DOCSLIB.ORG

T Lymphocytes Mrna, and Protein Expression in Activated Networks

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology , 31 of which you can access for free at: 2011; 187:2233-2243; Prepublished online 25 from submission to initial decision 4 weeks from acceptance to publication July 2011; doi: 10.4049/jimmunol.1101233 http://www.jimmunol.org/content/187/5/2233 MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes Yevgeniy A. Grigoryev, Sunil M. Kurian, Traver Hart, Aleksey A. Nakorchevsky, Caifu Chen, Daniel Campbell, Steven R. Head, John R. Yates III and Daniel R. Salomon J Immunol cites 83 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2011/07/25/jimmunol.110123 3.DC1 This article http://www.jimmunol.org/content/187/5/2233.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2011 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 26, 2021. The Journal of Immunology MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes Yevgeniy A. Grigoryev,* Sunil M. Kurian,* Traver Hart,* Aleksey A. Nakorchevsky,† Caifu Chen,‡ Daniel Campbell,x Steven R. Head,x John R. Yates, III,† and Daniel R. Salomon* MicroRNAs (miRNAs) regulate specific immune mechanisms, but their genome-wide regulation of T lymphocyte activation is largely unknown. We performed a multidimensional functional genomics analysis to integrate genome-wide differential mRNA, miRNA, and protein expression as a function of human T lymphocyte activation and time. We surveyed expression of 420 human miRNAs in parallel with genome-wide mRNA expression. We identified a unique signature of 71 differentially expressed miRNAs, Downloaded from 57 of which were previously not known as regulators of immune activation. The majority of miRNAs are upregulated, mRNA expression of these target genes is downregulated, and this is a function of binding multiple miRNAs (combinatorial targeting). Our data reveal that consideration of this complex signature, rather than single miRNAs, is necessary to construct a full picture of miRNA-mediated regulation. Molecular network mapping of miRNA targets revealed the regulation of activation-induced immune signaling. In contrast, pathways populated by genes that are not miRNA targets are enriched for metabolism and biosynthesis. Finally, we specifically validated miR-155 (known) and miR-221 (novel in T lymphocytes) using locked nucleic acid inhibitors. http://www.jimmunol.org/ Inhibition of these two highly upregulated miRNAs in CD4+ T cells was shown to increase proliferation by removing suppression of four target genes linked to proliferation and survival. Thus, multiple lines of evidence link top functional networks directly to T lymphocyte immunity, underlining the value of mapping global gene, protein, and miRNA expression. The Journal of Immu- nology, 2011, 187: 2233–2243. lymphocytes regulate the adaptive immune response by coordinated fashion to achieve a balance among proliferation, serving as Ag-specific effector cells. Activation via TCR memory, and quiescence. T engagement and CD28 costimulation is characterized by MicroRNAs (miRNAs) have emerged as posttranscriptional by guest on September 26, 2021 gene upregulation (1) and is a highly regulated process requiring regulators of gene expression in a variety of biological processes coordination of multiple signaling pathways for proliferation, cyto- (3–7). The mode of miRNA regulation is protein repression via kines, and differentiation. After Ag clearance, some effector cells complementary sequence recognition in the 39 untranslated region must be reduced or eliminated by mechanisms like activation- of the target mRNA and/or degradation of the target transcript (8– induced cell death (2). Thus, activation must be regulated in a 11). A recent paper indicates the major effect of miRNAs is to decrease mRNA levels (12). miRNAs can potentially regulate hundreds of proteins (13) and *Department of Molecular and Experimental Medicine, The Scripps Research In- modulate concentration of proteins over a narrow range in a dose- † stitute, La Jolla, CA 92037; Department of Chemical Physiology, The Scripps Re- dependent manner (14, 15). miRNAs are involved in hematopoi- search Institute, La Jolla, CA 92037; ‡Applied Biosystems, Foster City, CA 94404; and xDNA Microarray Core, The Scripps Research Institute, La Jolla, CA 92037 etic cell function and development (as summarized in Refs. 16– Received for publication May 2, 2011. Accepted for publication June 17, 2011. 