DOCSLIB.ORG

Stomach-Specific Activation of Oncogenic KRAS and STAT3-Dependent Inflammation Cooperatively Promote Gastric Tumorigenesis in a Preclinical Model

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Stomach-Specific Activation of Oncogenic KRAS and STAT3-Dependent Inflammation Cooperatively Promote Gastric Tumorigenesis in a Preclinical Model Published OnlineFirst February 2, 2016; DOI: 10.1158/0008-5472.CAN-15-3089 Cancer Molecular and Cellular Pathobiology Research Stomach-Specific Activation of Oncogenic KRAS and STAT3-Dependent Inflammation Cooperatively Promote Gastric Tumorigenesis in a Preclinical Model Stefan Thiem1, Moritz F. Eissmann1, Joachim Elzer1, Anna Jonas2, Tracy L. Putoczki3, Ashleigh Poh1,3, Paul Nguyen1,3, Adele Preaudet3, Dustin Flanagan4, Elizabeth Vincan4, Paul Waring5, Michael Buchert1, Andrew Jarnicki1,6, and Matthias Ernst1 Abstract About 5% to 10% of human gastric tumors harbor oncogenic terized by excessive STAT3 activity. To assess the contribution of mutations in the KRAS pathway, but their presence alone is often STAT3 to the spontaneously developing gastric adenomas in insufficient for inducing gastric tumorigenesis, suggesting a gp130F/F mice, which carry a knockin mutation in the Il6 requirement for additional mutagenic events or microenviron- signal transducer (Il6st), we generated Tg(Tff1-CreERT2); fl fl mental stimuli, including inflammation. Assessing the contribu- Stat3 / ;gp130F/F mice that also harbor a conditional Stat3 knock- tion of such events in preclinical mouse models requires Cre out allele and found that tamoxifen administration conferred a recombinase–mediated conditional gene expression in stem or significant reduction in their tumor burden. Conversely, excessive þ progenitor cells of normal and transformed gastric epithelium. Kras activity in Tg(Tff1-CreERT2);KrasLSL-G12D/ ;gp130F/F mice We therefore constructed a bacterial artificial chromosome con- promoted more extensive gastric inflammation, metaplastic taining transgene (Tg), comprising the regulatory elements of the transformation, and tumorigenesis than observed in Tg(Tff1- þ trefoil factor 1 (Tff1) gene and the tamoxifen-inducible Cre CreERT2);KrasLSL-G12D/ mice. Collectively, our findings demon- recombinase (CreERT2)–coding sequence. The resulting Tg strate that advanced gastric tumorigenesis requires oncogenic (Tff1-CreERT2) mice were crossed with mice harboring condi- KRAS or BRAF in concert with aberrant STAT3 activation in tional oncogenic mutations in Kras or Braf. The administration of epithelial precursor cells of the glandular stomach, providing a þ tamoxifen to the resulting adult Tg(Tff1-CreERT2);KrasLSL-G12D/ new conditional model of gastric cancer in which to investigate þ and Tg(Tff1-CreERT2);BrafLSL-V600E/ mice resulted in gastric candidate therapeutic targets and treatment strategies. Cancer Res; metaplasia, inflammation, and adenoma development, charac- 76(8); 1–11. Ó2016 AACR. Introduction ities (1). The most prevalent form of gastric cancer is intestinal- type gastric adenocarcinoma, which progresses from superficial Despite a recent decline in mortality and incidence, gastric gastritis through stages of chronic gastritis, atrophic gastritis, cancer still accounts for one of the largest cancer-related mortal- metaplastic transformation, and dysplasia to invasive adenocar- cinoma (2). Although chronic infection with Helicobacter pylori (H. pylori) remains the main risk factor for intestinal-type gastric 1Cancer and Inflammation, Olivia Newton-John Cancer Research Insti- tute and School of Cancer Medicine La Trobe University, Heidelberg, cancer, others include high-salt diet and viral infections (2). Australia. 2Department of Multiple Sclerosis, The Florey Institute of Tumor initiation and progression is a multistep process that Neuroscience and Mental Health, Melbourne, Australia. 3Inflammation requires the acquisition of genetic alterations and growth-pro- Division, The Walter & Eliza Hall Institute of Medical Research and Department of Medical Biology University of Melbourne, Melbourne, moting conditions in the microenvironment. The most common Australia. 4Department of Anatomy and Neuroscience, University of activating mutations in gastric cancer driver genes affect KRAS, Melbourne, Melbourne, Australia. 