DOCSLIB.ORG

0.5) in Stat3∆/∆ Compared with Stat3flox/Flox

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

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 1300002K09Rik RIKEN cDNA 1300002K09 gene 74152 1453144_at Pisd-ps3 phosphatidylserine decarboxylase, pseudogene 3 66776 1447831_s_at Mtmr7 myotubularin related protein 7 54384 1447655_x_at Sox6 SRY-box containing gene 6 20679 1447584_s_at Myct1 myc target 1 68632 1447343_at Nrp2 neuropilin 2 18187 1447299_at --- --- --- 1447284_at Trem1 triggering receptor expressed on myeloid cells 1 58217 1447260_at Gm10499 /// Gm8909 predicted gene 10499 /// predicted gene 8909 667977 /// 69717 1447223_at --- --- --- 1447116_at --- --- --- 1447075_at LOC100503847 hypothetical LOC100503847 100503847 1446337_at Htt huntingtin 15194 1446323_at Atf7ip activating transcription factor 7 interacting protein 54343 1445824_at Zfp458 zinc finger protein 458 238690 1445605_s_at Fam135a family with sequence similarity 135, member A 68187 1445188_at --- --- --- 1445101_at --- --- --- 1444900_at D18Ertd289e DNA segment, Chr 18, ERATO Doi 289, expressed 52490 1444790_at Hsbp1l1 heat shock factor binding protein 1-like 1 66255 1444740_at Lass3 LAG1 homolog, ceramide synthase 3 545975 1444620_at --- --- --- 1444619_x_at Psmb8 proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional 16913 peptidase 7) 1444487_at Lrat lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase) 79235 1443913_at --- --- --- 1443584_at 1110028C15Rik RIKEN cDNA 1110028C15 gene 68691 1443480_at --- --- --- 1443430_at --- --- --- 1442979_at --- --- --- 1442273_at Ccdc158 coiled-coil domain containing 158 320696 1441975_at Acpp acid phosphatase, prostate 56318 1441971_at --- --- --- 1441941_x_at Serpinb5 serine (or cysteine) peptidase inhibitor, clade B, member 5 20724 1441876_x_at Zfp93 zinc finger protein 93 22755 1441855_x_at Cxcl1 chemokine (C-X-C motif) ligand 1 14825 1441438_at Gpc6 glypican 6 23888 1441417_at Stt3a STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae) 16430 1441202_at --- --- --- 1440589_at --- --- --- 1440440_at --- --- --- 1440339_at Enpp1 ectonucleotide pyrophosphatase/phosphodiesterase 1 18605 1440336_at C130013H08Rik RIKEN cDNA C130013H08 gene 100327264 1440307_at Gtf3c2 general transcription factor IIIC, polypeptide 2, beta 71752 1440264_at --- --- --- 1440228_at Ranbp6 RAN binding protein 6 240614 1440052_at --- --- --- 1439878_at Ivl involucrin 16447 1439703_at Cd200r1 CD200 receptor 1 57781 1439695_a_at Kif20b kinesin family member 20B 240641 1439620_at Car13 carbonic anhydrase 13 71934 1439562_at F730047E07Rik RIKEN cDNA F730047E07 gene 212377 1439019_at Fras1 Fraser syndrome 1 homolog (human) 231470 1438987_at Fam71d family with sequence similarity 71, member D 70897 1438701_at Bicd1 bicaudal D homolog 1 (Drosophila) 12121 1438515_at Zfp207 zinc finger protein 207 22680 1438426_at Shisa4 shisa homolog 4 (Xenopus laevis) 77552 1437989_at Pde8b phosphodiesterase 8B 218461 1437842_at Plcxd1 phosphatidylinositol-specific phospholipase C, X domain containing 1 403178 1437789_at Birc6 baculoviral IAP repeat-containing 6 12211 1437673_at Wnt5a wingless-related MMTV integration site 5A 22418 1437580_s_at Nek2 NIMA (never in mitosis gene a)-related expressed kinase 2 18005 1437264_at BC051142 cDNA sequence BC051142 407788 1436852_at E130308A19Rik RIKEN cDNA E130308A19 gene 230259 1436706_at Mmgt1 membrane magnesium transporter 1 236792 1436590_at Ppp1r3b protein phosphatase 1, regulatory (inhibitor) subunit 3B 244416 1436538_at Ankrd37 ankyrin repeat domain 37 654824 1436251_at Pde1c phosphodiesterase 1C 18575 1436118_at Vangl2 vang-like 2 (van gogh, Drosophila) 93840 1435836_at Pdk1 pyruvate dehydrogenase kinase, isoenzyme 1 228026 1435752_s_at Abcc9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 20928 1435472_at Kremen1 kringle containing transmembrane protein 1 84035 1435307_at Ankrd34b ankyrin repeat domain 34B 218440 1435264_at Emilin2 elastin microfibril interfacer 2 246707 1435236_at Tceanc transcription elongation factor A (SII) N-terminal and central domain containing 245695 1435190_at Chl1 