64). A few miRNAs have been linked to specific T lymphocyte This work was supported by National Institutes of Health Grants U19 A1063603 and mechanisms—181a (37), 181c (39), 155 (28), 150 (18), 146 (20), R01 AI081757. and 142 (40)—via regulation of T cell sensitivity to Ag stimula- Y.A.G., S.M.K., and D.R.S. conceived and designed the experiments and wrote the tion, regulating transcription factors, and activation-induced cell manuscript; Y.A.G., S.M.K., and A.A.N. performed the experiments; Y.A.G., A.A.N., death. However, at the global level, little is known about the im- and T.H. analyzed the data; and C.C., D.C., S.R.H., and J.R.Y. contributed reagents/ materials/analysis tools. pact of activation-induced miRNAs on mRNA and protein ex- pression in human T lymphocytes, particularly in the context of The sequences presented in this article (entire set of CEL files) have been submitted to the National Center for Biotechnology Information Gene Expression Omnibus mapping miRNA-regulated molecular networks. under accession number GSE14352 (http://www.ncbi.nlm.nih.gov/geo/query/acc. In this study, we show that differentially upregulated miRNAs cgi?acc=GSE14352). regulate T lymphocyte activation by targeting highly differentially Address correspondence and reprint requests to Dr. Daniel R. Salomon, Department expressed genes involved in networks critical for cell activation, of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail Code MEM-L55, La Jolla, CA 92037. E-mail address: proliferation, and survival. We used a multidimensional approach [email protected] to integrate genome-wide miRNA, mRNA, and protein expression. The online version of this article contains supplemental material. We surveyed expression for 420 human miRNA sequences at 0, 24, Abbreviations used in this article: Ct, threshold cycle; FDR, false discovery rate; IPA, 48, and 72 h after activation. In parallel, we profiled global mRNA Ingenuity Pathways Analysis; LNA, locked nucleic acid; miRNA, microRNA; qPCR, and protein expression. We found 71 significantly differentially ex- quantitative real-time PCR. pressed miRNAs, of which 57 have not been previously linked to Copyright Ó 2011 by The American Association of Immunologists, Inc. 0022-1767/11/$16.00 T lymphocyte function. Testing several established miRNA target www.jimmunol.org/cgi/doi/10.4049/jimmunol.1101233 2234 microRNA-REGULATED NETWORKS IN T CELL ACTIVATION prediction algorithms, we demonstrated globally that targets of performed for specified pairwise comparisons among all time points of multiple upregulated miRNAs (combinatorial targeting) have de- activation. creased mRNA expression with activation. In validation, we In parallel, we performed our own analysis of differential gene ex- pression to corroborate AltAnalyze results. CEL files for each donor from showed that inhibition of two highly upregulated miRNAs in the 1.0ST HuEx Arrays were normalized by robust multiarray averaging CD4+ T cells increased proliferation by removing suppression of using a custom cumulative distribution function downloaded from the four target genes involved in proliferation and survival. Thus, University of Michigan (http://brainarray.mbni.med.umich.edu/Brainarray/ our studies provide novel evidence for a large number of func- Database/CustomCDF/genomic_curated_CDF.asp). Differential expression was measured with the Limma package (http://www.bioconductor.org/ tional molecular networks populated by downregulated targets of packages/2.6/bioc/html/limma.html) using a two-class model. All calcu- highly upregulated miRNAs. lations were performed in R/Bioconductor. Genes were filtered using a fold-change filter of 1.5 (0.58 in log2) and an FDR filter of 0.01. Genes that were detected as significantly differentially expressed by both AltA- Materials and Methods nalyze and Limma analysis were then selected for further analysis. T lymphocyte isolation The Multidimensional Protein Identification Tool proteomics Blood draw for this study was accepted by our institution’s ethical com- mission, and all subjects gave their written consent according to review The Multidimensional Protein Identification Tool (66) protocol was used board guidelines. CD2+ T
Recommended publications
  • Microdeletions in 16P11.2 and 13Q31.3 Associated with Developmental Delay and Generalized Overgrowth

