DOCSLIB.ORG

Supplemental Table 1A. Differential Gene Expression Profile of Adehcd40l and Adehnull Treated Cells Vs Untreated Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Supplemental Table 1a. Differential Gene Expression Profile of AdEHCD40L and AdEHNull treated cells vs Untreated Cells Fold change Regulation Fold change Regulation ([AdEHCD40L] vs ([AdEHCD40L] ([AdEHNull] vs ([AdEHNull] vs Probe Set ID [Untreated]) vs [Untreated]) [Untreated]) [Untreated]) Gene Symbol Gene Title RefSeq Transcript ID NM_001039468 /// NM_001039469 /// NM_004954 /// 203942_s_at 2.02 down 1.00 down MARK2 MAP/microtubule affinity-regulating kinase 2 NM_017490 217985_s_at 2.09 down 1.00 down BAZ1A fibroblastbromodomain growth adjacent factor receptorto zinc finger 2 (bacteria-expressed domain, 1A kinase, keratinocyte NM_013448 /// NM_182648 growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer 203638_s_at 2.10 down 1.01 down FGFR2 syndrome, Jackson-Weiss syndrome) NM_000141 /// NM_022970 1570445_a_at 2.07 down 1.01 down LOC643201 hypothetical protein LOC643201 XM_001716444 /// XM_001717933 /// XM_932161 231763_at 3.05 down 1.02 down POLR3A polymerase (RNA) III (DNA directed) polypeptide A, 155kDa NM_007055 1555368_x_at 2.08 down 1.04 down ZNF479 zinc finger protein 479 NM_033273 /// XM_001714591 /// XM_001719979 241627_x_at 2.15 down 1.05 down FLJ10357 hypothetical protein FLJ10357 NM_018071 223208_at 2.17 down 1.06 down KCTD10 potassium channel tetramerisation domain containing 10 NM_031954 219923_at 2.09 down 1.07 down TRIM45 tripartite motif-containing 45 NM_025188 242772_x_at 2.03 down 1.07 down Transcribed locus 233019_at 2.19 down 1.08 down CNOT7 CCR4-NOT transcription complex, subunit 7 NM_013354 /// NM_054026 223139_s_at 2.09 down 1.08 down DHX36 DEAH (Asp-Glu-Ala-His) box polypeptide 36 NM_001114397 /// NM_020865 1569594_a_at 2.17 down 1.09 down SDCCAG1 serologically defined colon cancer antigen 1 NM_004713 238518_x_at 2.13 down 1.09 down GLYCTK glycerate kinase NM_145262 217650_x_at 2.83 down 1.09 down ST3GAL2 ST3 beta-galactoside alpha-2,3-sialyltransferase 2 NM_006927 218862_at 2.12 down 1.13 down ASB13 ankyrin repeat and SOCS box-containing 13 NM_024701 215587_x_at 2.83 down 1.13 down CDNA FLJ13829 fis, clone THYRO1000625 215623_x_at 2.33 down 1.13 down SMC4 structural maintenance of chromosomes 4 NM_001002800 /// NM_005496 231479_at 2.00 down 1.14 down TTC33 tetratricopeptide repeat domain 33 NM_012382 222854_s_at 2.05 down 1.14 down GEMIN8 gem (nuclear organelle) associated protein 8 NM_001042479 /// NM_001042480 /// NM_017856 242766_at 2.13 down 1.14 down Homo sapiens, clone IMAGE:3660074, mRNA 228766_at 2.45 down 1.15 down 200598_s_at 2.11 down 1.16 down HSP90B1 heat shock protein 90kDa beta (Grp94), member 1 NM_003299 221755_at 2.10 down 1.17 down EHBP1L1 EH domain binding protein 1-like 1 NM_001099409 1556082_a_at 2.20 down 1.18 down CDNA FLJ33441 fis, clone BRACE2021932 205099_s_at 2.01 down 1.18 down CCR1 chemokine (C-C motif) receptor 1 NM_001295 203731_s_at 2.00 down 1.18 down ZKSCAN5 zinc finger with KRAB and SCAN domains 5 NM_014569 /// NM_145102 233511_at 2.07 down 1.18 down CDNA clone IMAGE:5271538 235985_at 2.89 down 1.18 down Transcribed locus 214987_at 2.41 down 1.19 down CDNA clone IMAGE:4801326 