cell adhesion molecule with homology to L1CAM 12661 1435075_at Tmem106b transmembrane protein 106B 71900 1435069_at BC064078 cDNA sequence BC064078 408064 1435065_x_at Vav2 vav 2 oncogene 22325 1434855_at Amdhd2 amidohydrolase domain containing 2 245847 1434749_at BC067068 cDNA sequence BC067068 216292 1434725_at Gramd1c GRAM domain containing 1C 207798 1434711_at BC030867 cDNA sequence BC030867 217216 1434539_at Lrrn3 leucine rich repeat protein 3, neuronal 16981 1433615_at Tmem117 transmembrane protein 117 320709 1432906_at --- --- --- 1432391_at Ccdc21 coiled-coil domain containing 21 70012 1432088_at Veph1 ventricular zone expressed PH domain homolog 1 (zebrafish) 72789 1431754_at 4930578N16Rik RIKEN cDNA 4930578N16 gene 75051 1431269_at Prdx4 peroxiredoxin 4 53381 1431220_at 2810416G20Rik RIKEN cDNA 2810416G20 gene 100040353 1431131_s_at A630007B06Rik RIKEN cDNA A630007B06 gene 213993 1430995_at Tmx3 thioredoxin-related transmembrane protein 3 67988 1430257_at Card11 caspase recruitment domain family, member 11 108723 1429277_at --- --- --- 1429197_s_at Rabgap1l RAB GTPase activating protein 1-like 29809 1429123_at Rab27a RAB27A, member RAS oncogene family 11891 1429098_s_at Nhej1 nonhomologous end-joining factor 1 75570 1429021_at Epha4 Eph receptor A4 13838 1428692_at Hddc3 HD domain containing 3 68695 1428304_at Esco2 establishment of cohesion 1 homolog 2 (S. cerevisiae) 71988 1460521_a_at Obfc2a oligonucleotide/oligosaccharide-binding fold containing 2A 109019 1460438_at Lysmd1 LysM, putative peptidoglycan-binding, domain containing 1 217779 1460427_a_at Adam28 a disintegrin and metallopeptidase domain 28 13522 1460423_x_at Gm5571 /// Igk-V1 predicted gene 5571 /// immunoglobulin kappa chain variable 1 (V1) 16081 /// 434025 1460364_at Gtf2ird1 general transcription factor II I repeat domain-containing 1 57080 1460329_at B4galt6 UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6 56386 1460247_a_at Skp2 S-phase kinase-associated protein 2 (p45) 27401 1460197_a_at Steap4 STEAP family member 4 117167 1459902_at 2700007P21Rik RIKEN cDNA 2700007P21 gene 212772 1456174_x_at Ndrg1 N-myc downstream regulated gene 1 17988 1456169_at Tstd1 thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 226654 1455898_x_at Slc2a3 solute carrier family 2 (facilitated glucose transporter), member 3 20527 1455892_x_at --- --- --- 1455475_at 3110057O12Rik RIKEN cDNA 3110057O12 gene 269423 1455466_at Gpr133 G protein-coupled receptor 133 243277 1455435_s_at Chdh choline dehydrogenase 218865 1455053_a_at Dcun1d1 DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae) 114893 1454849_x_at Clu clusterin 12759 1453748_a_at Kif23 kinesin family member 23 71819 1453596_at Id2 inhibitor of DNA binding 2 15902 1453427_at Csnk2a1 casein kinase 2, alpha 1 polypeptide 12995 1453360_a_at Tex9 testis expressed gene 9 21778 1453278_a_at Clip4 CAP-GLY domain containing linker protein family, member 4 78785 1452801_at Pigk phosphatidylinositol glycan anchor biosynthesis, class K 329777 1452614_at Bcl2l15 BCLl2-like 15 229672 1452593_a_at Tceb1 transcription elongation factor B (SIII), polypeptide 1 67923 1452557_a_at --- --- --- 1452463_x_at Gm10883 predicted gene 10883 384419 1452426_x_at --- --- --- 1452417_x_at Gm10883 /// Gm1420 /// predicted gene 10883 /// predicted gene 1420 /// predicted gene 7202 /// 110759 /// 16071 /// 16114 /// 384419 /// Gm7202 /// Igk-C /// Igk-J1 immunoglobulin kappa chain, constant region /// immunoglobulin kappa chain, 546213 /// 637227 /// Igk-V28 joining region, 1 /// immunoglobulin kappa chain variable 28 (V28) 1452415_at Actn1 actinin, alpha 1 109711 1452391_at Cxadr coxsackie virus and adenovirus receptor 13052 1452314_at Kif11 kinesin family member 11 16551 1452297_at Ccnt2 cyclin T2 72949 1452277_at Arsg arylsulfatase G 74008 1452114_s_at Igfbp5 insulin-like growth factor binding protein 5 16011 1452072_at Myct1 myc target 1 68632 1451671_at Gorasp1 golgi reassembly stacking protein 1 74498 1451538_at
Recommended publications
  • Table 2. Functional Classification of Genes Differentially Regulated After HOXB4 Inactivation in HSC/Hpcs