    Microdeletions in 16P11.2 and 13Q31.3 Associated with Developmental Delay and Generalized Overgrowth

    Microdeletions in 16p11.2 and 13q31.3 associated with developmental delay and generalized overgrowth A.M. George1, J. Taylor2 and D.R. Love1 1Diagnostic Genetics, LabPlus, Auckland City Hospital, Auckland, New Zealand 2Northern Regional Genetic Service, Auckland City Hospital, Auckland, New Zealand Corresponding author: D.R. Love E-mail: [email protected] Genet. Mol. Res. 11 (3): 3133-3137 (2012) Received November 28, 2011 Accepted July 18, 2012 Published September 3, 2012 DOI http://dx.doi.org/10.4238/2012.September.3.1 ABSTRACT. Chromosome microarray analysis of patients with developmental delay has provided evidence of small deletions or duplications associated with this clinical phenotype. In this context, a 7.1- to 8.7-Mb interstitial deletion of chromosome 16 is well documented, but within this interval a rare 200-kb deletion has recently been defined that appears to be associated with obesity, or developmental delay together with overgrowth. We report a patient carrying this rare deletion, who falls into the latter clinical category, but who also carries a second very rare deletion in 13q31.3. It remains unclear if this maternally inherited deletion acts as a second copy number variation leading to pathogenic variation, or is non-causal and the true modifiers are yet to be determined. Key words: Developmental delay; Obesity; Overgrowth; GPC5; SH2B1 Genetics and Molecular Research 11 (3): 3133-3137 (2012) ©FUNPEC-RP www.funpecrp.com.br A.M. George et al. 3134 INTRODUCTION Current referrals for chromosome microarray analysis (CMA) are primarily for de- termining the molecular basis of developmental delay and autistic spectrum disorder in child- hood.
  • The Ciliated Cell Transcriptome A

    The Ciliated Cell Transcriptome A

    THE CILIATED CELL TRANSCRIPTOME A DISSERTATION SUBMITTED TO THE DEPARTMENT OF BIOLOGICAL SCIENCES AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Ramona Hoh March 2010 ! © 2010 by Ramona Amy Hoh. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/sk794dv5857 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Timothy Stearns, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Mark Krasnow I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Maxence Nachury I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. William Nelson Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives.
  • (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002

    (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002

    USOO6395889B1 (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002 (54) NUCLEIC ACID MOLECULES ENCODING WO WO-98/56804 A1 * 12/1998 ........... CO7H/21/02 HUMAN PROTEASE HOMOLOGS WO WO-99/0785.0 A1 * 2/1999 ... C12N/15/12 WO WO-99/37660 A1 * 7/1999 ........... CO7H/21/04 (75) Inventor: fish E. Robison, Wilmington, MA OTHER PUBLICATIONS Vazquez, F., et al., 1999, “METH-1, a human ortholog of (73) Assignee: Millennium Pharmaceuticals, Inc., ADAMTS-1, and METH-2 are members of a new family of Cambridge, MA (US) proteins with angio-inhibitory activity', The Journal of c: - 0 Biological Chemistry, vol. 274, No. 33, pp. 23349–23357.* (*) Notice: Subject to any disclaimer, the term of this Descriptors of Protease Classes in Prosite and Pfam Data patent is extended or adjusted under 35 bases. U.S.C. 154(b) by 0 days. * cited by examiner (21) Appl. No.: 09/392, 184 Primary Examiner Ponnathapu Achutamurthy (22) Filed: Sep. 9, 1999 ASSistant Examiner William W. Moore (51) Int. Cl." C12N 15/57; C12N 15/12; (74) Attorney, Agent, or Firm-Alston & Bird LLP C12N 9/64; C12N 15/79 (57) ABSTRACT (52) U.S. Cl. .................... 536/23.2; 536/23.5; 435/69.1; 435/252.3; 435/320.1 The invention relates to polynucleotides encoding newly (58) Field of Search ............................... 536,232,235. identified protease homologs. The invention also relates to 435/6, 226, 69.1, 252.3 the proteases. The invention further relates to methods using s s s/ - - -us the protease polypeptides and polynucleotides as a target for (56) References Cited diagnosis and treatment in protease-mediated disorders.
  • Structure of Human Aspartyl Aminopeptidase Complexed With

    Structure of Human Aspartyl Aminopeptidase Complexed With

    Chaikuad et al. BMC Structural Biology 2012, 12:14 http://www.biomedcentral.com/1472-6807/12/14 RESEARCH ARTICLE Open Access Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family Apirat Chaikuad1, Ewa S Pilka1, Antonio De Riso2, Frank von Delft1, Kathryn L Kavanagh1, Catherine Vénien-Bryan2, Udo Oppermann1,3 and Wyatt W Yue1* Abstract Backround: Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results: The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β- hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions: The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference.
  • Injury by Mechanical Ventilation Gene Transcription and Promotion Of

