Association of Chromosome 19 to Lung Cancer Genotypes and Phenotypes

Total Page:16

File Type:pdf, Size:1020Kb

Association of Chromosome 19 to Lung Cancer Genotypes and Phenotypes Cancer Metastasis Rev DOI 10.1007/s10555-015-9556-2 Association of chromosome 19 to lung cancer genotypes and phenotypes Xiangdong Wang1 & Yong Zhang 1 & Carol L. Nilsson2 & Frode S. Berven3 & Per E. Andrén4 & Elisabet Carlsohn5 & Johan Malm7 & Manuel Fuentes7 & Ákos Végvári6,8 & Charlotte Welinder6,9 & Thomas E. Fehniger6,10 & Melinda Rezeli8 & Goutham Edula11 & Sophia Hober12 & Toshihide Nishimura13 & György Marko-Varga6,8,13 # Springer Science+Business Media New York 2015 Abstract The Chromosome 19 Consortium, a part of the aberrations include translocation t(15, 19) (q13, p13.1) fusion Chromosome-Centric Human Proteome Project (C-HPP, oncogene BRD4-NUT, DNA repair genes (ERCC1, ERCC2, http://www.C-HPP.org), is tasked with the understanding XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4) chromosome 19 functions at the gene and protein levels, as , Dyrk1B, and potential oncogenesis protector genes such as well as their roles in lung oncogenesis. Comparative genomic NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and hybridization (CGH) studies revealed chromosome aberration EGLN2. In conclusion, neXtProt is an effective resource for in lung cancer subtypes, including ADC, SCC, LCC, and the validation of gene aberrations identified in genomic SCLC. The most common abnormality is 19p loss and 19q studies. It promises to enhance our understanding of lung gain. Sixty-four aberrant genes identified in previous genomic cancer oncogenesis. studies and their encoded protein functions were further vali- dated in the neXtProt database (http://www.nextprot.org/). Among those, the loss of tumor suppressor genes STK11, Keywords Proteins . Genes . Antibodies . mRNA . Mass MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is spectrometry . Bioinformatics . Protein microarray . Human associated with lung oncogenesis or remote metastasis. Gene disease Xiangdong Wang and Yong Zhang contributed equally to this work. * Xiangdong Wang 7 Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, [email protected] Unidad de Proteomica, Departamento de Medicina and Servicio General de Citometría-Nucleus, University of Salamanca, * György Marko-Varga 37007 Salamanca, Spain [email protected] 8 Clinical Protein Science & Imaging, Biomedical Center, Department 1 Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, of Measurement Technology and Industrial Electrical Engineering, Fudan University, Shanghai, China Lund University, BMC C13, 221 84 Lund, Sweden 2 Department of Pharmacology and Toxicology, UTMB Cancer 9 Department of Oncology and Pathology, Clinical Sciences, Lund Center, University of Texas Medical Branch, Galveston, TX 77555, University, 221 85 Lund, Sweden USA 3 Department of Biomedicine, University of Bergen, 10 Institute of Clinical Medicine, Tallinn University of Technology, 5009 Bergen, Norway 12618 Tallinn, Estonia 4 Department of Pharmaceutical Biosciences, Uppsala University, 751 11 24 Uppsala, Sweden Clinnovo Research Labs, Hyderabad, India 5 Proteomics Core Facility, Göteborg University, 413 12 School of Biotechnology, Department of Proteomics, Royal Institute 90 Göteborg, Sweden of Technology, 106 91 Stockholm, Sweden 6 Department of Laboratory Medicine, Section for Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, 205 13 First Department of Surgery, Tokyo Medical University, 6-7-1 02 Malmö, Sweden Nishishinjiku Shinjiku-ku, Tokyo 160-0023, Japan Cancer Metastasis Rev 1 Introduction Lung cancer Lung cancer Lung cancer risk subtype prognosis Lung cancer is the leading diagnosed cancer as well as CGH study the leading cause of cancer death globally. It accounts for 13 % (1.82 million) of the total new cancer cases Gene aberraon in chromosome 19 and 18 % (1.59 million) of the deaths in cancer in 2012 around the world [1]. Lung cancer is also the leading Protein level validaon in cause of death accounting for 29 % and 26 % of total C-HPP based database cancer deaths in men and women, respectively. The five year survival for all stage lung cancer patients is only Gene and protein funcon annotaon about 15 %, and for stage IV patients, just 3–4%[2, 3]. Chromosome aberrations