Fez1/Lzts1 Alterations in Gastric Carcinoma1
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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. -
Differential Expression of FEZ1/LZTS1 Gene in Lung Cancers and Their Cell Cultures1
2292 Vol. 8, 2292–2297, July 2002 Clinical Cancer Research Differential Expression of FEZ1/LZTS1 Gene in Lung Cancers and Their Cell Cultures1 Shinichi Toyooka, Yasuro Fukuyama, NSCLC cell lines, it was strongly correlated to D8S261 Ignacio I. Wistuba, Melvyn S. Tockman, and LPL loci in SCLC cell lines. No mutation was found John D. Minna, and Adi F. Gazdar2 within cording region of FEZ1 by PCR-single-strand con- formational polymorphism. Hamon Center for Therapeutic Oncology Research [S. T., Y. F., Conclusions: We found differential FEZ1 expression in J. D. M., A. F. G.], and Departments of Pathology [A. F. G.], Internal Medicine [J. D. M.], and Pharmacology [J. D. M.], University of NSCLC and SCLC cell lines, and the absent expression in 3 Texas Southwestern Medical Center, Dallas, Texas 75390-8593; of 6 short-term cultures of NSCLC tumors. FEZ1 may be Department of Pathology, Pontificia Universidad Catolica de Chile, related to tumorigenesis of lung cancer. Santiago, Chile [I. I. W.]; and Molecular Screening Laboratory, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida 33612-9497 [M .S. T.] INTRODUCTION Lung cancer is the most common cause of cancer deaths in the United States (1) and on clinicopathological grounds is ABSTRACT divided into two major types, NSCLCs and SCLCs. The mo- Purpose: The FEZ1/LZTS1 (FEZ1) gene, located on lecular genetic changes in these two types of lung cancer are chromosome 8p22 (8p22), was identified recently as a can- very different, including specific patterns of allelic loss (2–5). didate tumor suppressor gene. -
8P22 MTUS1 Gene Product ATIP3 Is a Novel Anti-Mitotic Protein Underexpressed in Invasive Breast Carcinoma of Poor Prognosis
8p22 MTUS1 Gene Product ATIP3 Is a Novel Anti-Mitotic Protein Underexpressed in Invasive Breast Carcinoma of Poor Prognosis Sylvie Rodrigues-Ferreira1, Anne Di Tommaso1, Ariane Dimitrov2, Sylvie Cazaubon1, Nade`ge Gruel3,4, He´le`ne Colasson1, Andre´ Nicolas5, Nathalie Chaverot1, Vincent Molinie´ 6, Fabien Reyal2, Brigitte Sigal-Zafrani4,5, Benoit Terris7, Olivier Delattre3,4, Franc¸ois Radvanyi2, Franck Perez2, Anne Vincent-Salomon4,5, Clara Nahmias1* 1 Institut Cochin, Universite´ Paris Descartes, Inserm U567, CNRS UMR8104, Paris, France, 2 CNRS UMR144, Institut Curie, Paris, France, 3 Inserm U830, Institut Curie, Paris, France, 4 Translational Research Department, Institut Curie, Paris, France, 5 Pathology Department, Hopital Curie, Paris, France, 6 Pathology Department, Hopital St. Joseph, Paris, France, 7 Pathology Department, Hopital Cochin, Paris, France Abstract Background: Breast cancer is a heterogeneous disease that is not totally eradicated by current therapies. The classification of breast tumors into distinct molecular subtypes by gene profiling and immunodetection of surrogate markers has proven useful for tumor prognosis and prediction of effective targeted treatments. The challenge now is to identify molecular biomarkers that may be of functional relevance for personalized therapy of breast tumors with poor outcome that do not respond to available treatments. The Mitochondrial Tumor Suppressor (MTUS1) gene is an interesting candidate whose expression is reduced in colon, pancreas, ovary and oral cancers. The present study investigates the expression and functional effects of MTUS1 gene products in breast cancer. Methods and Findings: By means of gene array analysis, real-time RT-PCR and immunohistochemistry, we show here that MTUS1/ATIP3 is significantly down-regulated in a series of 151 infiltrating breast cancer carcinomas as compared to normal breast tissue. -
Convergent Functional Genomics of Schizophrenia: from Comprehensive Understanding to Genetic Risk Prediction
Molecular Psychiatry (2012) 17, 887 -- 905 & 2012 Macmillan Publishers Limited All rights reserved 1359-4184/12 www.nature.com/mp IMMEDIATE COMMUNICATION Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction M Ayalew1,2,9, H Le-Niculescu1,9, DF Levey1, N Jain1, B Changala1, SD Patel1, E Winiger1, A Breier1, A Shekhar1, R Amdur3, D Koller4, JI Nurnberger1, A Corvin5, M Geyer6, MT Tsuang6, D Salomon7, NJ Schork7, AH Fanous3, MC O’Donovan8 and AB Niculescu1,2 We have used a translational convergent functional genomics (CFG) approach to identify and prioritize genes involved in schizophrenia, by gene-level integration of genome-wide association study data with other genetic and gene expression studies in humans and animal models. Using this polyevidence scoring and pathway analyses, we identify top genes (DISC1, TCF4, MBP, MOBP, NCAM1, NRCAM, NDUFV2, RAB18, as well as ADCYAP1, BDNF, CNR1, COMT, DRD2, DTNBP1, GAD1, GRIA1, GRIN2B, HTR2A, NRG1, RELN, SNAP-25, TNIK), brain