Ret Is a Multifunctional Coreceptor That Integrates Diffusible- and Contact-Axon Guidance Signals
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Legends for Supplemental Figures and Tables Figure S1. Expression of Tlx during retinogenesis. (A) Staged embryos were stained for β- galactosidase knocked into the Tlx locus to indicate Tlx expression. Tlx was expressed in the neural blast layer in the early phase of neural retina development (blue signal). (B) Expression of Tlx in neural retina was quantified using Q-PCR at multiple developmental stages. Figure S2. Expression of p27kip1 and cyclin D1 (Ccnd1) at various developmental stages in wild-type or Tlx-/- retinas. (A) Q-PCR analysis of p27kip1 mRNA expression. (B) Western blotting analysis of p27kip1 protein expression. (C) Q-PCR analysis of cyclin D1 mRNA expression. Figure S3. Q-PCR analysis of mRNA expression of Sf1 (A), Lrh1 (B), and Atn1 (C) in wild-type mouse retinas. RNAs from testis and liver were used as controls. Table S1. List of genes dysregulated both at E15.5 and P0 Tlx-/- retinas. Gene E15.5 P0 Cluste Gene Title Fold Fold r Name p-value p-value Change Change nuclear receptor subfamily 0, group B, Nr0b1 1.65 0.0024 2.99 0.0035 member 1 1 Pou4f3 1.91 0.0162 2.39 0.0031 POU domain, class 4, transcription factor 3 1 Tcfap2d 2.18 0.0000 2.37 0.0001 transcription factor AP-2, delta 1 Zic5 1.66 0.0002 2.02 0.0218 zinc finger protein of the cerebellum 5 1 Zfpm1 1.85 0.0030 1.88 0.0025 zinc finger protein, multitype 1 1 Pten 1.60 0.0155 1.82 0.0131 phospatase and tensin homolog 2 Itgb5 -1.85 0.0063 -1.85 0.0007 integrin beta 5 2 Gpr49 6.86 0.0001 15.16 0.0001 G protein-coupled receptor 49 3 Cmkor1 2.60 0.0007 2.72 0.0013 -
Gene Expression Profiles of Estrogen Receptor–Positive and Estrogen Receptor–Negative Breast Cancers Are Detectable in Histologically Normal Breast Epithelium
Published OnlineFirst November 8, 2010; DOI: 10.1158/1078-0432.CCR-10-1369 Clinical Cancer Human Cancer Biology Research Gene Expression Profiles of Estrogen Receptor–Positive and Estrogen Receptor–Negative Breast Cancers Are Detectable in Histologically Normal Breast Epithelium Kelly Graham1, Xijin Ge4, Antonio de las Morenas2, Anusri Tripathi3, and Carol L. Rosenberg1,2,3 Abstract Purpose: Previously, we found that gene expression in histologically normal breast epithelium (NlEpi) from women at high breast cancer risk can resemble gene expression in NlEpi from cancer-containing breasts. Therefore, we hypothesized that gene expression characteristic of a cancer subtype might be seen in NlEpi of breasts containing that subtype. Experimental Design: We examined gene expression in 46 cases of microdissected NlEpi from untreated women undergoing breast cancer surgery. From 30 age-matched cases [15 estrogen receptor (ER)þ,15ERÀ] we used Affymetryix U133A arrays. From 16 independent cases (9 ERþ,7ERÀ), we validated selected genes using quantitative real-time PCR (qPCR). We then compared gene expression between NlEpi and invasive breast cancer using four publicly available data sets. Results: We identified 198 genes that are differentially expressed between NlEpi from breasts with ERþ (NlEpiERþ) compared with ERÀ cancers (NlEpiERÀ). These include genes characteristic of ERþ and ERÀ cancers (e.g., ESR1, GATA3, and CX3CL1, FABP7). qPCR validated the microarray results in both the 30 original cases and the 16 independent cases. Gene expression in NlEpiERþ and NlEpiERÀ resembled gene expression in ERþ and ERÀ cancers, respectively: 25% to 53% of the genes or probes examined in four external data sets overlapped between NlEpi and the corresponding cancer subtype. -
Supplementary Table 1: Genes Affected by Anoikis. A, Ratio of Signal