    Table 2. Functional Classification of Genes Differentially Regulated After HOXB4 Inactivation in HSC/Hpcs

    Table 2. Functional classification of genes differentially regulated after HOXB4 inactivation in HSC/HPCs Symbol Gene description Fold-change (mean ± SD) Signal transduction Adam8 A disintegrin and metalloprotease domain 8 1.91 ± 0.51 Arl4 ADP-ribosylation factor-like 4 - 1.80 ± 0.40 Dusp6 Dual specificity phosphatase 6 (Mkp3) - 2.30 ± 0.46 Ksr1 Kinase suppressor of ras 1 1.92 ± 0.42 Lyst Lysosomal trafficking regulator 1.89 ± 0.34 Mapk1ip1 Mitogen activated protein kinase 1 interacting protein 1 1.84 ± 0.22 Narf* Nuclear prelamin A recognition factor 2.12 ± 0.04 Plekha2 Pleckstrin homology domain-containing. family A. (phosphoinosite 2.15 ± 0.22 binding specific) member 2 Ptp4a2 Protein tyrosine phosphatase 4a2 - 2.04 ± 0.94 Rasa2* RAS p21 activator protein 2 - 2.80 ± 0.13 Rassf4 RAS association (RalGDS/AF-6) domain family 4 3.44 ± 2.56 Rgs18 Regulator of G-protein signaling - 1.93 ± 0.57 Rrad Ras-related associated with diabetes 1.81 ± 0.73 Sh3kbp1 SH3 domain kinase bindings protein 1 - 2.19 ± 0.53 Senp2 SUMO/sentrin specific protease 2 - 1.97 ± 0.49 Socs2 Suppressor of cytokine signaling 2 - 2.82 ± 0.85 Socs5 Suppressor of cytokine signaling 5 2.13 ± 0.08 Socs6 Suppressor of cytokine signaling 6 - 2.18 ± 0.38 Spry1 Sprouty 1 - 2.69 ± 0.19 Sos1 Son of sevenless homolog 1 (Drosophila) 2.16 ± 0.71 Ywhag 3-monooxygenase/tryptophan 5- monooxygenase activation protein. - 2.37 ± 1.42 gamma polypeptide Zfyve21 Zinc finger. FYVE domain containing 21 1.93 ± 0.57 Ligands and receptors Bambi BMP and activin membrane-bound inhibitor - 2.94 ± 0.62
  • Diseasespecific and Inflammationindependent Stromal

