Upregulation of E3 Ubiquitin Ligase CBLC Enhances EGFR

Total Page:16

File Type:pdf, Size:1020Kb

Upregulation of E3 Ubiquitin Ligase CBLC Enhances EGFR Published OnlineFirst June 26, 2018; DOI: 10.1158/0008-5472.CAN-17-3858 Cancer Tumor Biology and Immunology Research Upregulation of E3 Ubiquitin Ligase CBLC Enhances EGFR Dysregulation and Signaling in Lung Adenocarcinoma Shiao-Ya Hong1, Yu-Rung Kao1, Te-Chang Lee1, and Cheng-Wen Wu1,2,3,4 Abstract CBLC (CBL proto-oncogene c) belongs to the CBL protein ubiquitinated and positively regulated aEGFR stability family, which has E3 ubiquitin ligase activity toward activated through the conjugation of polyubiquitin by K6 and K11 receptor tyrosine kinases. CBLC is frequently upregulated in linkages. This CBLC-mediated polyubiquitination promoted non–small cell lung cancer (NSCLC), yet very little is known either preferential recycling of aEGFR back to the plasma about the functions of CBLC in tumorigenesis. Here we show membrane or trafficking to the cell nucleus. IHC analyses that CBLC is an epigenetically demethylated target and its revealed a positive correlation between phospho-EGFR and expression can be upregulated in NSCLC after treatment with CBLC in lung adenocarcinoma. In summary, we demonstrate a the DNA methylation inhibitor 50-azacytidine. Depletion novel mechanism by which aEGFR escapes lysosomal degra- of CBLC significantly inhibited cell viability and clonogenicity dation in a CBLC/ubiquitin-dependent manner to sustain its in vitro and reduced tumor growth in a xenograft model. CBLC activation. Our work identifies CBLC as a potential diagnostic silencing further sensitized EGFR-mutated NSCLC cells to biomarker and also points to its utilization as a novel thera- treatment with tyrosine kinase inhibitors. Conversely, ectopic peutic target for NSCLC therapy. expression of CBLC enhanced the activation of EGFR and downstream ERK1/2 signaling after ligand stimulation by Significance: This work demonstrates the role of CBLC expres- competing with CBL for EGFR binding. Analysis of ubiquitin sion as a diagnostic biomarker and potential therapeutic target in linkages on activated EGFR (aEGFR) revealed that CBLC lung adenocarcinoma. Cancer Res; 78(17); 4984–96. Ó2018 AACR. Introduction a linker region, and a RING finger motif. CBLC differs from CBL and CBLB in that the latter two both have a proline-rich region, The activation of tyrosine kinase receptors (RTK) engages a wide several regulatory tyrosine phosphorylation sites, and an ubiqui- range of signaling pathways that regulate cellular processes and tin-associated (UBA) domain in their C-termini (2). While CBL functions (1, 2). Aberrant activation of RTKs can be triggered by and CBLB are ubiquitously expressed, the expression of CBLC is genetic alterations (e.g., amplification, somatic mutation, and specifically restricted to normal epithelial cells (5). deletion/insertion) or evading lysosomal degradation. The EGFR, The ubiquitination mediated by CBL can negatively regulate an important member of RTKs, is frequently hyperactivated in a EGFR signaling through lysosomal degradation. Upon ligand variety of cancers (3). Dysregulation of EGFR signaling can lead to stimulation, CBL binds to activated EGFR (aEGFR) through its uncontrolled cell proliferation,tumorigenesis, and cancer progres- TKB domain (6). Subsequently, CBL-interacting protein of 85 kDa sion (3). (CIN85) and endophilin are recruited to EGFR complexes by The CBL family of E3 ligases has emerged as a key negative tyrosine phosphorylation of CBL. This process has been found to regulator of activated RTKs. CBL family proteins belong to the be required for EGFR internalization into endosomal sorting (7). RING finger class of E3 ligases, which catalyze the transfer of The ubiquitin modification mediated by CBL then can serve as a ubiquitin from E2 to substrates (4). The CBL family proteins (CBL, signal for directing aEGFR toward lysosomal degradation (8). CBLB, and CBLC in mammals) share a highly conserved N- However, accumulating evidence also links CBL protein family to terminus consisting of a tyrosine-kinase binding (TKB) domain, a potential role of oncogenic driver in cancer progression. Muta- tions in CBL are associated with approximately 5% of myeloid 1Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. 