related to lung oncogenesis Potenal lung mechanisms have been revealed recently. About 50 % oncogenesis of the lung adenocarcinoma (ADC) tumors bear Bdriver mechanism mutations^. EGFR mutations are the most common Fig. 1 Workflow identifying molecular mechanism of lung oncogenesis. drive mutations in lung ADC, usually due to losses in To decipher the oncogenesis mechanism chromosome 19 gene exon 19, or point mutations of exon 21 in chromosome aberrations identified in GCH studies with lung cancer subtype, risk, 7[4]. About 4 % of lung ADCs are caused by EML4- and prognosis were enrolled. The indentified aberration genes were integrated and further inquired in chromosome centric neXProt to ALK fusion genes, usually intron 13 of EML4 in chro- explore potential lung oncogenesis mechanism mosome 1 fused to intron 20 of ALK in chromosome 2 [5]. Targeted treatments aimed at the driver mutation proteins remarkably increase the overall survival of lung Chromosome 19 has the highest gene density of all human ADC patients. With comparative genomic hybridization chromosomes, more than double the genome-wide average. (CGH) methods and high throughout genome-wide as- Furthermore, it has large clusters of gene families that corre- sociation studies (GWAS), more chromosomal variants spond to high G + C content and CpG islands which indicate associated with lung oncogenesis have been identified. its rich biological and evolutionary significance. Chromosome The importance of chromosome 19 gene aberrations was 19 is also unique in its density of repeat sequences (55 % vs clearly demonstrated by the previous studies. the genome average of 44.8 %) [14]. The Chromosome-Centric Human Proteome Project (C- The C-HPP project targets the identification of all HPP) is a global consortium dedicated to mapping the entire gene-coding proteins with a special emphasis on the human complement of proteins, with global membership missing proteins, which account for almost 30 % of (http://www.c-hpp.org)[6–10]. The Chromosome 19 the proteins in the human proteome. The ENCODE ini- Consortium has investigated gene expression using tiative has been linked to the C-HPP initiative and pro- complementary analysis platforms, to provide a genome- vides newly identified gene activity that may predict wide human protein resource database, and detailed maps of novel proteoforms [13]. The data resources of the HPP protein molecular pathways, interactions, and networks. The are comprised of Ensemble, which is linked to the Chromosome 19 project has already contributed to the anno- neXtProt, PeptideAtlas, and gpmDB databases. Recently, tations of severe diseases, especially glioblastoma [11–13]. the numbers of highly confident protein identifications The present article focuses on chromosome 19 gene aber- in these data resources that were announced recently by rations in different lung cancer subtypes, including non-small Marko-Varga et al [15]. The number of missing proteins cell lung cancer (NSCLC): ADC, squamous cell carcinoma during one year was decreased from 32.7 % in 2012 to (SCC), large cell carcinoma (LCC), and small cell lung cancer 26.2 % in 2013 (September, lecture by G. Omenn, at (SCLC), and their potential role in lung oncogenesis. We have HUPO World Congress, Yokohama, Japan). In the Sep- explored gene polymorphisms on chromosome 19 that are tember 19, 2014, release of neXtProt, the number of translated into protein variants, and offer potential mecha- protein-coding genes is about 20000. Roughly 18 % of nisms involved, as well as potential targeted therapeutics for the complete set of human protein coding genes is miss- the future (Fig. 1). ing at the protein level currently. As for chromosome 19, according to of neXtProt database released on Jan- uary 2015, there are estimated 1,432 protein-coding 2 Bioinformatic annotation of chromosome 19 genes, including 244 genes with transcript-based evi- dence (PE2) available. Of these 1,432 genes, 2,707 al- Chromosome 19 spans about 64 million base pairs, ternative splicing variants are listed, as well as 199N- representing more than 2 % of the human genome. acetylated and 407 phorphoproteins. Cancer Metastasis Rev 19P In SCC, the aberrations of chromosome 19 losses or gains DNA loss were both indentified. One CGH study in Eastern lung SCC DNA gain demonstrated DNA