    Diseasespecific and Inflammationindependent Stromal

    Full Length Arthritis & Rheumatism DOI 10.1002/art.37704 Disease-specific and inflammation-independent stromal alterations in spondyloarthritis synovitis Nataliya Yeremenko1,2, Troy Noordenbos1,2, Tineke Cantaert1,3, Melissa van Tok1,2, Marleen van de Sande1, Juan D. Cañete4, Paul P. Tak1,5*, Dominique Baeten1,2 1Department of Clinical Immunology and Rheumatology and 2Department of Experimental Immunology, Academic Medical Center/University of Amsterdam, the Netherlands. 3Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. 4Department of Rheumatology, Hospital Clinic de Barcelona and IDIBAPS, Spain. 5Arthrogen B.V., Amsterdam, the Netherlands. *Currently also: GlaxoSmithKline, Stevenage, U.K. Corresponding author: Dominique Baeten, MD, PhD, Department of Clinical Immunology and Rheumatology, F4-105, Academic Medical Center/University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands. E-mail: [email protected] This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1002/art.37704 © 2012 American College of Rheumatology Received: Apr 11, 2012; Revised: Jul 25, 2012; Accepted: Sep 06, 2012 Arthritis & Rheumatism Page 2 of 36 Abstract Objective: The molecular processes driving the distinct patterns of synovial inflammation and tissue remodelling in spondyloarthritis (SpA) versus rheumatoid arthritis (RA) remain largely unknown. Therefore, we aimed to identify novel and unsuspected disease- specific pathways in SpA by a systematic and unbiased synovial gene expression analysis. Methods: Differentially expressed genes were identified by pan-genomic microarray and confirmed by quantitative PCR and immunohistochemistry using synovial tissue biopsies of SpA (n=63), RA (n=28) and gout (n=9) patients.
  • Inherited Monogenic Defects of Ceramide Metabolism Molecular

    Inherited Monogenic Defects of Ceramide Metabolism Molecular

    Clinica Chimica Acta 495 (2019) 457–466 Contents lists available at ScienceDirect Clinica Chimica Acta journal homepage: www.elsevier.com/locate/cca Review Inherited monogenic defects of ceramide metabolism: Molecular bases and diagnoses T ⁎⁎ Patricia Dubota,b, Frédérique Sabourdya,b, Jitka Rybovac,Jeffrey A. Medinc,d, , ⁎ Thierry Levadea,b, a Laboratoire de Biochimie Métabolique, Centre de Référence en Maladies Héréditaires du Métabolisme, Institut Fédératif de Biologie, CHU de Toulouse, Toulouse, France b INSERM UMR1037, CRCT (Cancer Research Center of Toulouse), Université Paul Sabatier, Toulouse, France c Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA d Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA ABSTRACT Ceramides are membrane lipids implicated in the regulation of numerous biological functions. Recent evidence suggests that specific subsets of molecular species of ceramide may play distinct physiological roles. The importance of this family of molecules in vertebrates is witnessed by the deleterious consequences of genetic alterations in ceramide metabolism. This brief review summarizes the clinical presentation of human disorders due to the deficiency of enzymes involved either in the biosynthesis or the degradation of ceramides. Information on the possible underlying pathophysiological mechanisms is also provided, based on knowledge gathered from animal models of these inherited rare conditions. When appropriate, tools for chemical and molecular diagnosis of these disorders and therapeutic options are also presented. 1. Introduction/foreword relationships that are relevant for unraveling the biological role of these genes and gene products in humans. Studies on ceramides and sphingolipid metabolism have attracted a lot of attention recently. This is largely related to the multiplicity of 2.
  • Kinesin Family Member 18B Regulates the Proliferation and Invasion Of

    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.
  • Edinburgh Research Explorer

