have been identified in this complex (2). In addition, subunit composition of this complex has been shown to vary among different tissues (3). 1. Denis, C.L. and Chen, J. (2003) Prog Nucleic Acid Res Mol Biol 73, 221-50. 2. Lau, N.C. et al.
    [Show full text]
  • Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations
    IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. X, NO. X, MONTHXXX 20XX 1 Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations Davide Chicco, Fernando Palluzzi, and Marco Masseroli Abstract—Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand their test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and may contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new biomolecular annotations are both effective and efficient, especially if compared with the time-consuming trials of biological validation. To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritizing their results, we introduce here a new element that can improve the accuracy and relevance of the results of an annotation prediction and prioritization pipeline. We propose a novelty indicator able to state the level of ”newness” (or ”originality”) of the annotations predicted for a specific gene to Gene Ontology terms, and to help prioritizing the most novel and interesting annotations predicted. We performed a thorough biological functional analysis of the prioritized annotations predicted with high accuracy by using this indicator and our previously proposed prediction algorithms. The relevance
    [Show full text]
  • Gene Section Mini Review
    Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review SMAP1 (stromal membrane-associated protein 1) Kenji Tanabe, Shunsuke Kon, Masanobu Satake Department of Molecular Immunology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan (KT, SK, MS) Published in Atlas Database: March 2008 Online updated version: http://AtlasGeneticsOncology.org/Genes/SMAP1ID42974ch6q13.html DOI: 10.4267/2042/44388 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2009 Atlas of Genetics and Cytogenetics in Oncology and Haematology isoform A transcript is constituted by 467, and the other Identity from an isoform B is by 440 aa residues. A protein Other names: FLJ13159; FLJ42245; SMAP-1 diagram shown above represents an isoform B type. HGNC (Hugo): SMAP1 Expression Location: 6q13 Both isoform transcripts are detected in various human Local order: Between D6S455 and D6S1673. tissues. Expression appears to be almost ubiquitous. DNA/RNA Localisation SMAP1 protein is detected in the cytoplasm of cells, Description and appears to be highly concentrated near the plasma The gene spans an approximately 190 kb region, and is membrane. composed of 11 exons. Function Transcription SMAP1 functions as a GTPase-activating protein for an There is only one transcription initiation site. However, Arf6 GTPase. Arf6 is a Ras-related, small GTPase, and due to alternative splicing, generated are two types of regulates clathrin-dependent and -independent transcripts, isoforms A and B. The length of each endocytosis as well as actin dynamics. SMAP1 is transcript is either 3344 (isoform A) or 3263 nt specifically involved in the Arf6-regulated, clathrin- (isoform B).
    [Show full text]
  • The CCR4-NOT Complex Contributes to Repression of Major
    www.nature.com/scientificreports OPEN The CCR4-NOT complex contributes to repression of Major Histocompatibility Complex class II Received: 20 January 2017 Accepted: 3 May 2017 transcription Published: xx xx xxxx Alfonso Rodríguez-Gil 1, Olesja Ritter1, Vera V. Saul1, Jochen Wilhelm2, Chen-Yuan Yang3, Rudolf Grosschedl3, Yumiko Imai4, Keiji Kuba4, Michael Kracht5 & M. Lienhard Schmitz1 The multi-subunit CCR4 (carbon catabolite repressor 4)-NOT (Negative on TATA) complex serves as a central coordinator of all different steps of eukaryotic gene expression. Here we performed a systematic and comparative analysis of cells where the CCR4-NOT subunits CNOT1, CNOT2 or CNOT3 were individually downregulated using doxycycline-inducible shRNAs. Microarray experiments showed that downregulation of either CNOT subunit resulted in elevated expression of major histocompatibility complex class II (MHC II) genes which are found in a gene cluster on chromosome 6. Increased expression of MHC II genes after knock-down or knock-out of either CNOT subunit was seen in a variety of cell systems and also in naïve macrophages from CNOT3 conditional knock-out mice. CNOT2-mediated repression of MHC II genes occurred also in the absence of the master regulator class II transactivator (CIITA) and did not cause detectable changes of the chromatin structure at the chromosomal MHC II locus. CNOT2 downregulation resulted in an increased de novo transcription of mRNAs whereas tethering of CNOT2 to a regulatory region governing MHC II expression resulted in diminished transcription. These results expand the known repertoire of CCR4-NOT members for immune regulation and identify CNOT proteins as a novel group of corepressors restricting class II expression.
    [Show full text]
  • Transcriptional Regulator CNOT3 Defines an Aggressive Colorectal Cancer Subtype
    Published OnlineFirst November 29, 2016; DOI: 10.1158/0008-5472.CAN-16-1346 Cancer Tumor and Stem Cell Biology Research Transcriptional Regulator CNOT3 Defines an Aggressive Colorectal Cancer Subtype Paloma Cejas1,2,3, Alessia Cavazza1,2, C.N. Yandava1, Victor Moreno3, David Horst4, Juan Moreno-Rubio3, Emilio Burgos5, Marta Mendiola3,5, Len Taing1, Ajay Goel6, Jaime Feliu3, and Ramesh A. Shivdasani1,2 Abstract Cancer cells exhibit dramatic alterations of chromatin organi- primarily to genes whose expression was affected by CNOT3 loss, zation at cis-regulatory elements, but the molecular basis, extent, and also at sites modulated in certain types of colorectal cancers. and impact of these alterations are still being unraveled. Here, we These target genes were implicated in ESC and cancer self-renewal identify extensive genome-wide modification of sites bearing the and fell into two distinct groups: those dependent on CNOT3 and active histone mark H3K4me2 in primary human colorectal MYC for optimal transcription and those repressed by CNOT3 cancers, as compared with corresponding benign precursor ade- binding and promoter hypermethylation. Silencing CNOT3 in nomas. Modification of certain colorectal cancer sites highlighted colorectal cancer cells resulted in replication arrest. In clinical þ the activity of the transcription factor CNOT3, which is known to specimens, early-stage tumors that included >5% CNOT3 cells control self-renewal of embryonic stem cells (ESC). In primary exhibited a correlation to worse clinical outcomes compared with colorectal cancer cells, we observed a scattered pattern of CNOT3 tumors with little to no CNOT3 expression. Together, our findings expression, as might be expected for a tumor-initiating cell mark- implicate CNOT3 in the coordination of colonic epithelial cell er.