2Institute of neoplasms. The mutant proteins fail to ubiquitinate RTKs but Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, retain the adaptor function to activate downstream PI3K pathway. 3 Taiwan. Institute of Microbiology and Immunology, National Yang-Ming CBL mutations in the RING finger motif lost its E3 activity, 4 University, Taipei, Taiwan. Institute of Clinical Medicine, National Yang-Ming assuming an oncogenic role in cancer progression (9). University, Taipei, Taiwan. In comparison with CBL, the genetic variations of CBLC are less Note: Supplementary data for this article are available at Cancer Research common and little is known about its functions in tumorigenesis. Online (http://cancerres.aacrjournals.org/). Although previous reports suggest that CBLC may as well serve as a Corresponding Author: Cheng-Wen Wu, Institute of Biomedical Sciences, negative regulator of aEGFR (1, 5), it has been revealed that CBLC Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529, Taiwan. neither interacts nor colocalizes with CIN85 in mammalian cells Phone: 8862-2652-3015; Fax: 8862-2652-3075; E-mail: [email protected] due to the absence of the distal part of C-terminus found in CBL or doi: 10.1158/0008-5472.CAN-17-3858 CBLB proteins (10). Because CBL–CIN85–endophilin interaction Ó2018 American Association for Cancer Research. is required to initiate the endocytosis and degradation of EGFR, 4984 Cancer Res; 78(17) September 1, 2018 Downloaded from cancerres.aacrjournals.org on October 1, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst June 26, 2018; DOI: 10.1158/0008-5472.CAN-17-3858 CBLC Dysregulates EGFR Signaling the exact role of CBLC in regulating aEGFR turnover remains facturer's protocol. UPL probe-based qPCR (Roche) was carried elusive. Here, we identified that CBLC is an epigenetically out on a LightCycler 480 and analyzed using the manufacturer's demethylated target and its expression can be upregulated after software. The following primers and UPL probes were used for treatment with a DNA methylation inhibitor, 50-azacytidine in amplification: EGFR forward: 50-CATGTCGATGGACTTCCAGA- non–small cell lung cancer (NSCLC) cells. Our data revealed that 30, reverse: 50-GGGACAGCTTGGATCACACT-30, probe: 44; CBL CBLC knockdown renders EGFR-mutant NSCLC cells more sen- forward 50-TGACGTATGACGAAGTGAAAGC-30, reverse: 50- sitive to tyrosine kinase inhibitor (TKI) treatments, probably CAGCTCAGCCGGAAGATATAA-30, probe: 50; CBLB forward: through reducing the protein stability of aEGFR. We further found 50- GTGCACCTCTTGCCTTACG-30, reverse: 50-CCTTTTATTTCA- that CBLC overexpression reduces CBL-mediated ubiquitination CAACGACAGAAA, probe: 51; CBLC forward: 50-TGCTGAGAG- and degradation of aEGFR through the conjugation of ubiquitin CAACAAGGATG-30, reverse: 50-TCTGGCTGTCCGAGTGCT-30, K6 and K11 linkages. The CBLC-mediated stabilization of aEGFR probe: 71; b-actin forward: 50-AGAGCTACGAGCTGCCTGAC- is preferentially destined for the recycling program, leading to 30, reverse: 50-CGTGGATGCCACAGGACT-30, probe: 9. sustained EGFR activation in cancer cells. Immunoblotting Cultured cells were lysed with RIPA buffer (50 mmol/L Tris Materials and Methods HCl, pH 7.4, 150 mmol/L NaCl, 2 mmol/L EDTA, 1% NP-40, 1% Database and statistical analyses sodium deoxycholate, 0.1% SDS) supplemented with protease The level of CBLC promoter methylation was extracted from and phosphatase inhibitors (Roche). The protein concentration TCGA and analyzed by GraphPad Prism. Other statistical analyses was determined using the Bio-Rad protein assay Kit (Bio-Rad). were also performed using GraphPad Prism. P values less than Lysates were separated in a 8%–12% SDS-PAGE, transferred to 0.05 were considered significant. nitrocellulose membranes, incubated with specific antibodies overnight, and developed by enhanced chemiluminescence. Cell lines, plasmids, and antibodies Images were acquired with the LAS-3000 system (Fujifilm). The human lung normal cells (BEAS2B, NL-20), lung cancer cells (A549, H358, H1437, H3255, H1975, HCC827, H2170, Genomic DNA preparation and bisulfite conversion PCR H226, H520), and HEK293T were from ATCC. All cell lines were Genomic DNA from cultured cells was isolated by using a authenticatedbycytogeneticanalysisfromthisestablishedprovider. commercially available DNA Extraction kit (Macherey-Nagel) They were maintained according to ATCC's instructions and used followed by the corresponding manufacturer's protocols. DNA within 6 months after resuscitation. H928 lung adenocarcinoma samples were bisulfite converted using EpiTect Bisulfite Conver- cells were authenticated and provided by the National Health sion Kit (Qiagen) following the manufacturer's instructions. The Research Institute (Taipei, Taiwan), and cultured in RPMI1640 resulting modified DNA was amplified by PCR using methylation- medium supplemented with 10% FBS and 1% penicillin/strepto- specific and unmethylation-specific primer sets. The primer mycin.AllcellswereroutinelydetectedasMycoplasma-freebytheEZ- sequences were as follows: methylated forward primer: 50- PCR Mycoplasma Test Kit (Biological Industries). CBLC cDNA was TTTTTTTCGGTTTTTTAGGATTCGT-30, methylated reverse primer: cloned into pCDNA3/HA or pEGFP-C2 vector. Rab family (RAB5, 50-TAAACCACCTCTCGAAACAACTACG-30; unmethylated for- RAB7, and RAB11)
Recommended publications
  • CBL Mutations in Myeloproliferative Neoplasms Are Also Found in the Gene’S Proline-Rich Domain and in Patients with the V617FJAK2
    Articles and Brief Reports Chronic Myeloproliferative Disorders CBL mutations in myeloproliferative neoplasms are also found in the gene’s proline-rich domain and in patients with the V617FJAK2 Paula Aranaz,1 Cristina Hurtado,1 Ignacio Erquiaga,1 Itziar Miguéliz,1 Cristina Ormazábal,1 Ion Cristobal,2 Marina García-Delgado,1 Francisco Javier Novo,1 and José Luis Vizmanos1 1Department of Genetics, School of Sciences, University of Navarra, Pamplona; and 2CIMA, Center for Applied Medical Research, University of Navarra, Pamplona, Spain ABSTRACT Funding: this work was funded Background with the help of the Spanish Despite the discovery of the p.V617F in JAK2, the molecular pathogenesis of some chronic myelo- Ministry of Science and Innovation proliferative neoplasms remains unclear. Although very rare, different studies have identified CBL (SAF 2007-62473), the PIUNA (Cas-Br-Murine ecotropic retroviral transforming sequence) mutations in V617FJAK2-negative Program of the University of patients, mainly located in the RING finger domain. In order to determine the frequency of CBL Navarra, the Caja Navarra Foundation through the Program mutations in these diseases, we studied different regions of all CBL family genes (CBL, CBLB and “You choose, you decide” (Project CBLC) in a selected group of patients with myeloproliferative neoplasms. We also included 10.830) and ISCIII-RTICC V617FJAK2-positive patients to check whether mutations in CBL and JAK2 are mutually exclusive (RD06/0020/0078). events. PA received a predoctoral grant from the Government of Navarra. Design and Methods Using denaturing high performance liquid chromatography, we screened for mutations in CBL, Manuscript received on CBLB and CBLC in a group of 172 V617FJAK2-negative and 232 V617FJAK2-positive patients July 26, 2011.