230888_at 2.18 down 1.19 down WDR91 WD repeat domain 91 NM_014149 225272_at 2.04 down 1.20 down SAT2 spermidine/spermine N1-acetyltransferase family member 2 NM_133491 201491_at 2.02 down 1.20 down AHSA1 AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) NM_012111 205240_at 2.74 down 1.20 down GPSM2 G-protein signaling modulator 2 (AGS3-like, C. elegans) NM_013296 229466_at 2.14 down 1.21 down LOC256273 hypothetical protein LOC256273 227507_at 2.06 down 1.22 down ZNF592 zinc finger protein 592 NM_014630 225377_at 2.21 down 1.22 down C9orf86 chromosome 9 open reading frame 86 NM_017995 /// NM_024718 212601_at 2.47 down 1.22 down ZZEF1 zinc finger, ZZ-type with EF-hand domain 1 NM_015113 228789_at 2.92 down 1.24 down MTMR6 myotubularin related protein 6 NM_004685 205854_at 2.44 down 1.24 down TULP3 tubby like protein 3 NM_003324 214836_x_at 2.04 down 1.26 down IGKC immunoglobulin kappa constant 218895_at 2.82 down 1.26 down GPATCH3 G patch domain containing 3 NM_022078 215521_at 2.16 down 1.27 down PHC3 polyhomeotic homolog 3 (Drosophila) NM_024947 204492_at 2.26 down 1.27 down ARHGAP11A Rho GTPase activating protein 11A NM_014783 /// NM_199357 /// XM_001714495 221436_s_at 2.14 down 1.28 down CDCA3 cell division cycle associated 3 NM_031299 224736_at 2.63 down 1.28 down CCAR1 cell division cycle and apoptosis regulator 1 NM_018237 214965_at 2.17 down 1.29 down SPATA2L spermatogenesis associated 2-like NM_152339 235084_x_at 2.56 down 1.30 down Transcribed locus 244792_at 2.06 down 1.31 down 235696_at 2.33 down 1.31 down CDNA clone IMAGE:4837650 229483_at 2.09 down 1.31 down CDNA FLJ42331 fis, clone TSTOM2000588 64488_at 2.31 down 1.31 down CDNA FLJ38849 fis, clone MESAN2008936 201674_s_at 2.40 down 1.32 down AKAP1 A kinase (PRKA) anchor protein 1 NM_003488 220342_x_at 2.41 down 1.32 down EDEM3 ER degradation enhancer, mannosidase alpha-like 3 NM_025191 233509_at 2.26 down 1.33 down HERC4 hect domain and RLD 4 NM_015601 /// NM_022079 202386_s_at 2.02 down 1.33 down KIAA0430 KIAA0430 NM_014647 220305_at 2.08 down 1.34 down MGC3260 hypothetical LOC78993 228897_at 2.08 down 1.34 down DERL3 Der1-like domain family, member 3 NM_001002862 /// NM_198440 228723_at 2.14 down 1.34 down CDNA FLJ30445 fis, clone BRACE2009238 239294_at 2.31 down 1.35 down Transcribed locus 208993_s_at 3.01 down 1.35 down PPIG peptidylprolyl isomerase G (cyclophilin G) NM_004792 203264_s_at 2.17 down 1.36 down ARHGEF9 Cdc42 guanine nucleotide exchange factor (GEF) 9 NM_015185 217164_at 2.16 down 1.36 down 218756_s_at 2.12 down 1.36 down MGC4172 short-chain dehydrogenase/reductase NM_024308 228252_at 2.09 down 1.36 down PIF1 PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae) NM_025049 235782_at 2.52 down 1.36 down Transcribed locus 211969_at 2.13 down 1.37 down HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 NM_001017963 /// NM_005348 215942_s_at 2.01 down 1.37 down GTSE1 G-2 and S-phase expressed 1 NM_016426 227811_at 2.17 down 1.38 down FGD3 FYVE, RhoGEF and PH domain containing 3 NM_001083536 /// NM_033086 210625_s_at 2.35 down 1.38 down AKAP1 A kinase (PRKA) anchor protein 1 NM_003488 210993_s_at 2.24 down 1.38 down SMAD1 SMAD family member 1 NM_001003688 /// NM_005900 224520_s_at 5.02 down 1.39 down BEST3 bestrophin 3 NM_032735 /// NM_152439 227254_at 3.15 down 1.39 down POU2F1 POU class 2 homeobox 1 NM_002697 236090_at 2.16 down 1.39 down Transcribed locus 233642_s_at 2.06 down 1.39 down HEATR5B HEAT repeat containing 5B NM_019024 222305_at 2.08 down 1.39 down HK2 hexokinase 2 NM_000189 214550_s_at 2.60 down 1.40 down TNPO3 transportin 3 NM_012470 222713_s_at 2.03 down 1.40 down FANCF Fanconi anemia, complementation group F NM_022725 242578_x_at 2.83 down 1.40 down SLC22A3 Solute carrier family 22 (extraneuronal monoamine transporter), member 3 NM_021977 222045_s_at 2.23 down 1.41 down PCIF1 PDX1 C-terminal inhibiting factor 1 NM_022104 243560_at 2.54 down 1.42 down Transcribed locus 219949_at 4.30 down 1.42 down LRRC2 leucine rich repeat containing 2 NM_024512 /// NM_024750 203345_s_at 2.28 down 1.42 down MTF2 metal response element binding transcription factor 2 NM_007358 223174_at 2.14 down 1.42 down BTBD10 BTB (POZ) domain containing 10 NM_032320 217807_s_at 2.01 down 1.42 down GLTSCR2 glioma tumor suppressor candidate region gene 2 NM_015710 232682_at 2.06 down 1.42 down MREG melanoregulin NM_018000 242691_at 2.31 down 1.43 down CDNA FLJ41369 fis, clone BRCAN2006117 226413_at 2.05 down 1.43 down LOC400027 hypothetical gene supported by BC047417 XM_001718517 /// XM_931434 /// XM_943193 203725_at 2.08 down 1.43 down GADD45A growth arrest and DNA-damage-inducible, alpha NM_001924 225108_at 2.47 down 1.44 down 229050_s_at 2.11 down 1.44 down SNHG7 small nucleolar RNA host gene (non-protein coding) 7 NR_003672 228167_at 2.01 down 1.44 down KLHL6 kelch-like 6 (Drosophila) NM_130446 1552621_at 2.45 down 1.44 down POLR2J2 DNA directed RNA polymerase II polypeptide J-related NM_032959 239024_at 2.03 down 1.45 down ZNF148 zinc finger protein 148 NM_021964 1558755_x_at 2.66 down 1.45 down ZNF763 zinc finger protein 763 NM_001012753 225330_at 2.20 down 1.45 down IGF1R insulin-like growth factor 1 receptor NM_000875 223487_x_at 2.04 down 1.45 down GNB4 guanine nucleotide binding protein (G protein), beta polypeptide 4 NM_021629 1552427_at 2.35 down 1.46 down ZNF485 zinc finger protein 485 NM_145312 33646_g_at 2.24 down 1.46 down GM2A GM2 ganglioside activator NM_000405 201737_s_at 2.92 down 1.46 down 7-Mar membrane-associated ring finger (C3HC4) 6 NM_005885 212086_x_at 2.03 down 1.47 down LMNA lamin A/C NM_005572 /// NM_170707 /// NM_170708 minichromosome maintenance complex component 3 associated protein 220459_at 2.13 down 1.47 down MCM3APAS antisense NR_002776 230178_s_at 2.02 down 1.47 down CDNA FLJ38461 fis, clone FEBRA2020977 209162_s_at 2.03 down 1.47 down PRPF4 PRP4 pre-mRNA processing factor 4 homolog (yeast) NM_004697 238908_at 2.94 down 1.48 down CALU Calumenin NM_001219 205132_at 2.29 down 1.48 down ACTC1 actin, alpha, cardiac muscle 1 NM_005159 217142_at 2.30 down 1.49 down NM_001042749 /// NM_001042750 /// NM_001042751 /// 207983_s_at 2.21 down 1.49 down STAG2 stromal antigen 2 NM_006603 225640_at 2.15 down 1.49 down LOC401504 hypothetical gene supported by AK091718 241773_at 2.14 down 1.49 down 1553286_at 2.17 down 1.50 down ZNF555 zinc finger protein 555 NM_152791 216606_x_at 2.14 down 1.50 down LYPLA2P1 lysophospholipase II pseudogene 1 NR_001444
Recommended publications
  • Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach

    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
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model

    Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model

    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.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 © 2016 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 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
  • Identification of Candidate Substrates of the Leucine Rich Repeat Kinase 2 by Mass Spectrometry

    Identification of Candidate Substrates of the Leucine Rich Repeat Kinase 2 by Mass Spectrometry

    Identification of candidate substrates of the leucine rich repeat kinase 2 by mass spectrometry- based phosphoproteomics William Carl Edelman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2016 Reading Committee: Judit Villén, Chair Leo Pallanck Deborah Nickerson Program Authorized to Offer Degree: Department of Genome Sciences 2 © Copyright 2016 William Carl Edelman 3 University of Washington Abstract Identification of candidate substrates of the leucine rich repeat kinase 2 by mass spectrometry-based phosphoproteomics William Carl Edelman Chair of the Supervisory Committee: Assistant Professor, Judit Villén Department of Genome Sciences Mutations in the kinase domain of the leucine rich repeat kinase (LRRK2) have been implicated in heritable forms of Parkinson’s disease (PD). Specifically, a glycine to serine mutation (G2019S) has demonstrated hyperactive autophosphorylation, neuronal toxicity, and locomotor deficits in the fruit fly Drosophila melanogaster— all of which are related to its pathogenicity in PD. My dissertation focuses on identifying novel substrates of LRRK2 through analysis of proteome-wide changes in protein abundance as well as identifying changes in phosphorylation of proteins in vitro and in the in vivo fruit fly model. Using mass spectrometry, I provide quantitative information on thousands of proteins and phosphorylation sites. In vitro kinase assays on peptides derived from fly heads or a neuroblastoma cell line provide evidence for direct substrates of LRRK2, while the in vivo experiment in flies expressing LRRK2 identifies both direct and indirect phosphorylation substrates of the kinase. Herein, I present evidence for novel, LRRK2-mediated phosphorylation sites in the Drosophila melanogaster and the neuroblastoma models of PD.
  • An Interactive Web Application to Explore Regeneration-Associated Gene Expression and Chromatin Accessibility

    An Interactive Web Application to Explore Regeneration-Associated Gene Expression and Chromatin Accessibility

    Supplementary Materials Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer 1. Table S1. List of cholesterol metabolic genes from MGI database 2. Table S2. List of differentially expressed transcripts during optic nerve regeneration in zebrafish using the MGI cholesterol metabolic gene queries in the Regeneration Rosetta app 3. Table S3. List of transcription factor encoding genes from brain cell bodies following spinal cord injury in lamprey over a course of 12 weeKs 4. Table S4. List of transcription factor encoding genes from spinal cell bodies following spinal cord injury in lamprey over a course of 12 weeks Ensembl ID MGI Gene ID Symbol Name ENSMUSG00000015243 MGI:99607 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 ENSMUSG00000026944 MGI:99606 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 ENSMUSG00000024030 MGI:107704 Abcg1 ATP binding cassette subfamily G member 1 ENSMUSG00000026003 MGI:87866 Acadl acyl-Coenzyme A dehydrogenase, long-chain ENSMUSG00000018574 MGI:895149 Acadvl acyl-Coenzyme A dehydrogenase, very long chain ENSMUSG00000038641 MGI:2384785 Akr1d1 aldo-keto reductase family 1, member D1 ENSMUSG00000028553 MGI:1353627 Angptl3 angiopoietin-like 3 ENSMUSG00000031996 MGI:88047 Aplp2 amyloid beta (A4) precursor-like protein 2 ENSMUSG00000032083 MGI:88049 Apoa1 apolipoprotein A-I ENSMUSG00000005681 MGI:88050 Apoa2 apolipoprotein A-II ENSMUSG00000032080 MGI:88051 Apoa4
  • Enzymatic Encoding Methods for Efficient Synthesis Of

    Enzymatic Encoding Methods for Efficient Synthesis Of

    (19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN,
  • Molecular Markers of Serine Protease Evolution

    Molecular Markers of Serine Protease Evolution

    The EMBO Journal Vol. 20 No. 12 pp. 3036±3045, 2001 Molecular markers of serine protease evolution Maxwell M.Krem and Enrico Di Cera1 ment and specialization of the catalytic architecture should correspond to signi®cant evolutionary transitions in the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St Louis, history of protease clans. Evolutionary markers encoun- MO 63110-1093, USA tered in the sequences contributing to the catalytic apparatus would thus give an account of the history of 1Corresponding author e-mail: [email protected] an enzyme family or clan and provide for comparative analysis with other families and clans. Therefore, the use The evolutionary history of serine proteases can be of sequence markers associated with active site structure accounted for by highly conserved amino acids that generates a model for protease evolution with broad form crucial structural and chemical elements of applicability and potential for extension to other classes of the catalytic apparatus. These residues display non- enzymes. random dichotomies in either amino acid choice or The ®rst report of a sequence marker associated with serine codon usage and serve as discrete markers for active site chemistry was the observation that both AGY tracking changes in the active site environment and and TCN codons were used to encode active site serines in supporting structures. These markers categorize a variety of enzyme families (Brenner, 1988). Since serine proteases of the chymotrypsin-like, subtilisin- AGY®TCN interconversion is an uncommon event, it like and a/b-hydrolase fold clans according to phylo- was reasoned that enzymes within the same family genetic lineages, and indicate the relative ages and utilizing different active site codons belonged to different order of appearance of those lineages.
  • Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers

    Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers

    Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers. by Kelly Kennaley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2019 Doctoral Committee: Associate Professor Zaneta Nikolovska-Coleska, Co-Chair Adjunct Associate Professor Scott A. Tomlins, Co-Chair Associate Professor Eric R. Fearon Associate Professor Alexey I. Nesvizhskii Kelly R. Kennaley [email protected] ORCID iD: 0000-0003-2439-9020 © Kelly R. Kennaley 2019 Acknowledgements I have immeasurable gratitude for the unwavering support and guidance I received throughout my dissertation. First and foremost, I would like to thank my thesis advisor and mentor Dr. Scott Tomlins for entrusting me with a challenging, interesting, and impactful project. He taught me how to drive a project forward through set-backs, ask the important questions, and always consider the impact of my work. I’m truly appreciative for his commitment to ensuring that I would get the most from my graduate education. I am also grateful to the many members of the Tomlins lab that made it the supportive, collaborative, and educational environment that it was. I would like to give special thanks to those I’ve worked closely with on this project, particularly Dr. Moloy Goswami for his mentorship, Lei Lucy Wang, Dr. Sumin Han, and undergraduate students Bhavneet Singh, Travis Weiss, and Myles Barlow. I am also grateful for the support of my thesis committee, Dr. Eric Fearon, Dr. Alexey Nesvizhskii, and my co-mentor Dr. Zaneta Nikolovska-Coleska, who have offered guidance and critical evaluation since project inception.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Palmitoyl-Protein Thioesterase 1 Deficiency in Drosophila Melanogaster Causes Accumulation

    Palmitoyl-Protein Thioesterase 1 Deficiency in Drosophila Melanogaster Causes Accumulation

    Genetics: Published Articles Ahead of Print, published on February 1, 2006 as 10.1534/genetics.105.053306 Palmitoyl-protein thioesterase 1 deficiency in Drosophila melanogaster causes accumulation of abnormal storage material and reduced lifespan Anthony J. Hickey*,†,1, Heather L. Chotkowski*, Navjot Singh*, Jeffrey G. Ault*, Christopher A. Korey‡,2, Marcy E. MacDonald‡, and Robert L. Glaser*,†,3 * Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002 † Department of Biomedical Sciences, State University of New York, Albany, NY 12201-0509 ‡ Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114 1 current address: Albany Medical College, Albany, NY 12208 2 current address: Department of Biology, College of Charleston, Charleston, SC 294243 3 corresponding author: Wadsworth Center, NYS Dept. Health, P. O. Box 22002, Albany, NY 12201-2002 E-mail: [email protected] 1 running title: Phenotypes of Ppt1-deficient Drosophila key words: Batten disease infantile neuronal ceroid lipofuscinosis palmitoyl-protein thioesterase CLN1 Drosophila corresponding author: Robert L. Glaser Wadsworth Center, NYS Dept. Health P. O. Box 22002 Albany, NY 12201-2002 E-mail: [email protected] phone: 518-473-4201 fax: 518-474-3181 2 ABSTRACT Human neuronal ceroid lipofuscinoses (NCLs) are a group of genetic neurodegenerative diseases characterized by progressive death of neurons in the central nervous system (CNS) and accumulation of abnormal lysosomal storage material. Infantile NCL (INCL), the most severe form of NCL, is caused by mutations in the Ppt1 gene, which encodes the lysosomal enzyme palmitoyl-protein thioesterase 1 (Ppt1). We generated mutations in the Ppt1 ortholog of Drosophila melanogaster in order to characterize phenotypes caused by Ppt1-deficiency in flies.
  • Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases

    Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases

    International Journal of Molecular Sciences Review Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases Peter Goettig Structural Biology Group, Faculty of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria; [email protected]; Tel.: +43-662-8044-7283; Fax: +43-662-8044-7209 Academic Editor: Cheorl-Ho Kim Received: 30 July 2016; Accepted: 10 November 2016; Published: 25 November 2016 Abstract: Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications. Keywords: secreted protease; sequon; N-glycosylation; O-glycosylation; core glycan; enzyme kinetics; substrate recognition; flexible loops; Michaelis constant; turnover number 1.
  • Mouse Carboxypeptidase M / CPM Protein (His Tag)

    Mouse Carboxypeptidase M / CPM Protein (His Tag)

    Mouse Carboxypeptidase M / CPM Protein (His Tag) Catalog Number: 50990-M08H General Information SDS-PAGE: Gene Name Synonym: 1110060I01Rik; 5730456K23Rik; AA589379; E030045M14Rik Protein Construction: A DNA sequence encoding the extracellular domain of mouse CPM isoform 1 (Q80V42-1) (Met 1-His 422), without the propeptide, was fused with a C- terminal polyhistidine tag. Source: Mouse Expression Host: HEK293 Cells QC Testing Purity: > 97 % as determined by SDS-PAGE Bio Activity： Protein Description Measured by its ability to release Larginine from BenzoylAlaArg, with Carboxypeptidase M, also known as CPM, is a membrane-bound detection of the arginine amino group by ophthaldialdehyde. The arginine/lysine carboxypeptidase which is a member of the specific activity is >40,000 pmoles/min/μg. carboxypeptidases family. These enzymes remove C-terminal amino acids from peptides and proteins and exert roles in the physiological processes Endotoxin: of blood coagulation/fibrinolysis, inflammation, food digestion and pro- hormone and neuropeptide processing. Among the carboxypeptidases < 1.0 EU per μg of the protein as determined by the LAL method CPM is of particular importance because of its constitutive expression in an active form at the surface of specialized cells and tissues in the human Stability: body. CPM in the brain appears to be membrane-bound via a Samples are stable for up to twelve months from date of receipt at -70 ℃ phosphatidylinositol glycan anchor. CPM is widely distributed in a variety of tissues and cells. The amino acid sequence of CPM indicated that the C- Predicted N terminal: Leu 18 terminal hydrophobic region might be a signal for membrane attachment via a glycosylphosphatidylinositol (GPI) anchor.
  • IL21R Expressing CD14+CD16+ Monocytes Expand in Multiple

    IL21R Expressing CD14+CD16+ Monocytes Expand in Multiple

    Plasma Cell Disorders SUPPLEMENTARY APPENDIX IL21R expressing CD14 +CD16 + monocytes expand in multiple myeloma patients leading to increased osteoclasts Marina Bolzoni, 1 Domenica Ronchetti, 2,3 Paola Storti, 1,4 Gaetano Donofrio, 5 Valentina Marchica, 1,4 Federica Costa, 1 Luca Agnelli, 2,3 Denise Toscani, 1 Rosanna Vescovini, 1 Katia Todoerti, 6 Sabrina Bonomini, 7 Gabriella Sammarelli, 1,7 Andrea Vecchi, 8 Daniela Guasco, 1 Fabrizio Accardi, 1,7 Benedetta Dalla Palma, 1,7 Barbara Gamberi, 9 Carlo Ferrari, 8 Antonino Neri, 2,3 Franco Aversa 1,4,7 and Nicola Giuliani 1,4,7 1Myeloma Unit, Dept. of Medicine and Surgery, University of Parma; 2Dept. of Oncology and Hemato-Oncology, University of Milan; 3Hematology Unit, “Fondazione IRCCS Ca’ Granda”, Ospedale Maggiore Policlinico, Milan; 4CoreLab, University Hospital of Parma; 5Dept. of Medical-Veterinary Science, University of Parma; 6Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture; 7Hematology and BMT Center, University Hospital of Parma; 8Infectious Disease Unit, University Hospital of Parma and 9“Dip. Oncologico e Tecnologie Avanzate”, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy ©2017 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2016.153841 Received: August 5, 2016. Accepted: December 23, 2016. Pre-published: January 5, 2017. Correspondence: [email protected] SUPPLEMENTAL METHODS Immunophenotype of BM CD14+ in patients with monoclonal gammopathies. Briefly, 100 μl of total BM aspirate was incubated in the dark with anti-human HLA-DR-PE (clone L243; BD), anti-human CD14-PerCP-Cy 5.5, anti-human CD16-PE-Cy7 (clone B73.1; BD) and anti-human CD45-APC-H 7 (clone 2D1; BD) for 20 min.