    Injury by Mechanical Ventilation Gene Transcription and Promotion Of

    Modulation of Lipopolysaccharide-Induced Gene Transcription and Promotion of Lung Injury by Mechanical Ventilation This information is current as William A. Altemeier, Gustavo Matute-Bello, Sina A. of September 29, 2021. Gharib, Robb W. Glenny, Thomas R. Martin and W. Conrad Liles J Immunol 2005; 175:3369-3376; ; doi: 10.4049/jimmunol.175.5.3369 http://www.jimmunol.org/content/175/5/3369 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2005/08/23/175.5.3369.DC1 Material http://www.jimmunol.org/ References This article cites 37 articles, 7 of which you can access for free at: http://www.jimmunol.org/content/175/5/3369.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 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 © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Modulation of Lipopolysaccharide-Induced Gene Transcription and Promotion of Lung Injury by Mechanical Ventilation1 William A.
  • Katalog 2015 Cover Paul Lin *Hinweis Förderung.Indd

    Katalog 2015 Cover Paul Lin *Hinweis Förderung.Indd

    Product List 2015 WE LIVE SERVICE Certificates quartett owns two productions sites that are certified according to EN ISO 9001:2008 Quality management systems - Requirements EN ISO 13485:2012 + AC:2012 Medical devices - Quality management systems - Requirements for regulatory purposes GMP Conformity Our quality management guarantees products of highest quality! 2 Foreword to the quartett product list 2015 quartett Immunodiagnostika, Biotechnologie + Kosmetik Vertriebs GmbH welcomes you as one of our new business partners as well as all of our previous loyal clients. You are now member of quartett´s worldwide customers. First of all we would like to introduce ourselves to you. Founded as a family-run company in 1986, quartett ensures for more than a quarter of a century consistent quality of products. Service and support of our valued customers are our daily businesses. And we will continue! In the end 80´s quartett offered radioimmunoassay and enzyme immunoassay kits from different manufacturers in the USA. In the beginning 90´s the company changed its strategy from offering products for routine diagnostic to the increasing field of research and development. Setting up a production plant in 1997 and a second one in 2011 supported this decision. The company specialized its product profile in the field of manufacturing synthetic peptides for antibody production, peptides such as protease inhibitors, biochemical reagents and products for histology, cytology and immunohistology. All products are exclusively manufactured in Germany without outsourcing any production step. Nowadays, we expand into all other diagnostic and research fields and supply our customers in universities, government institutes, pharmaceutical and biotechnological companies, hospitals, and private doctor offices.
  • Blimp1 Regulates the Transition of Neonatal to Adult Intestinal Epithelium

    Blimp1 Regulates the Transition of Neonatal to Adult Intestinal Epithelium

    UCLA UCLA Previously Published Works Title Blimp1 regulates the transition of neonatal to adult intestinal epithelium. Permalink https://escholarship.org/uc/item/01x184nd Journal Nature communications, 2(1) ISSN 2041-1723 Authors Muncan, Vanesa Heijmans, Jarom Krasinski, Stephen D et al. Publication Date 2011-08-30 DOI 10.1038/ncomms1463 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLE Received 11 May 2011 | Accepted 28 Jul 2011 | Published 30 Aug 2011 DOI: 10.1038/ncomms1463 Blimp1 regulates the transition of neonatal to adult intestinal epithelium Vanesa Muncan1,2,3, Jarom Heijmans1,2,3, Stephen D. Krasinski4, Nikè V. Büller1,2,3, Manon E. Wildenberg1,2,3, Sander Meisner1, Marijana Radonjic5, Kelly A. Stapleton4, Wout H. Lamers1, Izak Biemond3, Marius A. van den Bergh Weerman6, Dónal O’Carroll7, James C. Hardwick3, Daniel W. Hommes3 & Gijs R. van den Brink1,2,3 In many mammalian species, the intestinal epithelium undergoes major changes that allow a dietary transition from mother’s milk to the adult diet at the end of the suckling period. These complex developmental changes are the result of a genetic programme intrinsic to the gut tube, but its regulators have not been identified. Here we show that transcriptional repressor B lymphocyte-induced maturation protein 1 (Blimp1) is highly expressed in the developing and postnatal intestinal epithelium until the suckling to weaning transition. Intestine-specific deletion of Blimp1 results in growth retardation and excessive neonatal mortality. Mutant mice lack all of the typical epithelial features of the suckling period and are born with features of an adult-like intestine.
  • Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother

    Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother

    European Journal of Human Genetics (2012) 20, 540–546 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother Anne-Claude Tabet1,2,3,4, Marion Pilorge2,3,4, Richard Delorme5,6,Fre´de´rique Amsellem5,6, Jean-Marc Pinard7, Marion Leboyer6,8,9, Alain Verloes10, Brigitte Benzacken1,11,12 and Catalina Betancur*,2,3,4 The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5–30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5–30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28–30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40–29.25 Mb), inherited from his apparently healthy father.
  • The Purification and Identification of Interactors to Elucidate Novel Connections in the HEK 293 Cell Line