development, myelination, cell adhesion, glutamate receptor signaling, G-protein-- coupled receptor signaling and cAMP-mediated signaling as key to pathophysiology and as targets for therapeutic intervention. Overall, the data are consistent with a model of disrupted connectivity in schizophrenia, resulting from the effects of neurodevelopmental environmental stress on a background of genetic vulnerability. In addition, we show how the top candidate genes identified by CFG can be used to generate a genetic risk prediction score (GRPS) to aid schizophrenia diagnostics, with predictive ability in independent cohorts. The GRPS also differentiates classic age of onset schizophrenia from early onset and late-onset disease. -
W J B C Biological Chemistry
World Journal of W J B C Biological Chemistry Submit a Manuscript: https://www.f6publishing.com World J Biol Chem 2019 February 21; 10(2): 28-43 DOI: 10.4331/wjbc.v10.i2.28 ISSN 1949-8454 (online) REVIEW Fasciculation and elongation zeta proteins 1 and 2: From structural flexibility to functional diversity Mariana Bertini Teixeira, Marcos Rodrigo Alborghetti, Jörg Kobarg ORCID number: Mariana Bertini Mariana Bertini Teixeira, Jörg Kobarg, Institute of Biology, Department of Biochemistry and Teixeira (0000-0002-3431-3131); Tissue Biology, University of Campinas, Campinas 13083-862, Brazil Marcos Rodrigo Alborghetti (0000-0003-4517-5579); Jörg Kobarg Marcos Rodrigo Alborghetti, Department of Cell Biology, University of Brasilia, Brasilia (0000-0002-9419-0145). 70919-970, Brazil Author contributions: Teixeira MB, Jörg Kobarg, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083- Alborghetti MR and Kobarg J 862, Brazil performed the literature search, analyses and interpretation of the Corresponding author: Jörg Kobarg, PhD, Full Professor, Molecular Biologist, Faculty of data; elaborated the figures; Pharmaceutical Sciences, University of Campinas, Rua Monteiro Lobato 255, Bloco F, Sala conceived the overall idea of the 03, Campinas 13083-862, Brazil. [email protected] review, elaborated the final version Telephone: +55-19-35211443 of the text together; all the authors read, revised and approved the final version. Conflict-of-interest statement: The Abstract authors declare no conflict-of- Fasciculation and elongation zeta/zygin (FEZ) proteins are a family of hub interest. proteins and share many characteristics like high connectivity in interaction Open-Access: This article is an networks, they are involved in several cellular processes, evolve slowly and in open-access article which was general have intrinsically disordered regions. -
FEZ1) in the Brain
Review TheScientificWorldJOURNAL (2010) 10, 1646–1654 ISSN 1537-744X; DOI 10.1100/tsw.2010.151 Functions of Fasciculation and Elongation Protein Zeta-1 (FEZ1) in the Brain Andrés D. Maturana1,*, Toshitsugu Fujita2, and Shun’ichi Kuroda3,* 1Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan; 2Research Institute for Microbial Diseases, Osaka University, Osaka, Japan; 3Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan E-mail: [email protected]; [email protected] Received March 16, 2010; Revised June 9, 2010; Accepted June 30, 2010; Published August 17, 2010 Fasciculation and elongation protein zeta-1 (FEZ1) is a mammalian ortholog of the Caenorhabditis elegans UNC-76 protein that possesses four coiled-coil domains and a nuclear localization signal. It is mainly expressed in the brain. Suppression of FEZ1 expression in cultured embryonic neurons causes deficiency of neuronal differentiation. Recently, proteomic techniques revealed that FEZ1 interacts with various intracellular partners, such as signaling, motor, and structural proteins. FEZ1 was shown to act as an antiviral factor. The findings reported so far indicate that FEZ1 is associated with neuronal development, neuropathologies, and viral infection. Based on these accumulating evidences, we herein review the biological functions of FEZ1. KEYWORDS: FEZ1, neuronal differentiation, neuronal disorders, virus infection, organelle transport DISCOVERY OF FASCICULATION AND ELONGATION PROTEIN ZETA-1 (FEZ1) FEZ1 is a mammalian ortholog of UNC-76, a protein found in the nematode Caenorhabditis elegans. UNC-76 has been used in an attempt to elucidate the mechanisms of locomotory defects. Genetic screenings of C. elegans mutants showing locomotory defects (uncoordinated or unc mutants) allowed the identification of various genes related to deficiencies in axonal guidance. -
Mir-285–Yki/Mask Double-Negative Feedback Loop Mediates Blood