    [Show full text]
  • Supplementary Information Method CLEAR-CLIP. Mouse Keratinocytes
    Supplementary Information Method CLEAR-CLIP. Mouse keratinocytes of the designated genotype were maintained in E-low calcium medium. Inducible cells were treated with 3 ug/ml final concentration doxycycline for 24 hours before performing CLEAR-CLIP. One 15cm dish of confluent cells was used per sample. Cells were washed once with cold PBS. 10mls of cold PBS was then added and cells were irradiated with 300mJ/cm2 UVC (254nM wavelength). Cells were then scraped from the plates in cold PBS and pelleted by centrifugation at 1,000g for 2 minutes. Pellets were frozen at -80oC until needed. Cells were then lysed on ice with occasional vortexing in 1ml of lysis buffer (50mM Tris-HCl pH 7.4, 100mM NaCl, 1mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) containing 1X protease inhibitors (Roche #88665) and RNaseOUT (Invitrogen #10777019) at 4ul/ml final concentration. Next, TurboDNase (Invitrogen #AM2238, 10U), RNase A (0.13ug) and RNase T1 (0.13U) were added and samples were incubated at 37oC for 5 minutes with occasional mixing. Samples were immediately placed on ice and then centrifuged at 16,160g at 4oC for 20 minutes to clear lysate. 25ul of Protein-G Dynabeads (Invitrogen #10004D) were used per IP. Dynabeads were pre-washed with lysis buffer and pre- incubated with 3ul of Wako Anti-Mouse-Ago2 (2D4) antibody. The dynabead/antibody mixture was added to the lysate and rocked for 2 hours at 4oC. All steps after the IP were done on bead until samples were loaded into the polyacrylamide gel.
    [Show full text]
  • Anti-CBLB Antibody (ARG57312)
    Product datasheet [email protected] ARG57312 Package: 100 μl anti-CBLB antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes CBLB Tested Reactivity Hu, Ms Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name CBLB Antigen Species Human Immunogen Recombinant Protein of Human CBLB. Conjugation Un-conjugated Alternate Names Nbla00127; EC 6.3.2.-; RNF56; Signal transduction protein CBL-B; Casitas B-lineage lymphoma proto- oncogene b; SH3-binding protein CBL-B; Cbl-b; E3 ubiquitin-protein ligase CBL-B; RING finger protein 56 Application Instructions Application table Application Dilution IHC-P 1:50 - 1:200 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Jurkat Calculated Mw 109 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. www.arigobio.com 1/2 Bioinformation Gene Symbol CBLB Gene Full Name Cbl proto-oncogene B, E3 ubiquitin protein ligase Function E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome.
    [Show full text]
  • Brief Genetics Report
    Brief Genetics Report The Rat Diabetes Susceptibility Locus Iddm4 and at Least One Additional Gene Are Required for Autoimmune Diabetes Induced by Viral Infection Elizabeth P. Blankenhorn,1 Lucy Rodemich,1 Cristina Martin-Fernandez,1 Jean Leif,2 Dale L. Greiner,2 and John P. Mordes2 BBDR rats develop autoimmune diabetes only after challenge with environmental perturbants. These per- turbants include polyinosinic:polycytidylic acid (poly ype 1 diabetes results from inflammatory infiltra- I:C, a ligand of toll-like receptor 3), agents that deplete tion of pancreatic islets and selective ␤-cell regulatory T-cell (Treg) populations, and a non–␤-cell destruction. It is thought to be caused by envi- cytopathic parvovirus (Kilham rat virus [KRV]). The Tronmental factors operating in a genetically sus- dominant diabetes susceptibility locus Iddm4 is re- ceptible host (1,2). Susceptibility loci include the major quired for diabetes induced by treatment with poly I:C histocompatibility complex (MHC), a promoter polymor- plus Treg depletion. Iddm4 is penetrant in congenic phism of the insulin gene, and an allelic variant of CTLA4 heterozygous rats on the resistant WF background and (3). Among candidate environmental perturbants, viral is 79% sensitive and 80% specific as a predictor of infection is one of the most likely (4). How genes interact induced diabetes. Surprisingly, an analysis of 190 BBDR ؋ WF)F2 rats treated with KRV after brief with the environment to transform diabetes susceptibility) exposure to poly I:C revealed that the BBDR-origin into overt disease is unknown. allele of Iddm4 is necessary but not entirely sufficient BBDR rats model virus-induced autoimmune diabetes for diabetes expression.