5Department of Pathology, Univer- PI3K, and the receptor tyrosine kinases FGFR2, ERBB2, EGFR, 6 sity of Melbourne, Melbourne, Australia. School of Biomedical MET, and related signaling molecules (3). Meanwhile, chronic Sciences and Pharmacy, University of Newcastle, Newcastle, Australia. inflammation of the gastric mucosa, triggered by bacterial infec- Note: Supplementary data for this article are available at Cancer Research tion or other environmental factors, can initiate premalignant Online (http://cancerres.aacrjournals.org/). metaplastic transformation, which often results in the loss of acid- S. Thiem and M.F. Eissmann contributed equally to this article. producing parietal cells (4). Accordingly, the excessive inflamma- Corresponding Author: Matthias Ernst, Olivia Newton-John Cancer Research tory response of the gastric epithelium of gp130F/F mice, a vali- Institute and School of Cancer Medicine at La Trobe University, 145 Studley Rd, dated preclinical model for early stage intestinal-type gastric Heidelberg, Victoria 3084, Australia. Phone: 613-9496-9775; Fax: 613-9496- cancer in humans, is associated with intestinal metaplasia and 5334; E-mail: [email protected] inevitably triggers adenoma formation in the most distal part of doi: 10.1158/0008-5472.CAN-15-3089 the stomach, referred to as antrum (5). Meanwhile, aberrant Ó2016 American Association for Cancer Research. activation of Kras induces hyperplasia in many epithelial tissues www.aacrjournals.org OF1 Downloaded from cancerres.aacrjournals.org on October 2, 2021. © 2016 American Association for Cancer Research. Published OnlineFirst February 2, 2016; DOI: 10.1158/0008-5472.CAN-15-3089 Thiem et al. and, in the gastric epithelium, is associated with some hallmarks ATG initiation codon in the Tff1 locus. We injected the resulting of spasmolytic peptide–expressing metaplasia (SPEM) and pseu- BAC transgene in the pronucleus of CBB6F1-derived one-cell dointestinal metaplasia (6). However, oncogenic Kras activation embryos and genotyped transgenic founder mice and their off- in isolation is usually insufficient to trigger the formation of spring by PCR (refer to Supplementary Methods). gastric adenomas (7, 8). Thus, akin to the paradigms for the intestinal epithelium, gastric tumorigenesis may also depend on Tamoxifen administration the sequential acquisition of mutations within the precancerous Tamoxifen (Sigma T5648) was dissolved in 100% ethanol metaplastic epithelium or require a permissive tumor microen- (Sigma) and diluted 1:10 in sunflower oil (Sigma). Mice were fl vironment characterized by subclinical in ammation. injected intraperitoneally (100 mL) for 5 consecutive days with The formation of solid tumors is widely believed to depend on tamoxifen (1 mg/20 g body weight; twice daily) or vehicle, unless cancer stem cells, which, at least in the case of the intestinal indicated otherwise. The tamoxifen-containing emulsions were epithelium, express similar markers as their nontransformed prepared freshly every 3 days. tissue stem cells. Accordingly, the gastrointestinal stem cell marker locus Lgr5 can confer Cre recombinase–mediated cellular trans- b formation at the base of the glands of the pylorus and corpus -Gal staining region of the stomach (9). However, the higher abundance of Stomachs and intestines were opened longitudinally, washed Lgr5-positive stem cells in the intestinal epithelium results in three times in PBS by vigorous shaking, and pinned out on fi lethal intestinal tumorigenesis, preventing the analysis of gastric silicone-coated plates. Tissues were pre xed in 4% paraformal- fl fl tumor formation in corresponding Lgr5CreERT2;Apc / mice, which dehyde (PFA; Sigma) for one hour at 4 C, washed three times with b harbor conditional null alleles of the tumor suppressor gene Apc -Gal Wash Buffer (20 minutes/room temperature), and incu- fi bated in b-Gal Staining Solution (refer to Supplementary Meth- (9). Meanwhile, Cre expression that is largely con ned to com- mitted gastric epithelial progenitors in Atp4b-Cre or Tg(Tff2- ods) at 37 C overnight. Photographs were taken and the organs fi CreERT2) mice is insufficient to reproducibly and reliably trans- were xed in 2% PFA (Sigma) at 4 C overnight, transferred to 70% fi duce tumorigenesis, and neither of these Cre-drivers have been ethanol, paraf n sectioned, and counterstained with Nuclear Fast tested for their capacity to confer recombinase activity within Red. established tumors (10, 11). We therefore exploited the regulatory sequences of the stomach-specific trefoil factor 1 (Tff1) gene, YFP detection which is primarily expressed in the epithelium of the glandular Following stomach dissection, specimens were washed in PBS, stomach within the corpus and antrum, and to a lesser extent also fixed in 4% PFA solution (Electron Microscopy Sciences) over- in the neoplastic counterpart in gastric cancer (12, 13). Impor- night, incubated in 30% and 50% sucrose/PBS (w/v) solution, tantly, Tff1 deficiency can give rise to gastric tumorigenesis in mice embedded in OCT (Tissue-Tek Sakura), and snap frozen on dry through a cell-intrinsic mechanism (14), arguing that Tff1-expres- ice. Frozen stomach sections (8 mm) were counterstained with sing gastric epithelium can provide the cell of origin for gastric DAPI before mounting. YFP (shown as green) and DAPI (shown cancer. We therefore exploited bacterial artificial chromosome as blue) were imaged using a confocal microscope (Zeiss LSM (BAC) transgenesis to confer tamoxifen-inducible CreERT2 activ- 780). ity in the glandular stomach of corresponding transgenic Tg(Tff1- CreERT2) mice.
