DOCSLIB.ORG

Supplementary Table I Genes Regulated by Myc/Ras Transformation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Table I Genes Regulated by Myc/Ras Transformation Supplementary Table I Genes regulated by myc/ras transformation signal Probe set Gene symbol gene + dox/ - E2 - dox/ - E2 - dox/ +E2 100011_at Klf3 Kruppel-like factor 3 (basic) 308 120 270 100013_at 2010008K16Rik RIKEN cDNA 2010008K16 gene 127 215 859 100016_at Mmp11 matrix metalloproteinase 11 187 71 150 100019_at Cspg2 chondroitin sulfate proteoglycan 2 1148 342 669 100023_at Mybl2 myeloblastosis oncogene-like 2 13 105 12 100030_at Upp uridine phosphorylase 18 39 110 100033_at Msh2 mutS homolog 2 (E. coli) 120 246 92 100037_at 2310005B10Rik RIKEN cDNA 2310005B10 gene 178 351 188 100039_at Tmem4 transmembrane protein 4 316 135 274 100040_at Mrpl17 mitochondrial ribosomal protein L17 88 142 89 100041_at 3010027G13Rik RIKEN cDNA 3010027G13 gene 818 1430 1033 methylenetetrahydrofolate dehydrogenase, methenyltetrahydrofolate 100046_at Mthfd2 cyclohydrolase 213 720 376 100064_f_at Gja1 gap junction membrane channel protein alpha 1 143 574 92 100066_at Gart phosphoribosylglycinamide formyltransferase 133 385 180 100071_at Mup2 major urinary protein 2 26 74 30 100081_at Stip1 stress-induced phosphoprotein 1 148 341 163 100089_at Ppic peptidylprolyl isomerase C 358 214 181 100091_at Ugalt2 UDP-galactose translocator 2 1456 896 1530 100095_at Scarb1 scavenger receptor class B, member 1 638 1044 570 100113_s_at Kifap3 kinesin-associated protein 3 482 168 311 100116_at 2810417H13Rik RIKEN cDNA 2810417H13 gene 134 261 53 100120_at Nid1 nidogen 1 81 47 54 100125_at Pa2g4 proliferation-associated 2G4, 38kD 62 286 44 100128_at Cdc2a cell division cycle 2 homolog A (S. pombe) 459 1382 247 100133_at Fyn Fyn proto-oncogene 168 44 82 100144_at Ncl nucleolin 1283 3452 1215 100151_at Tde1 tumor differentially expressed 1 620 351 620 100153_at Ncam1 neural cell adhesion molecule 1 302 144 234 100155_at Ddr1 discoidin domain receptor family, member 1 304 117 310 100156_at Mcmd5 mini chromosome maintenance deficient 5 (S. cerevisiae) 347 717 153 100272_at Smcy selected mouse cDNA on the Y 11 21 45 100279_at Siat5 sialyltransferase 5 125 75 76 100286_at Mst1 macrophage stimulating 1 (hepatocyte growth factor-like) 51 18 17 100290_f_at 6230416J20Rik RIKEN cDNA 6230416J20 gene 52 96 31 100291_at Cbl Casitas B-lineage lymphoma 31 56 43 100297_at 1600024A01Rik RIKEN cDNA 1600024A01 gene 120 73 90 100302_at Maff v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian) 21 53 26 100308_at Col8a1 procollagen, type VIII, alpha 1 931 262 949 100309_at Met met proto-oncogene 76 21 35 100342_i_at Tuba1 tubulin, alpha 1 5791 1931 4214 100353_g_at Hspa4 heat shock protein 4 435 703 466 100371_at Hnrpa1 heterogeneous nuclear ribonucleoprotein A1 31 64 28 100380_at H3f3a H3 histone, family 3A 1121 654 756 100412_g_at Aebp1 AE binding protein 1 2071 898 1427 100420_at Flg filaggrin 44 15 25 100429_at Ppox protoporphyrinogen oxidase 112 59 112 100435_at Edg2 endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2 847 309 391 100453_at Camk2b calcium/calmodulin-dependent protein kinase