The Nore1b/Mst1 Complex Restrains Antigen Receptor-Induced Proliferation of Naïve T Cells
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Transcriptional Control of Tissue-Resident Memory T Cell Generation
Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. -
Supplemental Table 1. Complete Gene Lists and GO Terms from Figure 3C
Supplemental Table 1. Complete gene lists and GO terms from Figure 3C. Path 1 Genes: RP11-34P13.15, RP4-758J18.10, VWA1, CHD5, AZIN2, FOXO6, RP11-403I13.8, ARHGAP30, RGS4, LRRN2, RASSF5, SERTAD4, GJC2, RHOU, REEP1, FOXI3, SH3RF3, COL4A4, ZDHHC23, FGFR3, PPP2R2C, CTD-2031P19.4, RNF182, GRM4, PRR15, DGKI, CHMP4C, CALB1, SPAG1, KLF4, ENG, RET, GDF10, ADAMTS14, SPOCK2, MBL1P, ADAM8, LRP4-AS1, CARNS1, DGAT2, CRYAB, AP000783.1, OPCML, PLEKHG6, GDF3, EMP1, RASSF9, FAM101A, STON2, GREM1, ACTC1, CORO2B, FURIN, WFIKKN1, BAIAP3, TMC5, HS3ST4, ZFHX3, NLRP1, RASD1, CACNG4, EMILIN2, L3MBTL4, KLHL14, HMSD, RP11-849I19.1, SALL3, GADD45B, KANK3, CTC- 526N19.1, ZNF888, MMP9, BMP7, PIK3IP1, MCHR1, SYTL5, CAMK2N1, PINK1, ID3, PTPRU, MANEAL, MCOLN3, LRRC8C, NTNG1, KCNC4, RP11, 430C7.5, C1orf95, ID2-AS1, ID2, GDF7, KCNG3, RGPD8, PSD4, CCDC74B, BMPR2, KAT2B, LINC00693, ZNF654, FILIP1L, SH3TC1, CPEB2, NPFFR2, TRPC3, RP11-752L20.3, FAM198B, TLL1, CDH9, PDZD2, CHSY3, GALNT10, FOXQ1, ATXN1, ID4, COL11A2, CNR1, GTF2IP4, FZD1, PAX5, RP11-35N6.1, UNC5B, NKX1-2, FAM196A, EBF3, PRRG4, LRP4, SYT7, PLBD1, GRASP, ALX1, HIP1R, LPAR6, SLITRK6, C16orf89, RP11-491F9.1, MMP2, B3GNT9, NXPH3, TNRC6C-AS1, LDLRAD4, NOL4, SMAD7, HCN2, PDE4A, KANK2, SAMD1, EXOC3L2, IL11, EMILIN3, KCNB1, DOK5, EEF1A2, A4GALT, ADGRG2, ELF4, ABCD1 Term Count % PValue Genes regulation of pathway-restricted GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, SMAD protein phosphorylation 9 6.34 1.31E-08 ENG pathway-restricted SMAD protein GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, phosphorylation -
Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5
Structure Article Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Lisheng Ni,1 Sheng Li,1,4 Jianzhong Yu,3 Jungki Min,1,5 Chad A. Brautigam,2 Diana R. Tomchick,2 Duojia Pan,3 and Xuelian Luo1,* 1Department of Pharmacology 2Department of Biophysics The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA 3Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA 4Present address: Biologics Department, Shanghai ChemPartner Co. Ltd., Shanghai 201203, China 5Present address: Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.str.2013.07.008 SUMMARY dor (Sav1), the NDR family kinases Lats1 and Lats2 (Lats1/2), and the adaptor protein Mob1. They form a central kinase The tumor-suppressive Hippo pathway controls cascade to transduce signals from cell-surface receptors tissue homeostasis through balancing cell prolifera- (Avruch et al., 2012; Hergovich, 2012). tion and apoptosis. Activation of the kinases Mst1 In the canonical Hippo kinase cascade, Mst1/2, in complex and Mst2 (Mst1/2) is a key upstream event in this with Sav1, phosphorylate and activate the Lats1/2-Mob1 com- pathway and remains poorly understood. Mst1/2 plexes, which then phosphorylate the transcriptional coactivator and their critical regulators RASSFs contain Yes-associated protein (YAP), a major downstream target of the Hippo pathway (Dong et al., 2007; Hao et al., 2008; Hong and Salvador/RASSF1A/Hippo (SARAH) domains that Guan, 2012; Huang et al., 2005; Zhao et al., 2007). -
STRIPAK Complexes in Cell Signaling and Cancer
Oncogene (2016), 1–9 © 2016 Macmillan Publishers Limited All rights reserved 0950-9232/16 www.nature.com/onc REVIEW STRIPAK complexes in cell signaling and cancer Z Shi1,2, S Jiao1 and Z Zhou1,3 Striatin-interacting phosphatase and kinase (STRIPAK) complexes are striatin-centered multicomponent supramolecular structures containing both kinases and phosphatases. STRIPAK complexes are evolutionarily conserved and have critical roles in protein (de) phosphorylation. Recent studies indicate that STRIPAK complexes are emerging mediators and regulators of multiple vital signaling pathways including Hippo, MAPK (mitogen-activated protein kinase), nuclear receptor and cytoskeleton remodeling. Different types of STRIPAK complexes are extensively involved in a variety of fundamental biological processes ranging from cell growth, differentiation, proliferation and apoptosis to metabolism, immune regulation and tumorigenesis. Growing evidence correlates dysregulation of STRIPAK complexes with human diseases including cancer. In this review, we summarize the current understanding of the assembly and functions of STRIPAK complexes, with a special focus on cell signaling and cancer. Oncogene advance online publication, 15 February 2016; doi:10.1038/onc.2016.9 INTRODUCTION in the central nervous system and STRN4 is mostly abundant in Recent proteomic studies identified a group of novel multi- the brain and lung, whereas STRN3 is ubiquitously expressed in 5–9 component complexes named striatin (STRN)-interacting phos- almost all tissues. STRNs share a -