    [Show full text]
  • Full-Text.Pdf
    Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility This information is current as Ramesh Ram, Munish Mehta, Quang T. Nguyen, Irma of September 23, 2021. Larma, Bernhard O. Boehm, Flemming Pociot, Patrick Concannon and Grant Morahan J Immunol 2016; 196:3043-3053; Prepublished online 24 February 2016; doi: 10.4049/jimmunol.1502056 Downloaded from http://www.jimmunol.org/content/196/7/3043 Supplementary http://www.jimmunol.org/content/suppl/2016/02/19/jimmunol.150205 Material 6.DCSupplemental http://www.jimmunol.org/ References This article cites 44 articles, 5 of which you can access for free at: http://www.jimmunol.org/content/196/7/3043.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 23, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility Ramesh Ram,*,† Munish Mehta,*,† Quang T.
    [Show full text]
  • Lineage-Specific Proteins Essential for Endocytosis in Trypanosomes Paul T
    © 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 1379-1392 doi:10.1242/jcs.191478 RESEARCH ARTICLE Lineage-specific proteins essential for endocytosis in trypanosomes Paul T. Manna1, Samson O. Obado2, Cordula Boehm1, Catarina Gadelha3, Andrej Sali4, Brian T. Chait2, Michael P. Rout2 and Mark C. Field1,* ABSTRACT year period since this radiation is vast, and while core metabolic and Clathrin-mediated endocytosis (CME) is the most evolutionarily gene expression pathways are frequently well conserved, many ancient endocytic mechanism known, and in many lineages the cellular features have experienced extensive specialisations, in part sole mechanism for internalisation. Significantly, in mammalian as a response to adaptive evolutionary forces. cells CME is responsible for the vast bulk of endocytic flux and One aspect of this diversity that has received considerable attention has likely undergone multiple adaptations to accommodate specific is the endomembrane system, on account of this feature representing requirements by individual species. In African trypanosomes, we one of the more unique, yet flexible, aspects of eukaryotic cells. The previously demonstrated that CME is independent of the AP-2 primitive endomembrane system in the earliest eukaryotes gave rise adaptor protein complex, that orthologues to many of the animal and to all of the endogenously derived internal compartments present in fungal CME protein cohort are absent, and that a novel, trypanosome- modern lineages (Schlacht et al., 2014). As a consequence of this restricted protein cohort interacts with clathrin and drives CME. Here, extensive evolutionary history, compartments have experienced we used a novel cryomilling affinity isolation strategy to preserve significant divergence, resulting in vastly different morphologies transient low-affinity interactions, giving the most comprehensive and functions, as reflected in diversification of the Golgi complex, trypanosome clathrin interactome to date.
    [Show full text]
  • UNIVERSITY of CALIFORNIA, IRVINE Gene Regulatory
    UNIVERSITY OF CALIFORNIA, IRVINE Gene Regulatory Mechanisms in Epithelial Specification and Function DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Sciences by Rachel Herndon Klein Dissertation Committee: Professor Bogi Andersen, M.D., Chair Professor Xing Dai, Ph.D. Professor Anand Ganesan, M.D. Professor Ali Mortazavi, Ph.D Professor Kyoko Yokomori, Ph.D 2015 © 2015 Rachel Herndon Klein DEDICATION To My parents, my sisters, my husband, and my friends for your love and support, and to Ben with all my love. ii TABLE OF CONTENTS Page LIST OF FIGURES iv LIST OF TABLES vi ACKNOWLEDGMENTS vii CURRICULUM VITAE viii-ix ABSTRACT OF THE DISSERTATION x-xi CHAPTER 1: INTRODUCTION 1 CHAPTER 2: Cofactors of LIM domain (CLIM) proteins regulate corneal epithelial progenitor cell function through noncoding RNA H19 22 CHAPTER 3: KLF7 regulates the corneal epithelial progenitor cell state acting antagonistically to KLF4 49 CHAPTER 4: GRHL3 interacts with super enhancers and the neuronal repressor REST to regulate keratinocyte differentiation and migration 77 CHAPTER 5: Methods 103 CHAPTER 6: Summary and Conclusions 111 REFERENCES 115 iii LIST OF FIGURES Page Figure 1-1. Structure and organization of the epidermis. 3 Figure 1-2. Structure of the limbus, and cornea epithelium. 4 Figure 1-3. Comparison of H3K4 methylating SET enzymes between S. cerevisiae, D. melanogaster, and H. sapiens. 18 Figure 1-4. The WRAD complex associates with Trithorax SET enzymes. 18 Figure 1-5. Model for GRHL3, PcG, and TrX –mediated regulation of epidermal differentiation genes. 19 Figure 2-1. Microarray gene expression analysis of postnatal day 3 (P3) whole mouse corneas reveals genes and pathways with altered expression in K14-DN-Clim mice.
    [Show full text]