II, beta 5 44 24 100465_i_at --- Mus musculus, clone IMAGE:3371572, mRNA 280 161 143 100482_at --- Mus musculus, clone IMAGE:5355325, mRNA 259 450 366 100483_at Ifnar1 interferon (alpha and beta) receptor 1 108 30 79 100486_at Ezh1 enhancer of zeste homolog 1 (Drosophila) 70 31 90 100488_at Gba acid beta glucosidase 659 309 845 100512_at Uchl5 ubiquitin carboxyl-terminal esterase L5 30 93 26 100539_at Bach-pending brain acyl-CoA hydrolase 208 353 201 100547_at 4921506I22Rik RIKEN cDNA 4921506I22 gene 237 99 99 100553_at Trim27 tripartite motif protein 27 226 606 230 100554_at Pdlim1 PDZ and LIM domain 1 (elfin) 72 221 188 100562_at Rangnrf-pending RAN guanine nucleotide release factor 107 280 73 100565_at Gnpi glucosamine-6-phosphate deaminase 140 67 101 100573_f_at Gpi1 glucose phosphate isomerase 1 191 329 221 100575_at Ard1 N-acetyltransferase ARD1 homolog (S. cerevisiae) 82 228 82 100577_at Snrpd1 small nuclear ribonucleoprotein D1 40 65 41 100578_at Impdh2 inosine 5'-phosphate dehydrogenase 2 502 1415 371 100580_at Clta clathrin, light polypeptide (Lca) 23 49 62 100593_at Tnnt2 troponin T2, cardiac 14 53 21 100596_at Selenbp1 selenium binding protein 1 8 53 36 100600_at Cd24a CD24a antigen 122 35 42 100603_at Dncic2 dynein, cytoplasmic, intermediate chain 2 118 56 89 100606_at Prnp prion protein 2702 1282 2648 100607_at Pld3 phospholipase D3 293 101 285 100636_at Eif4ebp1 eukaryotic translation initiation factor 4E binding protein 1 95 225 161 100697_at Pax3 paired box gene 3 11 21 11 100756_r_at Tyms-ps thymidylate synthase, pseudogene 86 214 148 100828_at Myla myosin light chain, alkali, cardiac atria 49 19 49 100877_at 1810058I24Rik RIKEN cDNA 1810058I24 gene 1074 585 744 100885_at Nek2 NIMA (never in mitosis gene a)-related expressed kinase 2 114 303 108 100886_f_at Mrpl45 mitochondrial ribosomal protein L45 154 296 180 100887_at 2810489L22Rik RIKEN cDNA 2810489L22 gene 44 80 41 100890_at 2600017H24Rik RIKEN cDNA 2600017H24 gene 90 214 106 100906_at Itgb7 integrin beta 7 178 468 627 100915_at Myh9 myosin heavy chain IX 2523 1461 2139 100923_at Myo10 myosin X 1122 293 776 100928_at Fbln2 fibulin 2 2508 1269 1442 100931_at Arsa arylsulfatase A 504 236 409 100953_at Timeless timeless homolog (Drosophila) 89 169 87 100955_at 2700084L22Rik RIKEN cDNA 2700084L22 gene 22 59 13 100974_at 1210002E11Rik RIKEN cDNA 1210002E11 gene 131 231 129 100977_at D530020C15Rik RIKEN cDNA D530020C15 gene 118 222 137 100983_at Prep prolyl endopeptidase 101 214 114 100986_at Fhl2 four and a half LIM domains 2 669 329 491 100988_at Bcl2l11 BCL2-like 11 (apoptosis facilitator) 321 164 211 100992_at Edr1 early development regulator 1 (homolog of polyhomeotic 1) 113 66 79 101015_s_at Ifnar2 interferon (alpha and beta) receptor 2 47 22 64 101027_s_at Pttg1 pituitary tumor-transforming 1 277 635 195 101039_at Col4a2 procollagen, type IV, alpha 2 1474 775 1095 101051_at S100a3 S100 calcium binding protein A3 66 109 80 101055_at Ppgb protective protein for beta-galactosidase 2084 1118 1996 101059_at Ndn necdin 336 171 193 101065_at Pcna proliferating cell nuclear antigen 291 826 204 101070_at Mkrn1 makorin, ring finger protein, 1 104 64 81 101073_at Lrp1 