amplifications on 19p [21]. Gains of 19q13.13 were increased in Western lung SCC patients ADC 19p13.11 [22]. Furthermore, gene losses of chromosome 19 in adja- cent bronchial mucosa were detected in SCC and LCC both in primary lung carcinomas. Chromosome 19 losses may be the early event in SCC oncogenesis [23]. Whole exon se- Asbstos 19p13.3 SCC quencing (n= 51) and copy number analysis (n=47) of induced ADC resected SCLC tumors was compared with matched non- cancer samples from Eastern SCLC patients. Genetic am- Smoker ADC 19p13.1 plifications in the PI3K/AKT/mTOR pathway were detect- ed in 36 % of SCLC, including AKT2 (9 %), located in 19q13.2 [24]. Western people showed two amplified re- gions in chromosome 19q13.2-3 in 4 types of lung cancer (ADC, SCC, LCC, and SCLC). 265 lung cancer samples were compared with 272 non-malignant samples. Single 19q12 SCC nucleotide polymorphism (SNP) RT-PCR revealed a vari- Non-smoker ADC 19q13.1 Smoker SCC ant allele of DNA repair gene ERCC2 rs1052559a and rs1799793 in 19q13.2–3 were significantly
Recommended publications
  • Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach
    Mafalda Rita Avó Bacalhau Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach Tese de doutoramento do Programa de Doutoramento em Ciências da Saúde, ramo de Ciências Biomédicas, orientada pela Professora Doutora Maria Manuela Monteiro Grazina e co-orientada pelo Professor Doutor Henrique Manuel Paixão dos Santos Girão e pela Professora Doutora Lee-Jun C. Wong e apresentada à Faculdade de Medicina da Universidade de Coimbra Julho 2017 Faculty of Medicine Establishing the pathogenicity of novel mitochondrial DNA sequence variations: a cell and molecular biology approach Mafalda Rita Avó Bacalhau Tese de doutoramento do programa em Ciências da Saúde, ramo de Ciências Biomédicas, realizada sob a orientação científica da Professora Doutora Maria Manuela Monteiro Grazina; e co-orientação do Professor Doutor Henrique Manuel Paixão dos Santos Girão e da Professora Doutora Lee-Jun C. Wong, apresentada à Faculdade de Medicina da Universidade de Coimbra. Julho, 2017 Copyright© Mafalda Bacalhau e Manuela Grazina, 2017 Esta cópia da tese é fornecida na condição de que quem a consulta reconhece que os direitos de autor são pertença do autor da tese e do orientador científico e que nenhuma citação ou informação obtida a partir dela pode ser publicada sem a referência apropriada e autorização. This copy of the thesis has been supplied on the condition that anyone who consults it recognizes that its copyright belongs to its author and scientific supervisor and that no quotation from the
    [Show full text]
  • Transcriptome Analysis of Four Arabidopsis Thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation
    G3: Genes|Genomes|Genetics Early Online, published on July 26, 2018 as doi:10.1534/g3.118.200573 Title: Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation Authors: Whitney L. Dolan and Clint Chapple Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA and Purdue Center for Plant Biology, West Lafayette, IN 47907, USA. Reference numbers: Gene expression data are available in the Gene Expression Omnibus under accession GSE95574. 1 © The Author(s) 2013. Published by the Genetics Society of America. Running title: RNAseq of Four Arabidopsis MED Mutants Keywords: Mediator, Arabidopsis, transcription regulation, gene expression Corresponding author: Clint Chapple Department of Biochemistry Purdue University 175 South University St. West Lafayette, IN 47907 Telephone: 765-494-0494 Fax: 765-494-7897 E-mail: [email protected] 2 1 ABSTRACT 2 3 The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The 4 complex is structurally divided into four modules known as the head, middle, tail and kinase 5 modules, and in Arabidopsis thaliana, comprises 28-34 subunits. Here, we explore the functions 6 of four Arabidopsis Mediator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing 7 the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits 8 affect both unique and overlapping sets of genes, providing insight into the functional and 9 structural relationships between them. The mutants primarily exhibit changes in the expression 10 of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for 11 MED23, as well as in the production of alternative transcripts.