    [Show full text]
  • Polymorphic Variation in the CBLB Gene in Human Type 1 Diabetes
    Genes and Immunity (2004) 5, 232–235 & 2004 Nature Publishing Group All rights reserved 1466-4879/04 $25.00 www.nature.com/gene BRIEF COMMUNICATION Polymorphic variation in the CBLB gene in human type 1 diabetes R Kosoy1,2, N Yokoi3, S Seino3,4 and P Concannon1,2 1Molecular Genetics Program, Benaroya Research Institute, Seattle, WA, USA; 2Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA; 3Division of Cellular and Molecular Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; 4Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan CBLB was evaluated as a candidate gene for type 1 diabetes (T1D) susceptibility based on its association with autoimmunity in animal models and its role in T-cell costimulatory signaling. Cblb is one of the two major diabetes predisposing loci in the Komeda diabetes-prone (KDP) rat. Cbl-b, a ubiquitin ligase, couples TCR-mediated stimulation with the requirement for CD28 costimulation, regulating T-cell activation. To identify variants with possible effects on gene function as well as haplotype tagging polymorphisms, the human CBLB coding region was sequenced in 16 individuals with T1D: no variants predicted to change the amino-acid sequence were identified. Seven single-nucleotide polymorphism (SNP) markers spanning the CBLB gene were genotyped in multiplex T1D families and assessed for disease association by transmission disequilibrium testing. No significant evidence of association was obtained for either individual markers or marker haplotypes. Genes and Immunity (2004) 5, 232–235. doi:10.1038/sj.gene.6364057 Published online 12 February 2004 Keywords: diabetes; T cell; SNP; haplotype Introduction studies in human T1D families and studies in the NOD mouse model of T1D.9,10 Type I diabetes (T1D) arises from autoimmune destruc- In the current study, we have evaluated another tion of the insulin-secreting b-cells of the pancreas candidate T1D gene, CBLB, which is implicated based requiring insulin replacement therapy for survival.
    [Show full text]
  • Downloaded from the App Store and Nucleobase, Nucleotide and Nucleic Acid Metabolism 7 Google Play
    Hoytema van Konijnenburg et al. Orphanet J Rare Dis (2021) 16:170 https://doi.org/10.1186/s13023-021-01727-2 REVIEW Open Access Treatable inherited metabolic disorders causing intellectual disability: 2021 review and digital app Eva M. M. Hoytema van Konijnenburg1†, Saskia B. Wortmann2,3,4†, Marina J. Koelewijn2, Laura A. Tseng1,4, Roderick Houben6, Sylvia Stöckler‑Ipsiroglu5, Carlos R. Ferreira7 and Clara D. M. van Karnebeek1,2,4,8* Abstract Background: The Treatable ID App was created in 2012 as digital tool to improve early recognition and intervention for treatable inherited metabolic disorders (IMDs) presenting with global developmental delay and intellectual disabil‑ ity (collectively ‘treatable IDs’). Our aim is to update the 2012 review on treatable IDs and App to capture the advances made in the identifcation of new IMDs along with increased pathophysiological insights catalyzing therapeutic development and implementation. Methods: Two independent reviewers queried PubMed, OMIM and Orphanet databases to reassess all previously included disorders and therapies and to identify all reports on Treatable IDs published between 2012 and 2021. These were included if listed in the International Classifcation of IMDs (ICIMD) and presenting with ID as a major feature, and if published evidence for a therapeutic intervention improving ID primary and/or secondary outcomes is avail‑ able. Data on clinical symptoms, diagnostic testing, treatment strategies, efects on outcomes, and evidence levels were extracted and evaluated by the reviewers and external experts. The generated knowledge was translated into a diagnostic algorithm and updated version of the App with novel features. Results: Our review identifed 116 treatable IDs (139 genes), of which 44 newly identifed, belonging to 17 ICIMD categories.
    [Show full text]
  • An X-Linked Cobalamin Disorder Caused by Mutations in Transcriptional Coregulator HCFC1
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector ARTICLE An X-Linked Cobalamin Disorder Caused by Mutations in Transcriptional Coregulator HCFC1 Hung-Chun Yu,1 Jennifer L. Sloan,2 Gunter Scharer,1,3,4,9 Alison Brebner,5 Anita M. Quintana,1 Nathan P. Achilly,2 Irini Manoli,2 Curtis R. Coughlin II,1,3 Elizabeth A. Geiger,1 Una Schneck,1 David Watkins,5 Terttu Suormala,6,7 Johan L.K. Van Hove,1,3 Brian Fowler,6,7 Matthias R. Baumgartner,6,7,8 David S. Rosenblatt,5 Charles P. Venditti,2 and Tamim H. Shaikh1,3,4,* Derivatives of vitamin B12 (cobalamin) are essential cofactors for enzymes required in intermediary metabolism. Defects in cobalamin metabolism lead to disorders characterized by the accumulation of methylmalonic acid and/or homocysteine in blood and urine. The most common inborn error of cobalamin metabolism, combined methylmalonic acidemia and hyperhomocysteinemia, cblC type, is caused by mutations in MMACHC. However, several individuals with presumed cblC based on cellular and biochemical analysis do not have mutations in MMACHC. We used exome sequencing to identify the genetic basis of an X-linked form of combined methylmalonic acidemia and hyperhomocysteinemia, designated cblX. A missense mutation in a global transcriptional coregulator, HCFC1, was identi- fied in the index case. Additional male subjects were ascertained through two international diagnostic laboratories, and 13/17 had one of five distinct missense mutations affecting three highly conserved amino acids within the HCFC1 kelch domain. A common phenotype of severe neurological symptoms including intractable epilepsy and profound neurocognitive impairment, along with variable biochemical manifestations, was observed in all affected subjects compared to individuals with early-onset cblC.