low density lipoprotein receptor-related protein 1 2161 979 2043 101083_s_at D17H6S56E-2 DNA segment, Chr 17, human D6S56E 2 266 578 183 101086_f_at Cnbp cellular nucleic acid binding protein 869 1657 882 101093_at Col4a1 procollagen, type IV, alpha 1 1164 552 787 101094_at Hig1-pending hypoxia induced gene 1 33 91 53 101099_at Nsg1 neuron specific gene family member 1 91 27 32 101105_at Bcrp1-pending breakpoint cluster region protein 1 1018 2228 1276 101108_at Nasp nuclear autoantigenic sperm protein (histone-binding) 41 73 34 101123_at Itm2b integral membrane protein 2B 1707 741 2165 101130_at Col1a2 procollagen, type I, alpha 2 7639 4621 8498 101180_at Atm ataxia telangiectasia mutated homolog (human) 87 176 194 101214_f_at Gapd glyceraldehyde-3-phosphate dehydrogenase 2161 3891 2701 101254_at Ran RAN, member RAS oncogene family 3763 6742 3389 101341_at H2-M9 histocompatibility 2, M region locus 9 21 44 50 101356_at Tk2 thymidine kinase 2, mitochondrial 102 56 76 101367_at Dctn1 dynactin 1 525 313 428 101384_at 2210008A03Rik RIKEN cDNA 2210008A03 gene 49 15 16 101385_at Mbd3 methyl-CpG binding domain protein 3 586 1060 533 101407_at Frda Friedreich ataxia 42 93 58 101414_at Lmnb2 lamin B2 67 118 52 101429_at Ddit3 DNA-damage inducible transcript 3 213 111 501 101433_at H2ls histocompatibility-2 complex class 1-like sequence 83 32 66 101435_at Akap2 A kinase (PRKA) anchor protein 2 96 41 68 101450_at Csf1 colony stimulating factor 1 (macrophage) 1316 609 1499 101451_at Peg3 paternally expressed 3 208 72 88 101453_at Mia melanoma inhibitory activity 18 35 29 101455_at Umps uridine monophosphate synthetase 40 91 16 101457_at Jak2 Janus kinase 2 54 30 66 101465_at Stat1 signal transducer and activator of transcription 1 103 57 679 101472_s_at Pklr pyruvate kinase liver and red blood cell 10 42 12 101484_at Nbr1 next to the Brca1 830 466 782 101485_at 2400003O03Rik RIKEN cDNA 2400003O03 gene 757 1231 722 101486_at Psmb10 proteasome (prosome, macropain) subunit, beta type 10 187 611 1047 101487_f_at Ly6e lymphocyte antigen 6 complex, locus E 3872 6614 10091 101489_at Amd1 S-adenosylmethionine decarboxylase 1 482 812 413 101494_at Afp alpha fetoprotein 19 45 40 101503_at Dpysl3 dihydropyrimidinase-like 3 119 55 61 101507_at 3110001I17Rik RIKEN cDNA 3110001I17 gene 31 7 43 101509_at Vbp1 von Hippel-Lindau binding protein 1 374 648 307 101515_at Acox1 acyl-Coenzyme A oxidase 1, palmitoyl 114 60 108 101516_at Cd59a CD59a antigen 88 31 88 101521_at Birc5 baculoviral IAP repeat-containing 5 89 232 55 101527_at Tcea1 transcription elongation factor A (SII) 1 509 829 521 101551_s_at Tes testis derived transcript 225 129 224 101554_at Nfkbia nuclear factor of kappa light chain gene enhancer in B-cells inhibitor, alpha 401 257 249 101560_at Emb embigin 2077 437 732 101576_f_at Spi1-2 serine protease inhibitor 1-2 80 43 68 101588_at Slc16a1 solute carrier family 16 (monocarboxylic acid transporters), member 1 28 64 34 101590_at Lamp2 lysosomal membrane glycoprotein 2 1238 506 1222 101623_at Slc16a8 solute carrier family 16 (monocarboxylic acid transporters), member 8 19 53 35 101624_at Kcns1 K+ voltage-gated channel, subfamily S, 1 38 22 39 101632_at Tnfrsf11a tumor necrosis factor receptor superfamily, member 11a 42 14 64 101634_at Npm1 nucleophosmin 1 2077 3442 1622 101650_at Pcdha6 protocadherin alpha 6 83 20 52 101764_at