    [Show full text]
  • Gprc5b Modulates Inflammatory Response in Glomerular Diseases
    BASIC RESEARCH www.jasn.org GPRC5b Modulates Inflammatory Response in Glomerular Diseases via NF-kB Pathway Sonia Zambrano,1 Katja Möller-Hackbarth,1 Xidan Li,1 Patricia Q. Rodriguez,1 Emmanuelle Charrin,1 Angelina Schwarz,1 Jenny Nyström,2 Annika Östman Wernerson,3 Mark Lal,4 and Jaakko Patrakka1 1Karolinska Insitutet/AstraZeneca Integrated Cardio Metabolic Center, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden; 2Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden; 3Division of Renal Medicine, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; and 4Division of Bioscience, Department of Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines Biotech Unit, AstraZeneca, Gothenburg, Sweden ABSTRACT Background Inflammatory processes play an important role in the pathogenesis of glomerulopathies. Finding novel ways to suppress glomerular inflammation may offer a new way to stop disease progression. However, the molecular mechanisms that initiate and drive inflammation in the glomerulus are still poorly understood. Methods We performed large-scale gene expression profiling of glomerulus-associated G protein– coupled receptors (GPCRs) to identify new potential therapeutic targets for glomerulopathies. The expression of Gprc5b in disease was analyzed using quantitative PCR and immunofluorescence, and by analyzing published microarray data sets. In vivo studies were carried out in a podocyte-specificGprc5b knockout mouse line. Mechanistic studies were performed in cultured human podocytes. Results We identified an orphan GPCR, Gprc5b, as a novel gene highly enriched in podocytes that was significantly upregulated in common human glomerulopathies, including diabetic nephropathy, IgA ne- phropathy, and lupus nephritis. Similar upregulation of Gprc5b was detected in LPS-induced nephropathy in mice.
    [Show full text]
  • A Network Propagation Approach to Prioritize Long Tail Genes in Cancer
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.05.429983; this version posted February 8, 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-ND 4.0 International license. A Network Propagation Approach to Prioritize Long Tail Genes in Cancer Hussein Mohsen1,*, Vignesh Gunasekharan2, Tao Qing2, Sahand Negahban3, Zoltan Szallasi4, Lajos Pusztai2,*, Mark B. Gerstein1,5,6,3,* 1 Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06511, USA 2 Breast Medical Oncology, Yale School of Medicine, New Haven, CT 06511, USA 3 Department of Statistics & Data Science, Yale University, New Haven, CT 06511, USA 4 Children’s Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA 5 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA 6 Department of Computer Science, Yale University, New Haven, CT 06511, USA * Corresponding author Abstract Introduction. The diversity of genomic alterations in cancer pose challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the “long tail” of the mutational distribution, uncovered new genes with significant implication in cancer development. The study of these genes often requires integrative approaches with multiple types of biological data. Network propagation methods have demonstrated high efficacy in uncovering genomic patterns underlying cancer using biological interaction networks. Yet, the majority of these analyses have focused their assessment on detecting known cancer genes or identifying altered subnetworks.
    [Show full text]
  • Environmental Influences on Endothelial Gene Expression
    ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community.