    Edinburgh Research Explorer

    Edinburgh Research Explorer International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list Citation for published version: Davenport, AP, Alexander, SPH, Sharman, JL, Pawson, AJ, Benson, HE, Monaghan, AE, Liew, WC, Mpamhanga, CP, Bonner, TI, Neubig, RR, Pin, JP, Spedding, M & Harmar, AJ 2013, 'International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list: recommendations for new pairings with cognate ligands', Pharmacological reviews, vol. 65, no. 3, pp. 967-86. https://doi.org/10.1124/pr.112.007179 Digital Object Identifier (DOI): 10.1124/pr.112.007179 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Pharmacological reviews Publisher Rights Statement: U.S. Government work not protected by U.S. copyright General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. 2021 1521-0081/65/3/967–986$25.00 http://dx.doi.org/10.1124/pr.112.007179 PHARMACOLOGICAL REVIEWS Pharmacol Rev 65:967–986, July 2013 U.S.
  • Enhancing Skin Health: by Oral Administration of Natural Compounds and Minerals with Implications to the Dermal Microbiome

    Enhancing Skin Health: by Oral Administration of Natural Compounds and Minerals with Implications to the Dermal Microbiome

    Review Enhancing Skin Health: By Oral Administration of Natural Compounds and Minerals with Implications to the Dermal Microbiome David L. Vollmer 1, Virginia A. West 1 and Edwin D. Lephart 2,* 1 4Life Research, Scientific Research Division, Sandy, Utah 84070, USA; [email protected] (D.L.V.); [email protected] (V.A.W) 2 Department of Physiology, Developmental Biology and The Neuroscience Center, Brigham Young University, Provo, Utah 84602, USA * Correspondence: [email protected]; Tel.: +1-801-422-2006 Received: 23 August 2018; Accepted: 1 October 2018; Published: 7 October 2018 Abstract: The history of cosmetics goes back to early Egyptian times for hygiene and health benefits while the history of topical applications that provide a medicinal treatment to combat dermal aging is relatively new. For example, the term cosmeceutical was first coined by Albert Kligman in 1984 to describe topical products that afford both cosmetic and therapeutic benefits. However, beauty comes from the inside. Therefore, for some time scientists have considered how nutrition reflects healthy skin and the aging process. The more recent link between nutrition and skin aging began in earnest around the year 2000 with the demonstrated increase in peer-reviewed scientific journal reports on this topic that included biochemical and molecular mechanisms of action. Thus, the application of: (a) topical administration from outside into the skin and (b) inside by oral consumption of nutritionals to the outer skin layers is now common place and many journal reports exhibit significant improvement for both on a variety of dermal parameters. Therefore, this review covers, where applicable, the history, chemical structure, and sources such as biological and biomedical properties in the skin along with animal and clinical data on the oral applications of: (a) collagen, (b) ceramide, (c) β-carotene, (d) astaxanthin, (e) coenzyme Q10, (f) colostrum, (g) zinc, and (h) selenium in their mode of action or function in improving dermal health by various quantified endpoints.
  • 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.
  • Genome-Wide DNA Methylation Profiling Identifies Differential Methylation in Uninvolved Psoriatic Epidermis

    Genome-Wide DNA Methylation Profiling Identifies Differential Methylation in Uninvolved Psoriatic Epidermis

    Genome-Wide DNA Methylation Profiling Identifies Differential Methylation in Uninvolved Psoriatic Epidermis Deepti Verma, Anna-Karin Ekman, Cecilia Bivik Eding and Charlotta Enerbäck The self-archived postprint version of this journal article is available at Linköping University Institutional Repository (DiVA): http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-147791 N.B.: When citing this work, cite the original publication. Verma, D., Ekman, A., Bivik Eding, C., Enerbäck, C., (2018), Genome-Wide DNA Methylation Profiling Identifies Differential Methylation in Uninvolved Psoriatic Epidermis, Journal of Investigative Dermatology, 138(5), 1088-1093. https://doi.org/10.1016/j.jid.2017.11.036 Original publication available at: https://doi.org/10.1016/j.jid.2017.11.036 Copyright: Elsevier http://www.elsevier.com/ Genome-Wide DNA Methylation Profiling Identifies Differential Methylation in Uninvolved Psoriatic Epidermis Deepti Verma*a, Anna-Karin Ekman*a, Cecilia Bivik Edinga and Charlotta Enerbäcka *Authors contributed equally aIngrid Asp Psoriasis Research Center, Department of Clinical and Experimental Medicine, Division of Dermatology, Linköping University, Linköping, Sweden Corresponding author: Charlotta Enerbäck Ingrid Asp Psoriasis Research Center, Department of Clinical and Experimental Medicine, Linköping University SE-581 85 Linköping, Sweden Phone: +46 10 103 7429 E-mail: [email protected] Short title Differential methylation in psoriasis Abbreviations CGI, CpG island; DMS, differentially methylated site; RRBS, reduced representation bisulphite sequencing Keywords (max 6) psoriasis, epidermis, methylation, Wnt, susceptibility, expression 1 ABSTRACT Psoriasis is a chronic inflammatory skin disease with both local and systemic components. Genome-wide approaches have identified more than 60 psoriasis-susceptibility loci, but genes are estimated to explain only one third of the heritability in psoriasis, suggesting additional, yet unidentified, sources of heritability.
  • Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS

    Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS

    Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen,
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
  • Long, Noncoding RNA Dysregulation in Glioblastoma

    Long, Noncoding RNA Dysregulation in Glioblastoma

    cancers Review Long, Noncoding RNA Dysregulation in Glioblastoma Patrick A. DeSouza 1,2 , Xuan Qu 1, Hao Chen 1,3, Bhuvic Patel 1 , Christopher A. Maher 2,4,5,6 and Albert H. Kim 1,6,* 1 Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] (P.A.D.); [email protected] (X.Q.); [email protected] (H.C.); [email protected] (B.P.) 2 Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] 3 Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 4 Department of Biomedical Engineering, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 5 McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 6 Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA * Correspondence: [email protected] Simple Summary: Developing effective therapies for glioblastoma (GBM), the most common primary brain cancer, remains challenging due to the heterogeneity within tumors and therapeutic resistance that drives recurrence. Noncoding RNAs are transcribed from a large proportion of the genome and remain largely unexplored in their contribution to the evolution of GBM tumors. Here, we will review the general mechanisms of long, noncoding RNAs and the current knowledge of how these impact heterogeneity and therapeutic resistance in GBM. A better understanding of the molecular drivers required for these aggressive tumors is necessary to improve the management and outcomes Citation: DeSouza, P.A.; Qu, X.; of this challenging disease.
  • Product Description SALSA MLPA Probemix P476-A1 ZNRF3

    Product Description SALSA MLPA Probemix P476-A1 ZNRF3

    MRC-Holland ® Product Description version A1-02; Issued 25 September 2018 MLPA Product Description SALSA ® MLPA ® Probemix P476-A1 ZNRF3 To be used with the MLPA General Protocol. Version A1. New Product. Catalogue numbers: • P476-025R: SALSA MLPA Probemix P476 ZNRF3, 25 reactions. • P476-050R: SALSA MLPA Probemix P476 ZNRF3, 50 reactions. • P476-100R: SALSA MLPA Probemix P476 ZNRF3, 100 reactions. To be used in combination with a SALSA MLPA reagent kit, available for various number of reactions. MLPA reagent kits are either provided with FAM or Cy5.0 dye-labelled PCR primer, suitable for Applied Biosystems and Beckman capillary sequencers, respectively (see www.mlpa.com ). Certificate of Analysis: Information regarding storage conditions, quality tests, and a sample electropherogram from the current sales lot is available at www.mlpa.com . Precautions and warnings: For professional use only. Always consult the most recent product description AND the MLPA General Protocol before use: www.mlpa.com . It is the responsibility of the user to be aware of the latest scientific knowledge of the application before drawing any conclusions from findings generated with this product. General information: The SALSA MLPA Probemix P476 ZNRF3 is a research use only (RUO) assay for the detection of deletions and duplications in the ZNRF3 gene. ZNRF3 is an E3 ubiquitin-protein ligase that acts as a negative feedback regulator of Wnt signalling (Hao et al. 2012). Three independent studies show homozygous deletions of the ZNRF3 gene in 10 to 16% of adrenocortical carcinoma cases (Assié et al. 2014; Juhlin et al. 2015; Zheng et al. 2016). Moreover, in 51% of microsatellite stable colorectal cancers deletion events at the ZNRF3 locus are detected (Bond et al.