Supplementary Table 1: Genes affected by anoikis. a, ratio of signal intensity of nonanchored cells anchorage dependent cells (CasKoSrc) over anchored cells; b, induced by Src transformation of Cx43KO cells; c, decreased by Src transformation of Cx43Ko cells; *, induced by normalization of Src transformed cells by neighboring nontransformed cells. Gene Symbol Probe Set Fold Changea Gene Name increased Selenbp1 1450699_at 23.22 selenium binding protein 1 Dscr1l1 1450243_a_at 10.77 Down syndrome critical region gene 1-like 1 Dscr1l1 1421425_a_at 4.29 Down syndrome critical region gene 1-like 1 Ttyh1 1426617_a_at 6.70 tweety homolog 1 (Drosophila) 5730521E12Rik 1419065_at 6.16 RIKEN cDNA 5730521E12 gene c 6330406I15Rik 1452244_at 5.87 RIKEN cDNA 6330406I15 gene AF067063 1425160_at 5.73 clone L2 uniform group of 2-cell-stage gene family mRNA Morc 1419418_a_at 5.55 microrchidia c Gpr56 1421118_a_at 5.43 G protein-coupled receptor 56 Pax6 1452526_a_at 5.06 paired box gene 6 Tgfbi 1415871_at 3.73 transforming growth factor beta induced Adarb1 1434932_at 3.70 adenosine deaminase RNA-specific B1 Ddx3y 1452077_at 3.30 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3 Y-linked b Ampd3 1422573_at 3.20 AMP deaminase 3 Gli2 1459211_at 3.07 GLI-Kruppel family member GLI2 Selenbp2 1417580_s_at 2.96 selenium binding protein 2 Adamts1 1450716_at 2.80 a disintegrin-like and metalloprotease with thrombospondin type 1 motif 1 Dusp15 1426189_at 2.70 dual specificity phosphatase-like 15 Dpep3 1429035_at 2.60 dipeptidase 3 Sepp1 1452141_a_at 2.57 selenoprotein P plasma -
Transcriptomic Analysis of Neuregulin-1 Regulated Genes
UC Riverside UC Riverside Previously Published Works Title Transcriptomic analysis of neuregulin-1 regulated genes following ischemic stroke by computational identification of promoter binding sites: A role for the ETS-1 transcription factor. Permalink https://escholarship.org/uc/item/2020r225 Journal PloS one, 13(6) ISSN 1932-6203 Authors Surles-Zeigler, Monique C Li, Yonggang Distel, Timothy J et al. Publication Date 2018 DOI 10.1371/journal.pone.0197092 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESEARCH ARTICLE Transcriptomic analysis of neuregulin-1 regulated genes following ischemic stroke by computational identification of promoter binding sites: A role for the ETS-1 transcription factor Monique C. Surles-Zeigler1, Yonggang Li2,3, Timothy J. Distel2, Hakeem Omotayo2, a1111111111 Shaokui Ge2, Byron D. Ford2* a1111111111 a1111111111 1 Department of Neurobiology, Morehouse School of Medicine, Atlanta, Georgia, United States of America, 2 Department of Biomedical Sciences, University of California±Riverside School of Medicine, Riverside, a1111111111 California, United States of America, 3 ICF, Atlanta, GA, United States of America a1111111111 * [email protected] Abstract OPEN ACCESS Citation: Surles-Zeigler MC, Li Y, Distel TJ, Ischemic stroke is a major cause of mortality in the United States. We previously showed Omotayo H, Ge S, Ford BD (2018) Transcriptomic that neuregulin-1 (NRG1) was neuroprotective in rat models of ischemic stroke. We used analysis of neuregulin-1 regulated genes following gene expression profiling to understand the early cellular and molecular mechanisms of ischemic stroke by computational identification of promoter binding sites: A role for the ETS-1 NRG1's effects after the induction of ischemia. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Ssecks/Gravin/AKAP12 Attenuates Expression of Proliferative And
BMC Cancer BioMed Central Research article Open Access SSeCKS/Gravin/AKAP12 attenuates expression of proliferative and angiogenic genes during suppression of v-Src-induced oncogenesis Yongzhong Liu1, Lingqiu Gao2 and Irwin H Gelman*2 Address: 1Mucosal Immunology Unit, National Institutes of Health, Bethesda, MD 20892, USA and 2Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA Email: Yongzhong Liu - [email protected]; Lingqiu Gao - [email protected]; Irwin H Gelman* - [email protected] * Corresponding author Published: 25 April 2006 Received: 24 January 2006 Accepted: 25 April 2006 BMC Cancer2006, 6:105 doi:10.1186/1471-2407-6-105 This article is available from: http://www.biomedcentral.com/1471-2407/6/105 © 2006Liu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: SSeCKS is a major protein kinase