Load more

Recommended publications
  • Chromosomal Aberrations in Head and Neck Squamous Cell Carcinomas in Norwegian and Sudanese Populations by Array Comparative Genomic Hybridization
    825-843 12/9/08 15:31 Page 825 ONCOLOGY REPORTS 20: 825-843, 2008 825 Chromosomal aberrations in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization ERIC ROMAN1,2, LEONARDO A. MEZA-ZEPEDA3, STINE H. KRESSE3, OLA MYKLEBOST3,4, ENDRE N. VASSTRAND2 and SALAH O. IBRAHIM1,2 1Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91; 2Department of Oral Sciences - Periodontology, Faculty of Medicine and Dentistry, University of Bergen, Årstadveien 17, 5009 Bergen; 3Department of Tumor Biology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Montebello, 0310 Oslo; 4Department of Molecular Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway Received January 30, 2008; Accepted April 29, 2008 DOI: 10.3892/or_00000080 Abstract. We used microarray-based comparative genomic logical parameters showed little correlation, suggesting an hybridization to explore genome-wide profiles of chromosomal occurrence of gains/losses regardless of ethnic differences and aberrations in 26 samples of head and neck cancers compared clinicopathological status between the patients from the two to their pair-wise normal controls. The samples were obtained countries. Our findings indicate the existence of common from Sudanese (n=11) and Norwegian (n=15) patients. The gene-specific amplifications/deletions in these tumors, findings were correlated with clinicopathological variables. regardless of the source of the samples or attributed We identified the amplification of 41 common chromosomal carcinogenic risk factors. regions (harboring 149 candidate genes) and the deletion of 22 (28 candidate genes). Predominant chromosomal alterations Introduction that were observed included high-level amplification at 1q21 (harboring the S100A gene family) and 11q22 (including Head and neck squamous cell carcinoma (HNSCC), including several MMP family members).
    [Show full text]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2015/0072349 A1 Diamandis Et Al
    US 201500 72349A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0072349 A1 Diamandis et al. (43) Pub. Date: Mar. 12, 2015 (54) CANCER BOMARKERS AND METHODS OF (52) U.S. Cl. USE CPC. G0IN33/57484 (2013.01); G0IN 2333/705 (2013.01) (71) Applicant: University Health Network, Toronto USPC ......................................... 435/6.12: 435/7.94 (CA) (57) ABSTRACT A method of evaluating a probability a Subject has a cancer, (72) Inventors: Eleftherios P. Diamandis, Toronto diagnosing a cancer and/or monitoring cancer progression (CA); Ioannis Prassas, Toronto (CA); comprising: a. measuring an amount of a biomarker selected Shalini Makawita, Toronto (CA); from the group consisting of CUZD1 and/or LAMC2 and/or Caitlin Chrystoja, Toronto (CA); Hari the group CUZD1, LAMC2, AQP8, CELA2B, CELA3B, M. Kosanam, Maple (CA) CTRB1, CTRB2, GCG, IAPP, INS, KLK1, PNLIPRP1, PNLIPRP2, PPY, PRSS3, REG3G, SLC30A8, KLK3, NPY, (21) Appl. No.: 14/385,449 PSCA, RLN1, SLC45A3, DSP GP73, DSG2, CEACAM7, CLCA1, GPA33, LEFTY1, ZG16, IRX5, LAMP3, MFAP4, (22) PCT Fled: Mar. 15, 2013 SCGB1A1, SFTPC, TMEM100, NPY, PSCA RLN1 and/or SLC45A3 in a test sample from a subject with cancer; (86) PCT NO.: PCT/CA2O13/OOO248 wherein the cancer is pancreas cancer if CUZD1, LAMC2, S371 (c)(1), AQP8, CELA2B, CELA3B, CTRB1, CTRB2, GCG, LAPP (2) Date: Sep. 23, 2014 INS, KLK1, PNLIPRP1, PNLIPRP2, PPY, PRSS3, REG3G, SLC30A8, DSP GP73 and/or DSG2 is selected; the cancer is colon cancer if CEACAM7, CLCA1, GPA33, LEFTY 1 and/ Related U.S. Application Data or ZG16 is selected, the cancer is lung cancer if IRX5, (60) Provisional application No.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • PMC6851141.Pdf