    [Show full text]
  • Supplemental Table 7 HCC-Related Genes Differentially Expressed Between Control and RCLG/Alb-Cre Transgenic Mice
    Supplemental Table 7 HCC-related genes differentially expressed between control and RCLG/Alb-Cre transgenic mice (average of three biological replicates >2 fold-change, t-test p < 0.05) Fold difference Gene symbol Description (Full name) (RCLG/Alb-Cre vs con) Lcn2 lipocalin 2 7.8899 IGKV16-104 Immunoglobulin Kappa light chain V gene segment 6.5300 IGHG1 Immunoglobulin heavy chain C gene segment 6.4945 Orm2 orosomucoid 2 5.3184 IGHG2B Immunoglobulin heavy chain C gene segment 3.5573 Slpi secretory leukocyte peptidase inhibitor 3.5081 Rgs16 regulator of G-protein signaling 16 3.1999 Dffa DNA fragmentation factor, alpha subunit 3.0666 Saa1 serum amyloid A 1 2.9429 Tmem176b transmembrane protein 176B 2.8218 Orm3 orosomucoid 3 2.7805 IGHG2C Immunoglobulin heavy chain C gene segment 2.7015 S100a8 S100 calcium binding protein A8 (calgranulin A) 2.6769 Ocel1 occludin/ELL domain containing 1 2.6553 Ly6e lymphocyte antigen 6 complex, locus E 2.5509 Itih3 inter-alpha trypsin inhibitor, heavy chain 3 2.5345 Nr0b2 nuclear receptor subfamily 0, group B, member 2 2.5118 Saa3 serum amyloid A 3 2.4707 Spp1 secreted phosphoprotein 1 2.4077 Gats opposite strand transcription unit to Stag3 2.3934 Tmem176a transmembrane protein 176A 2.3734 Tsc22d3 TSC22 domain family 3 2.3724 Cp ceruloplasmin 2.2608 C4b complement component 4B (Childo blood group) 2.2089 Gm1381 gene model 1381, (NCBI) 2.1777 Itih4 inter alpha-trypsin inhibitor, heavy chain 4 2.1524 S100a9 S100 calcium binding protein A9 (calgranulin B) 2.124 Vnn3 vanin 3 2.0685 Cd5l CD5 antigen-like 2.0606
    [Show full text]
  • 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.
    [Show full text]
  • Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces Cerevisiae Received: 26 October 2016 Henriette Uthe, Jens T
    www.nature.com/scientificreports OPEN Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae Received: 26 October 2016 Henriette Uthe, Jens T. Vanselow & Andreas Schlosser Accepted: 25 January 2017 Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Published: 27 February 2017 Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis. The Mediator complex is an essential coactivator of eukaryotic transcription. Its major function is to communi- cate regulatory signals from gene-specific transcription factors upstream of the transcription start site to RNA Polymerase II (Pol II) and to promote activator-dependent assembly and stabilization of the preinitiation complex (PIC)1–3. The yeast Mediator complex is composed of 25 subunits and forms four distinct modules: the head, the middle, and the tail module, in addition to the four-subunit CDK8 kinase module (CKM), which can reversibly associate with the 21-subunit Mediator complex.
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Extrinsic Regulators of Mrna Translation in Developing Brain: Story of Wnts
    cells Article Extrinsic Regulators of mRNA Translation in Developing Brain: Story of WNTs Yongkyu Park * , Midori Lofton , Diana Li and Mladen-Roko Rasin * Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; [email protected] (M.L.); [email protected] (D.L.) * Correspondence: [email protected] (Y.P.); [email protected] (M.-R.R.) Abstract: Extrinsic molecules such as morphogens can regulate timed mRNA translation events in developing neurons. In particular, Wingless-type MMTV integration site family, member 3 (Wnt3), was shown to regulate the translation of Foxp2 mRNA encoding a Forkhead transcription factor P2 in the neocortex. However, the Wnt receptor that possibly mediates these translation events remains unknown. Here, we report Frizzled member 7 (Fzd7) as the Wnt3 receptor that lays downstream in Wnt3-regulated mRNA translation. Fzd7 proteins co-localize with Wnt3 ligands in developing neo- cortices. In addition, the Fzd7 proteins overlap in layer-specific neuronal subpopulations expressing different transcription factors, Foxp1 and Foxp2. When Fzd7 was silenced, we found decreased Foxp2 protein expression and increased Foxp1 protein expression, respectively. The Fzd7 silencing also dis- rupted the migration of neocortical glutamatergic neurons. In contrast, Fzd7 overexpression reversed the pattern of migratory defects and Foxp protein expression that we found in the Fzd7 silencing. We further discovered that Fzd7 is required for Wnt3-induced Foxp2 mRNA translation. Surprisingly, we also determined that the Fzd7 suppression of Foxp1 protein expression is not Wnt3 dependent. In conclusion, it is exhibited that the interaction between Wnt3 and Fzd7 regulates neuronal identity and the Fzd7 receptor functions as a downstream factor in ligand Wnt3 signaling for mRNA translation.