Load more

Recommended publications
  • Molecular, Genetic, and Nutritional Aspects of Major and Trace Minerals
    Molecular, Genetic, and Nutritional Aspects of Major and Trace Minerals Edited by James F. Collins AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW ORK • OFORD • PARIS SAN DIEGO • SAN FRANCISCO • SINGAPORE • SDNE • TOKO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom Copyright © 2017 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.
    [Show full text]
  • Unrip (STRAP) (NM 007178) Human Tagged ORF Clone Lentiviral Particle Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC209149L3V Unrip (STRAP) (NM_007178) Human Tagged ORF Clone Lentiviral Particle Product data: Product Type: Lentiviral Particles Product Name: Unrip (STRAP) (NM_007178) Human Tagged ORF Clone Lentiviral Particle Symbol: STRAP Synonyms: MAWD; PT-WD; UNRIP Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) ACCN: NM_007178 ORF Size: 1050 bp ORF Nucleotide The ORF insert of this clone is exactly the same as(RC209149). Sequence: OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_007178.2 RefSeq Size: 1924 bp RefSeq ORF: 1053 bp Locus ID: 11171 UniProt ID: Q9Y3F4 Domains: WD40 Protein Families: Druggable Genome MW: 38.4 kDa This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 Unrip (STRAP) (NM_007178) Human Tagged ORF Clone Lentiviral Particle – RC209149L3V Gene Summary: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome.
    [Show full text]
  • Assessment of NR4A Ligands That Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.22.109017; this version posted May 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Assessment of NR4A Ligands that Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1 Paola Munoz-Tello 1, Hua Lin 2,3, Pasha Khan 2, Ian Mitchelle S. de Vera 1,4, Theodore M. Kamenecka 2, and Douglas J. Kojetin 1,2,* 1 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA 2 Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA 3 Current address: Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China 4 Current address: Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA * Correspondence: [email protected] as ligands that increase Nurr1 transcription in human neuroblastoma SK- ABSTRACT N-BE(2)-C cells (11). Amodiaquine improves behavioral alterations in a Nurr1/NR4A2 is an orphan nuclear receptor transcription factor im- Parkinson’s disease animal model (11) and improves neuropathology and plicated as a potential drug target for neurological disorders including memory impairment in an Alzheimer’s disease animal model (12). Alzheimer’s and Parkinson’s diseases. Previous studies identified small molecule modulators of NR4A nuclear receptors including Nurr1 and Amodiaquine is the most potent and efficacious Nurr1 agonist of the Nur77/NR4A1; it remains unclear whether these ligands affect Nurr1 4-amino-7-chloroquinoline compounds, but these compounds are not through direct binding or indirect non-binding mechanisms.