    ARTICLE https://doi.org/10.1038/s41467-019-12515-9 OPEN Genome-wide association study of eosinophilic granulomatosis with polyangiitis reveals genomic loci stratified by ANCA status Paul A Lyons et al.# Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare inflammatory disease of unknown cause. 30% of patients have anti-neutrophil cytoplasmic antibodies (ANCA) spe- 1234567890():,; cific for myeloperoxidase (MPO). Here, we describe a genome-wide association study in 676 EGPA cases and 6809 controls, that identifies 4 EGPA-associated loci through conventional case-control analysis, and 4 additional associations through a conditional false discovery rate approach. Many variants are also associated with asthma and six are associated with eosi- nophil count in the general population. Through Mendelian randomisation, we show that a primary tendency to eosinophilia contributes to EGPA susceptibility. Stratification by ANCA reveals that EGPA comprises two genetically and clinically distinct syndromes. MPO+ ANCA EGPA is an eosinophilic autoimmune disease sharing certain clinical features and an HLA-DQ association with MPO+ ANCA-associated vasculitis, while ANCA-negative EGPA may instead have a mucosal/barrier dysfunction origin. Four candidate genes are targets of therapies in development, supporting their exploration in EGPA. *email: [email protected] #A full list of authors and their affiliations appears at the end of the paper. NATURE COMMUNICATIONS | (2019) 10:5120 | https://doi.org/10.1038/s41467-019-12515-9 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-12515-9 osinophilic granulomatosis with polyangiitis (EGPA), once 176 (33%) were positive for ANCA, and of the 164 who were Enamed Churg-Strauss syndrome, has a unique combination positive for specific ANCA by ELISA, 159 (97%) had MPO+ of clinical features that have some overlap with the other ANCA and five PR3 + ANCA.
    [Show full text]
  • GPA33 Antibody
    Efficient Professional Protein and Antibody Platforms GPA33 Antibody Basic information: Catalog No.: UPA61087 Source: Rabbit Size: 50ul/100ul Clonality: polyclonal Concentration: 1mg/ml Isotype: Rabbit IgG Purification: affinity purified by Protein A Useful Information: WB:1:500-2000 Applications: IHC-P:1:400-800 Reactivity: Human, Mouse, Rat Specificity: This antibody recognizes GPA33 protein. Immunogen: KLH conjugated synthetic peptide derived from human GPA33 151-280/319 Description: May play a role in cell-cell recognition and signaling. Uniprot: Q9JKA5 Human BiowMW: 33 KDa Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Storage: Store at 4°C short term and -20°C long term. Avoid freeze-thaw cycles. Note: For research use only, not for use in diagnostic procedure. Data: Tissue/cell: human gastric carcinoma; 4% Para- formaldehyde-fixed and paraffin-embedded; An- tigen retrieval: citrate buffer at 37℃ for 20 min; Incubation: Anti-GPA33 Polyclonal Antibody, Un- conjugated 1:200, overnight at 4℃, followed by conjugation to the secondary antibody and DAB- staining Tissue/cell: human gastric carcinoma; 4% Para- formaldehyde-fixed and paraffin-embedded; An- tigen retrieval: citrate buffer at 37℃ for 20 min; Incubation: Anti-GPA33 Polyclonal Antibody, Un- conjugated 1:200, overnight at 4℃, followed by conjugation to the secondary antibody and DAB- staining Gene Universal Technology Co. Ltd www.universalbiol.com Tel: 0550-3121009 E-mail: [email protected] Efficient Professional Protein and Antibody Platforms Sample: Stomach (Rat) Lysate at 40 ug Primary: Anti-GPA33 at 1/1000 dilution Secondary: IRDye800CW Goat Anti-Rabbit IgG at 1/20000 dilution Predicted band size: 33 kD Observed band size: 30 kD Paraformaldehyde-fixed, paraffin embedded at 37 ℃ for 30min; Antibody incubation with (GPA33) Polyclonal Antibody, Unconjugated at 1:400 overnight at 4℃, followed by operating according to SP Kit(Rabbit) instructionsand DAB staining.