The Discovery of a Novel, Ras-Mediated NORE1A/PMLIV Tumor Suppressor Complex." (2016)
University of Louisville ThinkIR: The University of Louisville's Institutional Repository Electronic Theses and Dissertations 8-2016 The discovery of a novel, Ras-mediated NORE1A/ PMLIV tumor suppressor complex. Jessica Mezzanotte Sharpe University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/etd Part of the Medical Biochemistry Commons, and the Medical Molecular Biology Commons Recommended Citation Sharpe, Jessica Mezzanotte, "The discovery of a novel, Ras-mediated NORE1A/PMLIV tumor suppressor complex." (2016). Electronic Theses and Dissertations. Paper 2539. https://doi.org/10.18297/etd/2539 This Doctoral Dissertation is brought to you for free and open access by ThinkIR: The nivU ersity of Louisville's Institutional Repository. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of ThinkIR: The nivU ersity of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. THE DISCOVERY OF A NOVEL, RAS-MEDIATED NORE1A/PMLIV TUMOR SUPPRESSOR COMPLEX By: Jessica Mezzanotte Sharpe B.A., Vanderbilt University, 2010 M.S., University of Louisville, 2014 A Dissertation Submitted to the Faculty of the School of Medicine of the University of Louisville in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biochemistry and Molecular Biology Department of Biochemistry and Molecular Genetics University of Louisville Louisville, KY August, 2016 Copyright 2016 by Jessica Mezzanotte Sharpe All Rights Reserved THE DISCOVERY OF A NOVEL, RAS-MEDIATED NORE1A/PMLIV TUMOR SUPPRESSOR COMPLEX By Jessica Mezzanotte Sharpe B.A., Vanderbilt University, 2010 M.S., University of Louisville, 2014 A Dissertation Approved on June 8, 2016 by the following Dissertation Committee: __________________________________________ Dr. -
Gene Section Short Communication
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Short Communication RASSF5 (Ras association (RalGDS/AF -6) domain family member 5) Lee Schmidt, Geoffrey J Clark University of Louisville, Room 119C, Baxter II Research Building, 580 S Preston Street, Louisville, KY 40202, USA (LS, GJC) Published in Atlas Database: October 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/RASSF5ID42059ch1q32.html DOI: 10.4267/2042/47279 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2012 Atlas of Genetics and Cytogenetics in Oncology and Haematology Identity DNA/RNA Other names: MGC10823, MGC17344, Maxp1, Description NORE1, NORE1A, NORE1B, RAPL, RASSF3 The human gene for RASSF5 is 81 kb in length and is HGNC (Hugo): RASSF5 located on chromosome 1(q32.1). The gene can Location: 1q32.1 produce 4 protein isoforms, two via differential exon usage, a third via differential promoter usage and the genesis of the 4 th (which can be found as an EST clone) is not yet clear. The largest isoform, A, is 418 amino acids long and has a molecular weight of about 47 kD. The protein structure of RASSF5A contains a proline- rich region at the N-terminus which contains potential SH3 binding sites and a nuclear localization signal. This is followed by a cystein rich domain, sometimes Note referred to as a zinc finger. Next is the Ras association Murine RASSF5 originally named Nore1a. Nore1B domain and this is followed by sequence containing the independently identified and designated RAPL. Rat SARAH motif required for binding to the pro-apoptotic RASSF5 also cloned independently and designated kinases MST1 and MST2. -
The Expression of RUNDC3B Is Associated with Promoter Methylation in Lymphoid Malignancies