    [Show full text]
  • Kinesin Family Member 18B Regulates the Proliferation and Invasion Of
    Wu et al. Cell Death and Disease (2021) 12:302 https://doi.org/10.1038/s41419-021-03582-2 Cell Death & Disease ARTICLE Open Access Kinesin family member 18B regulates the proliferation and invasion of human prostate cancer cells Yu-Peng Wu 1,Zhi-BinKe 1, Wen-Cai Zheng 1, Ye-Hui Chen 1,Jun-MingZhu 1,FeiLin 1,Xiao-DongLi 1, Shao-Hao Chen 1,HaiCai 1, Qing-Shui Zheng 1, Yong Wei 1, Xue-Yi Xue 1 and Ning Xu 1 Abstract Expression of kinesin family member 18B (KIF18B), an ATPase with key roles in cell division, is deregulated in many cancers, but its involvement in prostate cancer (PCa) is unclear. Here, we investigated the expression and function of KIF18B in human PCa specimens and cell lines using bioinformatics analyses, immunohistochemical and immunofluorescence microscopy, and RT-qPCR and western blot analyses. KIF18B was overexpressed in PCa specimens compared with paracancerous tissues and was associated with poorer disease-free survival. In vitro, KIF18B knockdown in PCa cell lines promoted cell proliferation, migration, and invasion, and inhibited cell apoptosis, while KIF18B overexpression had the opposite effects. In a mouse xenograft model, KIF18B overexpression accelerated and promoted the growth of PCa tumors. Bioinformatics analysis of control and KIF18B-overexpressing PCa cells showed that genes involved in the PI3K–AKT–mTOR signaling pathway were significantly enriched among the differentially expressed genes. Consistent with this observation, we found that KIF18B overexpression activates the PI3K–AKT–mTOR signaling pathway in PCa cells both in vitro and in vivo. Collectively, our results suggest that KIF18B plays a crucial role – – 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; in PCa via activation of the PI3K AKT mTOR signaling pathway, and raise the possibility that KIF18B could have utility as a novel biomarker for PCa.
    [Show full text]
  • Cyclin D1 Is a Direct Transcriptional Target of GATA3 in Neuroblastoma Tumor Cells
    Oncogene (2010) 29, 2739–2745 & 2010 Macmillan Publishers Limited All rights reserved 0950-9232/10 $32.00 www.nature.com/onc SHORT COMMUNICATION Cyclin D1 is a direct transcriptional target of GATA3 in neuroblastoma tumor cells JJ Molenaar1,2, ME Ebus1, J Koster1, E Santo1, D Geerts1, R Versteeg1 and HN Caron2 1Department of Human Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands and 2Department of Pediatric Oncology, Emma Kinderziekenhuis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands Almost all neuroblastoma tumors express excess levels of 2000). Several checkpoints normally prevent premature Cyclin D1 (CCND1) compared to normal tissues and cell-cycle progression and cell division. The crucial G1 other tumor types. Only a small percentage of these entry point is controlled by the D-type Cyclins that can neuroblastoma tumors have high-level amplification of the activate CDK4/6 that in turn phosphorylate the pRb Cyclin D1 gene. The other neuroblastoma tumors have protein. This results in a release of the E2F transcription equally high Cyclin D1 expression without amplification. factor that causes transcriptional upregulation of Silencing of Cyclin D1 expression was previously found to numerous genes involved in further progression of the trigger differentiation of neuroblastoma cells. Over- cell cycle (Sherr, 1996). expression of Cyclin D1 is therefore one of the most Neuroblastomas are embryonal tumors that originate frequent mechanisms with a postulated function in neuro- from precursor cells of the sympathetic nervous system. blastoma pathogenesis. The cause for the Cyclin D1 This tumor has a very poor prognosis and despite the overexpression is unknown.