    [Show full text]
  • Rna-Sequencing Applications: Gene Expression Quantification and Methylator Phenotype Identification
    The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 8-2013 RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION Guoshuai Cai Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Bioinformatics Commons, Computational Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Cai, Guoshuai, "RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION" (2013). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 386. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/386 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION
    [Show full text]
  • Precise Integration of Inducible Transcriptional Elements (Priite
    Published online 4 May 2017 Nucleic Acids Research, 2017, Vol. 45, No. 13 e123 doi: 10.1093/nar/gkx371 Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression Rita Pinto1,2,3,4, Lars Hansen4, John Hintze4, Raquel Almeida1,2,3,5, Sylvester Larsen6,7, Mehmet Coskun8,9, Johanne Davidsen6, Cathy Mitchelmore6, Leonor David1,2,3, Jesper Thorvald Troelsen6 and Eric Paul Bennett4,* 1i3S, Instituto de Investigac¸ao˜ e Inovac¸ao˜ em Saude,´ Universidade do Porto, Porto, Portugal, 2Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal, 3Faculty of Medicine of the University of Porto, Porto, Portugal, 4Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, 5Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal, 6Department of Science and Environment, Roskilde University, Roskilde, Denmark, 7Department of Clinical Immunology, Naestved Hospital, Naestved, Denmark, 8Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark and 9The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Received October 03, 2016; Revised March 30, 2017; Editorial Decision April 10, 2017; Accepted April 27, 2017 ABSTRACT INTRODUCTION Tetracycline-based inducible systems provide pow- Historically, analysis of the molecular genetic mechanisms erful methods for functional studies where gene ex- underlying cell fate and animal phenotypes has been studied pression can be controlled. However, the lack of tight by abrogating gene function in cellular and animal model control of the inducible system, leading to leakiness systems.
    [Show full text]
  • Anti-GPA33 Antibody
    D220703 Anti-GPA33 antibody Cat. No. D220703 Package 25 μl/100 μl/200 μl Storage -20°C, pH7.4 PBS, 0.05% NaN3, 40% Glycerol Product overview Description A n ti-GPA33 rabbit polyclonal antibody Applications ELISA, WB, IHC Immunogen Fusion protein of human GPA33 Reactivity Human Content 0 .2 mg/ml Host species Rabbit Ig class Immunogen-specific rabbit IgG Purification Antigen affinity purification Target information Symbol GPA33 Full name glycoprotein A33 (transmembrane) Synonyms A33 Swissprot Q99795 Target Background The glycoprotein encoded by this gene is a cell surface antigen that is expressed in greater than 95% of human colon cancers. The open reading frame encodes a 319-amino acid polypeptide having a putative secretory signal sequence and 3 potential glycosylation sites. The predicted mature protein has a 213-amino acid extracellular region, a single transmembrane domain, and a 62-amino acid intracellular tail. The sequence of the extracellular region contains 2 domains characteristic of the CD2 subgroup of the immunoglobulin (Ig) superfamily. Sangon Biotech Applications Immunohistochemistry Predicted cell location: Cytoplasm and membrane Predicted cell location: Cytoplasm and membrane Positive control: Human colon cancer Positive control: Human thyroid cancer Recommended dilution: 50-200 Recommended dilution: 50-200 The image on the left is immunohistochemistry of paraffin-embedded The image on the left is immunohistochemistry of paraffin-embedded Human colon cancer tissue using D220703(GPA33 Antibody) at Human thyroid cancer
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
    Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors.
    [Show full text]
  • Genome-Wide Association Study of Endo-Parasite Phenotypes Using
    Twomey et al. Genet Sel Evol (2019) 51:15 https://doi.org/10.1186/s12711-019-0457-7 Genetics Selection Evolution RESEARCH ARTICLE Open Access Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle Alan J. Twomey1,2, Donagh P. Berry1, Ross D. Evans3, Michael L. Doherty2, David A. Graham4 and Deirdre C. Purfeld1* Abstract Background: Quantitative genetic studies suggest the existence of variation at the genome level that afects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites. Methods: Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 geno- typed dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic efects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were avail- able for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals.
    [Show full text]