C substrate with kinase scaffolding and metastasis- suppressor activity whose expression is severely downregulated in Src- and Ras-transformed fibroblast and epithelial cells and in human prostate, breast, and gastric cancers. We previously used NIH3T3 cells with tetracycline-regulated SSeCKS expression plus a temperature-sensitive v-Src allele to show that SSeCKS re-expression inhibited parameters of v-Src-induced oncogenic growth without attenuating in vivo Src kinase activity. Methods: We use cDNA microarrays and semi-quantitative RT-PCR analysis to identify changes in gene expression correlating with i) SSeCKS expression in the absence of v-Src activity, ii) activation of v-Src activity alone, and iii) SSeCKS re-expression in the presence of active v-Src. -
Supplementary Table 2
Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942 -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
A Bioinformatics Model of Human Diseases on the Basis Of
SUPPLEMENTARY MATERIALS A Bioinformatics Model of Human Diseases on the basis of Differentially Expressed Genes (of Domestic versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes Vasiliev1,2 G, Chadaeva2 I, Rasskazov2 D, Ponomarenko2 P, Sharypova2 E, Drachkova2 I, Bogomolov2 A, Savinkova2 L, Ponomarenko2,* M, Kolchanov2 N, Osadchuk2 A, Oshchepkov2 D, Osadchuk2 L 1 Novosibirsk State University, Novosibirsk 630090, Russia; 2 Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; * Correspondence: [email protected]. Tel.: +7 (383) 363-4963 ext. 1311 (M.P.) Supplementary data on effects of the human gene underexpression or overexpression under this study on the reproductive potential Table S1. Effects of underexpression or overexpression of the human genes under this study on the reproductive potential according to our estimates [1-5]. ↓ ↑ Human Deficit ( ) Excess ( ) # Gene NSNP Effect on reproductive potential [Reference] ♂♀ NSNP Effect on reproductive potential [Reference] ♂♀ 1 increased risks of preeclampsia as one of the most challenging 1 ACKR1 ← increased risk of atherosclerosis and other coronary artery disease [9] ← [3] problems of modern obstetrics [8] 1 within a model of human diseases using Adcyap1-knockout mice, 3 in a model of human health using transgenic mice overexpressing 2 ADCYAP1 ← → [4] decreased fertility [10] [4] Adcyap1 within only pancreatic β-cells, ameliorated diabetes [11] 2 within a model of human diseases -
A Role for Glial Cell–Derived Neurotrophic Factor–Induced Expression by Inflammatory Cytokines and RET/GFRA1 Receptor Up-Regulation in Breast Cancer
Research Article A Role for Glial Cell–Derived Neurotrophic Factor–Induced Expression by Inflammatory Cytokines and RET/GFRA1 Receptor Up-regulation in Breast Cancer Selma Esseghir,1 S. Katrina Todd,1 Toby Hunt,2 Richard Poulsom,2 Ivan Plaza-Menacho,1 Jorge S. Reis-Filho,1 and Clare M. Isacke1 1Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research and 2In Situ Hybridisation Service and Histopathology Unit, Cancer Research UK-London Research Institute, London, United Kingdom Abstract system homeostasis and the inflammatory response (3, 4) and in By screening a tissue microarray of invasive breast tumors, we tumor progression (5). The neurotrophic factor glial cell–derived have shown that the receptor tyrosine kinase RET (REar- neurotrophic factor (GDNF) was first identified for its trophic ranged during Transfection) and its coreceptor GFRA1(GDNF activity on midbrain dopaminergic neurons; however, GDNF has receptor family A-1) are overexpressed in a subset of estrogen subsequently been shown to have broader effects in regulating receptor–positive tumors. Germ line–activating oncogenic growth, survival, and migration of neurons in the brain, spinal cord, mutations in RET allow this receptor to signal independently and periphery as well as having an essential role in the growth and A branching of the ureteric buds of the developing kidney (6, 7). Mice of GFR 1and its ligand glial cell–derived neurotrophic factor Gdnf (GDNF) to promote a spectrum of endocrine neoplasias. with a homozygous deletion of die shortly after birth due to However, it is not known whether tumor progression can also severe defects in renal differentiation and the absence of an enteric nervous system (8, 9). -