    [Show full text]
  • Ailanthone Inhibits Non-Small Cell Lung Cancer Cell Growth Through Repressing DNA Replication Via Downregulating RPA1
    FULL PAPER British Journal of Cancer (2017) 117, 1621–1630 | doi: 10.1038/bjc.2017.319 Keywords: ailanthone; non-small cell lung cancer; DNA replication; RPA1; Chinese medicine Ailanthone inhibits non-small cell lung cancer cell growth through repressing DNA replication via downregulating RPA1 Zhongya Ni1, Chao Yao1, Xiaowen Zhu1, Chenyuan Gong1, Zihang Xu2, Lixin Wang3, Suyun Li4, Chunpu Zou2 and Shiguo Zhu*,1,3 1Laboratory of Integrative Medicine, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai 201203, PR China; 2Department of Internal Classic of Medicine, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai 201203, PR China; 3Department of Immunology and Pathogenic Biology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai 201203, PR China and 4Department of Pathology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai 201203, PR China Background: The identification of bioactive compounds from Chinese medicine plays a crucial role in the development of novel reagents against non-small cell lung cancer (NSCLC). Methods: High throughput screening assay and analyses of cell growth, cell cycle, apoptosis, cDNA microarray, BrdU incorporation and gene expression were performed. Results: Ailanthone (Aila) suppressed NSCLC cell growth and colony formation in vitro and inhibited NSCLC tumour growth in subcutaneously xenografted and orthotopic lung tumour models, leading to prolonged survival of tumour-bearing mice. Moreover, Aila induced cell cycle arrest in a dose-independent manner but did not induce apoptosis in all NSCLC cells.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
    [Show full text]
  • 0.5) in Stat3∆/∆ Compared with Stat3flox/Flox
    Supplemental Table 2 Genes down-regulated (<0.5) in Stat3∆/∆ compared with Stat3flox/flox Probe ID Gene Symbol Gene Description Entrez gene ID 1460599_at Ermp1 endoplasmic reticulum metallopeptidase 1 226090 1460463_at H60c histocompatibility 60c 670558 1460431_at Gcnt1 glucosaminyl (N-acetyl) transferase 1, core 2 14537 1459979_x_at Zfp68 zinc finger protein 68 24135 1459747_at --- --- --- 1459608_at --- --- --- 1459168_at --- --- --- 1458718_at --- --- --- 1458618_at --- --- --- 1458466_at Ctsa cathepsin A 19025 1458345_s_at Colec11 collectin sub-family member 11 71693 1458046_at --- --- --- 1457769_at H60a histocompatibility 60a 15101 1457680_a_at Tmem69 transmembrane protein 69 230657 1457644_s_at Cxcl1 chemokine (C-X-C motif) ligand 1 14825 1457639_at Atp6v1h ATPase, H+ transporting, lysosomal V1 subunit H 108664 1457260_at 5730409E04Rik RIKEN cDNA 5730409E04Rik gene 230757 1457070_at --- --- --- 1456893_at --- --- --- 1456823_at Gm70 predicted gene 70 210762 1456671_at Tbrg3 transforming growth factor beta regulated gene 3 21378 1456211_at Nlrp10 NLR family, pyrin domain containing 10 244202 1455881_at Ier5l immediate early response 5-like 72500 1455576_at Rinl Ras and Rab interactor-like 320435 1455304_at Unc13c unc-13 homolog C (C. elegans) 208898 1455241_at BC037703 cDNA sequence BC037703 242125 1454866_s_at Clic6 chloride intracellular channel 6 209195 1453906_at Med13l mediator complex subunit 13-like 76199 1453522_at 6530401N04Rik RIKEN cDNA 6530401N04 gene 328092 1453354_at Gm11602 predicted gene 11602 100380944 1453234_at
    [Show full text]
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
    [Show full text]
  • Research Article Characterization of the Equine Skeletal Muscle
    McGivney et al. BMC Genomics 2010, 11:398 http://www.biomedcentral.com/1471-2164/11/398 RESEARCH ARTICLE Open Access CharacterizationResearch article of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney1, Paul A McGettigan1, John A Browne1, Alexander CO Evans1,3, Rita G Fonseca2, Brendan J Loftus3, Amanda Lohan3, David E MacHugh1,3, Barbara A Murphy1, Lisa M Katz2 and Emmeline W Hill*1 Abstract Background: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.
    [Show full text]