The expression of RUNDC3B is associated with promoter methylation in lymphoid malignancies Running Head: Epigenetic regulation of RUNDC3B Keywords: RUNDC3B, DNA methylation, lymphoma, leukemia, B-cell, gene expression Dane W. Burmeister1, Emily H. Smith1,2, Robert T. Cristel1, Stephanie D. McKay1,3, Huidong Shi4, Gerald L. Arthur1, J. Wade Davis5,6, and Kristen H. Taylor1,* 1Department of Pathology and Anatomical Sciences; University of Missouri; Columbia, MO USA; 2Department of Dermatology; University of Michigan Health System; Ann Arbor, MI USA; 3Department of Animal Science; University of Vermont; Burlington, VT USA; 4Department of Biochemistry and Molecular Biology; Georgia Regents University; Augusta, GA USA; 5Department of Health Management and Informatics; University of Missouri; Columbia, MO USA; 6Department of Statistics; University of Missouri, Columbia, MO USA *Corresponding author: Kristen H. Taylor PhD Department of Pathology and Anatomical Sciences One Hospital Drive University of Missouri-Columbia Columbia, Missouri 65212 USA E-mail: [email protected] Telephone: 573-882-5523 FAX: 573-884-4612 This work was supported by a National Institute of Health grant NCI R00 CA132784 (K.H. Taylor) No potential conflicts exist for the authors of this manuscript. Word Count: 2991 This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/HON.2238 1 This article is protected by copyright. All rights reserved. Abstract DNA methylation is an epigenetic modification that plays an important role in regulation of gene expression. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Insights from reconstructing cellular networks in transcription, stress, and cancer Permalink https://escholarship.org/uc/item/6s97497m Authors Ke, Eugene Yunghung Ke, Eugene Yunghung Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Insights from Reconstructing Cellular Networks in Transcription, Stress, and Cancer A dissertation submitted in the partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Eugene Yunghung Ke Committee in charge: Professor Shankar Subramaniam, Chair Professor Inder Verma, Co-Chair Professor Web Cavenee Professor Alexander Hoffmann Professor Bing Ren 2012 The Dissertation of Eugene Yunghung Ke is approved, and it is acceptable in quality and form for the publication on microfilm and electronically ________________________________________________________________ ________________________________________________________________ ________________________________________________________________ ________________________________________________________________ Co-Chair ________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION To my parents, Victor and Tai-Lee Ke iv EPIGRAPH [T]here are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there -
RASSF6; the Putative Tumor Suppressor of the RASSF Family
Review RASSF6; the Putative Tumor Suppressor of the RASSF Family Hiroaki Iwasa 1, Xinliang Jiang 2 and Yutaka Hata 1,2,* Received: 2 November 2015; Accepted: 1 December 2015; Published: 9 December 2015 Academic Editor: Reinhard Dammann 1 Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; [email protected] 2 Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-3-5803-5164; Fax: +81-3-5803-0121 Abstract: Humans have 10 genes that belong to the Ras association (RA) domain family (RASSF). Among them, RASSF7 to RASSF10 have the RA domain in the N-terminal region and are called the N-RASSF proteins. In contradistinction to them, RASSF1 to RASSF6 are referred to as the C-RASSF proteins. The C-RASSF proteins have the RA domain in the middle region and the Salvador/RASSF/Hippo domain in the C-terminal region. RASSF6 additionally harbors the PSD-95/Discs large/ZO-1 (PDZ)-binding motif. Expression of RASSF6 is epigenetically suppressed in human cancers and is generally regarded as a tumor suppressor. RASSF6 induces caspase-dependent and -independent apoptosis. RASSF6 interacts with mammalian Ste20-like kinases (homologs of Drosophila Hippo) and cross-talks with the Hippo pathway. RASSF6 binds MDM2 and regulates p53 expression. The interactions with Ras and Modulator of apoptosis 1 (MOAP1) are also suggested by heterologous protein-protein interaction experiments. RASSF6 regulates apoptosis and cell cycle through these protein-protein interactions, and is implicated in the NF-κB and JNK signaling pathways. -
Differences in Gene Expression Profiles and Carcinogenesis Pathways Involved in Cisplatin Resistance of Four Types of Cancer