    The Purification and Identification of Interactors to Elucidate Novel Connections in the HEK 293 Cell Line

    The Purification and Identification of Interactors to Elucidate Novel Connections in the HEK 293 Cell Line Brett Hawley Biochemistry, Microbiology and Immunology Faculty of Medicine University of Ottawa © Brett Hawley, Ottawa, Canada, 2012 ABSTRACT The field of proteomics studies the structure and function of proteins in a large scale and high throughput manner. My work in the field of proteomics focuses on identifying interactions between proteins and discovering novel interactions. The identification of these interactions provides new information on metabolic and disease pathways and the working proteome of a cell. Cells are lysed and purified using antibody based affinity purification followed by digestion and identification using an HPLC coupled to a mass spectrometer. In my studies, I looked at the interaction networks of several AD related genes (Apolipoprotein E, Clusterin variant 1 and 2, Low-density lipoprotein receptor, Phosphatidylinositol binding clathrin assembly protein, Alpha- synuclein and Platelet-activating factor receptor) and an endosomal recycling pathway involved in cholesterol metabolism (Eps15 homology domain 1,2 and 4, Proprotein convertase subtilisin/kexin type 9 and Low-density lipoprotein receptor). Several novel and existing interactors were identified and these interactions were validated using co-immunopurification, which could be the basis for future research. ii ACKNOWLEDGEMENTS I would like to take this opportunity to thank my supervisor, Dr. Daniel Figeys, for his support and guidance throughout my studies in his lab. It was a great experience to work in his lab and I am very thankful I was given the chance to learn and work under him. I would also like to thank the members of my lab for all their assistance in learning new techniques and equipment in the lab.
  • Download on 20

    Download on 20

    bioRxiv preprint doi: https://doi.org/10.1101/850776; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation Julia D. Knopf1, Nina Landscheidt1, Cassandra L. Pegg2, Benjamin L. Schulz2, Nathalie Kühnle1, Chao-Wei Chao1, Simon Huck1 and Marius K. Lemberg1, # 1Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany. 2School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia QLD 4072, Australia. #Corresponding author: [email protected] Running title: RHBDL4 triggers ERAD of OST subunits Key words: Rhomboid serine protease, Rhbdd1, ubiquitin-dependent proteolysis, post- translational protein abundance control, N-linked glycosylation. Abbreviations ERAD, ER-associated degradation; OST, oligosacharyltransferase; TM, transmembrane; UIM, ubiquitin-interacting motif. Abstract The Endoplasmic Reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosacharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalyzed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation.
  • ARID5B As a Critical Downstream Target of the TAL1 Complex That Activates the Oncogenic Transcriptional Program and Promotes T-Cell Leukemogenesis

    ARID5B As a Critical Downstream Target of the TAL1 Complex That Activates the Oncogenic Transcriptional Program and Promotes T-Cell Leukemogenesis

    Downloaded from genesdev.cshlp.org on October 10, 2021 - Published by Cold Spring Harbor Laboratory Press ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis Wei Zhong Leong,1 Shi Hao Tan,1 Phuong Cao Thi Ngoc,1 Stella Amanda,1 Alice Wei Yee Yam,1 Wei-Siang Liau,1 Zhiyuan Gong,2 Lee N. Lawton,1 Daniel G. Tenen,1,3,4 and Takaomi Sanda1,4 1Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore; 2Department of Biological Sciences, National University of Singapore, 117543 Singapore; 3Harvard Medical School, Boston, Massachusetts 02215, USA; 4Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore The oncogenic transcription factor TAL1/SCL induces an aberrant transcriptional program in T-cell acute lym- phoblastic leukemia (T-ALL) cells. However, the critical factors that are directly activated by TAL1 and contribute to T-ALL pathogenesis are largely unknown. Here, we identified AT-rich interactive domain 5B (ARID5B) as a col- laborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B expression is down-regulated at the double-negative 2–4 stages in normal thymocytes, while it is induced by the TAL1 complex in human T-ALL cells. The enhancer located 135 kb upstream of the ARID5B gene locus is activated under a superenhancer in T-ALL cells but not in normal T cells. Notably, ARID5B-bound regions are associated predominantly with active tran- scription. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression.
  • Endoglin Protein Interactome Profiling Identifies TRIM21 and Galectin-3 As

    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.