Human GFRA3 / GFR-Alpha-3 Protein (His Tag)
Human GFRA3 / GFR-alpha-3 Protein (His Tag) Catalog Number: 10213-H08H General Information SDS-PAGE: Gene Name Synonym: GDNFR3; GFRalpha3; Y15110 Protein Construction: A DNA sequence encoding the human GFRa3 (NP_001487.2) (Met 1-Trp 382) was expressed, fused with the a C-terminal polyhistidine tag. Source: Human Expression Host: Human Cells QC Testing Purity: > 90 % as determined by SDS-PAGE Endotoxin: Protein Description < 1.0 EU per μg of the protein as determined by the LAL method Glial cell line derived neurotrophic factor (GDNF) Family Receptor Alpha 3 Stability: (GFRA3) or GDNFRa3 is a member of the GDNF receptor family. It is a glycosylphosphatidylinositol (GPI)-linked cell surface receptor for both Samples are stable for up to twelve months from date of receipt at -70 ℃ GDNF and NTN, and mediates activation of the RET tyrosine kinase receptor. GFRA3 / GDNFRa3 is a potent survival factor for central and Predicted N terminal: Asp 32 peripheral neurons, and is essential for the development of kidneys and the Molecular Mass: enteric nervous system. Glial cell line-derived neurotrophic factor (GDNF) and neurturin (NTN) are its binding ligand which are two structurally related, The recombinant human GFRa3 consists of 362 amino acids and predicts potent neurotrophic factors that play key roles in the control of neuron a molecular mass of 40.8 kDa. As a result of glycosylation, the apparent survival and differentiation. GDNF promotes the formation of a physical molecular mass of rhGFRa3 is approximately 50 kDa in SDS-PAGE under complex between GFRA/GDNFRa and the orphan tyrosin kinase receptor reducing conditions. -
Axon Guidance Molecules in Vascular Patterning
Downloaded from http://cshperspectives.cshlp.org/ on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Axon Guidance Molecules in Vascular Patterning Ralf H. Adams1 and Anne Eichmann2 1Max-Planck-Institute for Molecular Biomedicine, Department of Tissue Morphogenesis, and University of Mu¨nster, Faculty of Medicine, Mu¨nster, Germany 2Inserm U833, College de France, 11 Place Marcelin Berthelot, 75005 Paris, France Correspondence: [email protected] Endothelial cells (ECs) form extensive, highly branched and hierarchically organized tubular networks in vertebrates to ensure the proper distribution of molecular and cellular cargo in the vertebrate body. The growth of this vascular system during development, tissue repair or in disease conditions involves the sprouting, migration and proliferation of endothelial cells in a process termed angiogenesis. Surprisingly, specialized ECs, so-called tip cells, which lead and guide endothelial sprouts, share many feature with another guidance struc- ture, the axonal growth cone. Tip cells are motile, invasive and extend numerous filopodial protrusions sensing growth factors, extracellular matrix and other attractive or repulsive cues in their tissue environment. Axonal growth cones and endothelial tip cells also respond to signals belonging to the same molecular families, such as Slits and Roundabouts, Netrins and UNC5 receptors, Semaphorins, Plexins and Neuropilins, and Eph receptors and ephrin ligands. Here we summarize fundamental principles of angiogenic growth, the selec- tion and function of tip cells and the underlying regulation by guidance cues, the Notch pathway and vascular endothelial growth factor signaling. PATTERNING OF THE VASCULAR SYSTEM The circulating blood travels from the heart he vasculature, like the nervous system, through the aorta, the largest axial vessel, into Tforms a highly branched, tree-like network a hierarchical system of arteries and smaller that reaches into every organ of vertebrate arterioles into distal capillary beds (Fig.