    [Show full text]
  • Cysteine-Mediated Decyanation of Vitamin B12 by the Predicted Membrane Transporter Btum
    ARTICLE DOI: 10.1038/s41467-018-05441-9 OPEN Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM S. Rempel 1, E. Colucci 1, J.W. de Gier 2, A. Guskov 1 & D.J. Slotboom 1,3 Uptake of vitamin B12 is essential for many prokaryotes, but in most cases the membrane proteins involved are yet to be identified. We present the biochemical characterization and high-resolution crystal structure of BtuM, a predicted bacterial vitamin B12 uptake system. 1234567890():,; BtuM binds vitamin B12 in its base-off conformation, with a cysteine residue as axial ligand of the corrin cobalt ion. Spectroscopic analysis indicates that the unusual thiolate coordination allows for decyanation of vitamin B12. Chemical modification of the substrate is a property other characterized vitamin B12-transport proteins do not exhibit. 1 Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9474 AG Groningen, The Netherlands. 2 Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden. 3 Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. Correspondence and requests for materials should be addressed to D.J.S. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:3038 | DOI: 10.1038/s41467-018-05441-9 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-05441-9 fi obalamin (Cbl) is one of the most complex cofactors well as re nement statistics are summarized in Table 1. BtuMTd C(Supplementary Figure 1a) known, and used by enzymes consists of six transmembrane helices with both termini located catalyzing for instance methyl-group transfer and ribo- on the predicted cytosolic side (Fig.
    [Show full text]
  • Brief Genetics Report
    Brief Genetics Report Haplotype Tag Single Nucleotide Polymorphism Analysis of the Human Orthologues of the Rat Type 1 Diabetes Genes Ian4 (Lyp/Iddm1) and Cblb Felicity Payne, Deborah J. Smyth, Rebecca Pask, Bryan J. Barratt, Jason D. Cooper, Rebecca C.J. Twells, Neil M. Walker, Alex C. Lam, Luc J. Smink, Sarah Nutland, Helen E. Rance, and John A. Todd The diabetes-prone BioBreeding (BB) and Komeda dia- animal model is the severe lymphopenia that is essential betes-prone (KDP) rats are both spontaneous animal for the development of the diabetic phenotype and that is models of human autoimmune, T-cell–associated type 1 inherited as a Mendelian trait (3). Life-long and profound diabetes. Both resemble the human disease, and conse- T-cell lymphopenia is characterized by a reduction in quently, susceptibility genes for diabetes found in these peripheral CD4ϩ T-cells, an even greater reduction of two strains can be considered as potential candidate CD8ϩ T-cells (4), and an almost total absence of RT6ϩ genes in humans. Recently, a frameshift deletion in T-cells (5). The lymphopenia gene is involved in the Ian4, a member of the immune-associated nucleotide regulation of apoptosis in the T-cell lineage and is, there- (Ian)-related gene family, has been shown to map to BB fore, responsible for loss of critical T-cells, resulting in rat Iddm1. In the KDP rat, a nonsense mutation in the T-cell regulatory gene, Cblb, has been described as a autoimmunity (6). Recently, two groups have indepen- major susceptibility locus. Following a strategy of ex- dently shown, by positional cloning of Iddm1/lyp, that amining the human orthologues of susceptibility genes lymphopenia is due to a frameshift deletion in Ian4 (also identified in animal models for association with type 1 called Ian5) of the immune-associated nucleotide (Ian)- diabetes, we identified single nucleotide polymorphisms related gene family (6,7), resulting in a truncated protein (SNPs) from each gene by resequencing PCR product product.