596 ONCOLOGY REPORTS 30: 596-614, 2013 Differences in gene expression profiles and carcinogenesis pathways involved in cisplatin resistance of four types of cancer YONG YANG1,2, HUI LI1,2, SHENGCAI HOU1,2, BIN HU1,2, JIE LIU1,3 and JUN WANG1,3 1Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Capital Medical University, Beijing 100069; 2Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020; 3Department of Physiology, Capital Medical University, Beijing 100069, P.R. China Received December 23, 2012; Accepted March 4, 2013 DOI: 10.3892/or.2013.2514 Abstract. Cisplatin-based chemotherapy is the standard Introduction therapy used for the treatment of several types of cancer. However, its efficacy is largely limited by the acquired drug Cisplatin is primarily effective through DNA damage and is resistance. To date, little is known about the RNA expression widely used for the treatment of several types of cancer, such changes in cisplatin-resistant cancers. Identification of the as testicular, lung and ovarian cancer. However, the ability RNAs related to cisplatin resistance may provide specific of cancer cells to become resistant to cisplatin remains a insight into cancer therapy. In the present study, expression significant impediment to successful chemotherapy. Although profiling of 7 cancer cell lines was performed using oligo- previous studies have identified numerous mechanisms in nucleotide microarray analysis data obtained from the GEO cisplatin resistance, it remains a major problem that severely database. Bioinformatic analyses such as the Gene Ontology limits the usefulness of this chemotherapeutic agent. Therefore, (GO) and KEGG pathway were used to identify genes and it is crucial to examine more elaborate mechanisms of cisplatin pathways specifically associated with cisplatin resistance. -
Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda
ORIGINAL RESEARCH published: 16 August 2021 doi: 10.3389/fgene.2021.723980 Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda Richard Habimana 1,2*, Kiplangat Ngeno 2, Tobias Otieno Okeno 2, Claire D’ andre Hirwa 3, Christian Keambou Tiambo 4 and Nasser Kouadio Yao 5 1 College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda, 2 Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya, 3 Rwanda Agricultural and Animal Resources Development Board, Kigali, Rwanda, 4 Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya, 5 Biosciences Eastern and Central Africa – International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya A chicken genome has several regions with quantitative trait loci (QTLs). However, Edited by: replication and confirmation of QTL effects are required particularly in African chicken Younes Miar, Dalhousie University, populations. This study identified single nucleotide polymorphisms (SNPs) and putative Canada genes responsible for body weight (BW) and antibody response (AbR) to Newcastle Reviewed by: disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies Sayed Haidar Abbas, Northwest A & F University, China (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and Suxu Tan, 10% for significant and suggestive thresholds, respectively. BioMart data mining and Michigan State University, variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. United States A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) *Correspondence: Richard Habimana significantly (p ≤ 7.6E−5) associated with BW were identified on chromosomes (CHRs) [email protected] 8, 11, and 19. -
The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Author Manuscript Published OnlineFirst on August 3, 2016; DOI: 10.1158/0008-5472.CAN-16-0658 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. The genomic landscape of pancreatic and periampullary adenocarcinoma Vandana Sandhu1,8, David C Wedge2,11, Inger Marie Bowitz Lothe1,3, Knut Jørgen Labori4, Stefan C Dentro2,11, Trond Buanes4,5, Martina L Skrede1, Astrid M Dalsgaard1, Else Munthe6, Ola Myklebost6, Ole Christian Lingjærde7, Anne-Lise Børresen-Dale1,5, Tone Ikdahl9,10, Peter Van Loo12,13, Silje Nord1, Elin H Kure1,8* 1Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 2Wellcome Trust Sanger Institute, Hinxton, UK 3Department of Pathology, Oslo University Hospital, Oslo, Norway 4Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway 5Institute of Clinical Medicine, University of Oslo, Oslo, Norway 6Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 7Department of Computer Science, University of Oslo, Oslo, Norway 8Department for Environmental Health and Science, University college of Southeast Norway, Bø in Telemark, Norway 9Department of Oncology, Oslo University Hospital, Oslo, Norway 10Akershus University Hospital, Nordbyhagen, Norway 11Department of Cancer Genomics, Big Data Institute, University of Oxford, Oxford, UK 12The Francis Crick Institute, London, UK 13Department of Human Genetics, University of Leuven, Leuven, Belgium *Corresponding author: Elin H. Kure, [email protected] Running title: Copy number aberrations in periampullary adenocarcinomas Keywords 1. Pancreatic cancer 2. Copy number aberrations 3. Integrative –omics analysis 4. Driver genes 5. Prognostic subtypes 1 Downloaded from cancerres.aacrjournals.org on September 27, 2021.