    [Show full text]
  • Exome-Wide Meta-Analysis Identifies Rare 3'-UTR Variant In
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Erasmus University Digital Repository ORIGINAL RESEARCH published: 18 October 2017 doi: 10.3389/fgene.2017.00151 Exome-Wide Meta-Analysis Identifies Rare 3′-UTR Variant in ERCC1/CD3EAP Associated with Symptoms of Sleep Apnea Ashley van der Spek 1, Annemarie I. Luik 2, Desana Kocevska 3, Chunyu Liu 4, 5, 6, Rutger W. W. Brouwer 7, Jeroen G. J. van Rooij 8, 9, 10, Mirjam C. G. N. van den Hout 7, Robert Kraaij 1, 8, 9, Albert Hofman 1, 11, André G. Uitterlinden 1, 8, 9, Wilfred F. J. van IJcken 7, Daniel J. Gottlieb 12, 13, 14, Henning Tiemeier 1, 15, Cornelia M. van Duijn 1 and Najaf Amin 1* 1 Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands, 2 Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom, 3 Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, Netherlands, 4 Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA, United States, 5 Population Sciences Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, United States, 6 Department of Biostatistics, School of Public Health, Boston University, Boston, MA, United States, 7 Center for Biomics, Erasmus Medical Center, Rotterdam, Netherlands, 8 Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands, 9 Netherlands Consortium for Healthy Ageing, Rotterdam, Netherlands, 10 Department of Neurology, Erasmus
    [Show full text]
  • Genome-Wide Sirna Screen for Mediators of NF-Κb Activation
    Genome-wide siRNA screen for mediators SEE COMMENTARY of NF-κB activation Benjamin E. Gewurza, Fadi Towficb,c,1, Jessica C. Marb,d,1, Nicholas P. Shinnersa,1, Kaoru Takasakia, Bo Zhaoa, Ellen D. Cahir-McFarlanda, John Quackenbushe, Ramnik J. Xavierb,c, and Elliott Kieffa,2 aDepartment of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; bCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; cProgram in Medical and Population Genetics, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142; dDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115; and eDepartment of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115 Contributed by Elliott Kieff, December 16, 2011 (sent for review October 2, 2011) Although canonical NFκB is frequently critical for cell proliferation, (RIPK1). TRADD engages TNFR-associated factor 2 (TRAF2), survival, or differentiation, NFκB hyperactivation can cause malig- which recruits the ubiquitin (Ub) E2 ligase UBC5 and the E3 nant, inflammatory, or autoimmune disorders. Despite intensive ligases cIAP1 and cIAP2. CIAP1/2 polyubiquitinate RIPK1 and study, mammalian NFκB pathway loss-of-function RNAi analyses TRAF2, which recruit and activate the K63-Ub binding proteins have been limited to specific protein classes. We therefore under- TAB1, TAB2, and TAB3, as well as their associated kinase took a human genome-wide siRNA screen for novel NFκB activa- MAP3K7 (TAK1). TAK1 in turn phosphorylates IKKβ activa- tion pathway components. Using an Epstein Barr virus latent tion loop serines to promote IKK activity (4).
    [Show full text]