    [Show full text]
  • Quantitative Interactomics in Primary T Cells Unveils TCR Signal
    Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics Guillaume Voisinne, Kristof Kersse, Karima Chaoui, Liaoxun Lu, Julie Chaix, Lichen Zhang, Marisa Goncalves Menoita, Laura Girard, Youcef Ounoughene, Hui Wang, et al. To cite this version: Guillaume Voisinne, Kristof Kersse, Karima Chaoui, Liaoxun Lu, Julie Chaix, et al.. Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics. Nature Immunology, Nature Publishing Group, 2019, 20 (11), pp.1530 - 1541. 10.1038/s41590-019-0489-8. hal-03013469 HAL Id: hal-03013469 https://hal.archives-ouvertes.fr/hal-03013469 Submitted on 23 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. RESOURCE https://doi.org/10.1038/s41590-019-0489-8 Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics Guillaume Voisinne 1, Kristof Kersse1, Karima Chaoui2, Liaoxun Lu3,4, Julie Chaix1, Lichen Zhang3, Marisa Goncalves Menoita1, Laura Girard1,5, Youcef Ounoughene1, Hui Wang3, Odile Burlet-Schiltz2, Hervé Luche5,6, Frédéric Fiore5, Marie Malissen1,5,6, Anne Gonzalez de Peredo 2, Yinming Liang 3,6*, Romain Roncagalli 1* and Bernard Malissen 1,5,6* The activation of T cells by the T cell antigen receptor (TCR) results in the formation of signaling protein complexes (signalo­ somes), the composition of which has not been analyzed at a systems level.
    [Show full text]
  • A Graph-Theoretic Approach to Model Genomic Data and Identify Biological Modules Asscociated with Cancer Outcomes
    A Graph-Theoretic Approach to Model Genomic Data and Identify Biological Modules Asscociated with Cancer Outcomes Deanna Petrochilos A dissertation presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Neil Abernethy, Chair John Gennari, Ali Shojaie Program Authorized to Offer Degree: Biomedical Informatics and Health Education UMI Number: 3588836 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3588836 Published by ProQuest LLC (2013). Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 ©Copyright 2013 Deanna Petrochilos University of Washington Abstract Using Graph-Based Methods to Integrate and Analyze Cancer Genomic Data Deanna Petrochilos Chair of the Supervisory Committee: Assistant Professor Neil Abernethy Biomedical Informatics and Health Education Studies of the genetic basis of complex disease present statistical and methodological challenges in the discovery of reliable and high-confidence genes that reveal biological phenomena underlying the etiology of disease or gene signatures prognostic of disease outcomes. This dissertation examines the capacity of graph-theoretical methods to model and analyze genomic information and thus facilitate using prior knowledge to create a more discrete and functionally relevant feature space.
    [Show full text]
  • Oncogenic Signaling by Leukemia-Associated Mutant Cbl Proteins Scott Nadeau1,2, Wei An1,2, Nick Palermo1, Dan Feng1, Gulzar Ahmad1, Lin Dong, Gloria E
    nalytic A al & B y i tr o s c i h e Nadeau et al., Biochem Anal Biochem 2012, S6 m m e Biochemistry & i h s c t r o DOI: 10.4172/2161-1009.S6-001 i y B ISSN: 2161-1009 Analytical Biochemistry Review Article Open Access Oncogenic Signaling by Leukemia-Associated Mutant Cbl Proteins Scott Nadeau1,2, Wei An1,2, Nick Palermo1, Dan Feng1, Gulzar Ahmad1, Lin Dong, Gloria E. O. Borgstahl1,3,6,7, Amarnath Natarajan1,2,7, Mayumi Naramura1,2,7, Vimla Band1,2,3,7 and Hamid Band1-5,7* 1Eppley Institute for Research in Cancer and Allied Diseases 2Departments of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA 3Departments of Biochemistry & Molecular Biology, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA 4Departments of Pathology & Microbiology, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA 5Departments of Pharmacology & Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA 6Departments of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA 7UNMC-Eppley Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center Omaha, NE 68198-5950, USA Abstract Members of the Cbl protein family (Cbl, Cbl-b, and Cbl-c) are E3 ubiquitin ligases that have emerged as critical negative regulators of protein tyrosine kinase (PTK) signaling. This function reflects their ability to directly interact with activated PTKs and to target them as well as their associated signaling components for ubiquitination.
    [Show full text]