miR-285–Yki/Mask double-negative feedback loop PNAS PLUS mediates blood–brain barrier integrity in Drosophila Dong Lia,b, Yanling Liua,b, Chunli Peic,d, Peng Zhangc,d, Linqing Pana,b, Jing Xiaoe, Songshu Mengb, Zengqiang Yuanc,d,1, and Xiaolin Bia,b,1 aDepartment of Biological Sciences, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; bInstitute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian 116044, China; cThe Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing 100850, China; dCenter of Alzheimer’s Disease, Beijing Institute for Brain Disorders, Beijing 100069, China; and eDepartment of Oral Basic Science, College of Stomatology, Dalian Medical University, Dalian 116044, China Edited by Norbert Perrimon, Harvard Medical School/HHMI, Boston, MA, and approved February 10, 2017 (received for review August 9, 2016) The Hippo signaling pathway is highly conserved from Drosophila to in size to maintain integrity of the BBB (7). Although an increased cell mammals and plays a central role in maintaining organ size and tissue size can be achieved through the accumulation of cell mass during the homeostasis. The blood–brain barrier (BBB) physiologically isolates growth of diploid cells, cell size is often correlated with the ploidy of the brain from circulating blood or the hemolymph system, and its DNA content and is increased via polyploidy during development, integrity is strictly maintained to perform sophisticated neuronal characteristics that are important for organogenesis, such as proper functions. Until now, the underlying mechanisms of subperineurial organ size, structure, and function (8–10). SPG cells have been shown glia (SPG) growth and BBB maintenance during development are to maintain the integrity of the BBB during development by increased not clear. -
Gene Section Review
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review EEF1G (Eukaryotic translation elongation factor 1 gamma) Luigi Cristiano Aesthetic and medical biotechnologies research unit, Prestige, Terranuova Bracciolini, Italy; [email protected] Published in Atlas Database: March 2019 Online updated version : http://AtlasGeneticsOncology.org/Genes/EEF1GID54272ch11q12.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/70656/03-2019-EEF1GID54272ch11q12.pdf DOI: 10.4267/2042/70656 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2020 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract Keywords EEF1G; Eukaryotic translation elongation factor 1 Eukaryotic translation elongation factor 1 gamma, gamma; Translation; Translation elongation factor; alias eEF1G, is a protein that plays a main function protein synthesis; cancer; oncogene; cancer marker in the elongation step of translation process but also covers numerous moonlighting roles. Considering its Identity importance in the cell it is found frequently Other names: EF1G, GIG35, PRO1608, EEF1γ, overexpressed in human cancer cells and thus this EEF1Bγ review wants to collect the state of the art about EEF1G, with insights on DNA, RNA, protein HGNC (Hugo): EEF1G encoded and the diseases where it is implicated. Location: 11q12.3 Figure. 1. Splice variants of EEF1G. The figure shows the locus on chromosome 11 of the EEF1G gene and its splicing variants (grey/blue box). The primary transcript is EEF1G-001 mRNA (green/red box), but also EEF1G-201 variant is able to codify for a protein (reworked from https://www.ncbi.nlm.nih.gov/gene/1937; http://grch37.ensembl.org; www.genecards.org) Atlas Genet Cytogenet Oncol Haematol. -
Phosphorylation-Regulated Axonal Dependent Transport of Syntaxin 1 Is Mediated by a Kinesin-1 Adapter
Phosphorylation-regulated axonal dependent transport of syntaxin 1 is mediated by a Kinesin-1 adapter John Jia En Chuaa, Eugenia Butkevichb, Josephine M. Worseckc, Maike Kittelmannd, Mads Grønborga, Elmar Behrmanna, Ulrich Stelzlc, Nathan J. Pavlosa, Maciej M. Lalowskie,1, Stefan Eimerd, Erich E. Wankere, Dieter Robert Klopfensteinb,f,2, and Reinhard Jahna,2 aDepartment of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; bGeorg-August-Universität Göttingen, Drittes Physikalisches Institut-Biophysik, 37077 Göttingen, Germany; fBiochemistry II, Georg-August-Universität Göttingen, 37073 Göttingen, Germany; cMax-Planck- Institute for Molecular Genetics, 14195 Berlin, Germany; dEuropean Neuroscience Institute Göttingen and German Research Foundation Research Center for Molecular Physiology of the Brain, 37077 Göttingen, Germany; and eMax Delbrueck Center for Molecular Medicine, 13092 Berlin-Buch, Germany Edited by Ronald D. Vale, University of California, San Francisco, CA, and approved March 5, 2012 (received for review August 22, 2011) Presynaptic nerve terminals are formed from preassembled vesicles knockouts (15), although in the latter case, a compensation by other that are delivered to the prospective synapse by kinesin-mediated Munc18 isoforms cannot be excluded. These defects were attrib- axonal transport. However, precisely how the various cargoes are uted to a need for Stx to be stabilized by Munc18 in the inactive linked to the motor proteins remains unclear. Here, we report conformation during transport to prevent it from being trapped in a transport complex linking syntaxin 1a (Stx) and Munc18, two pro- nonproductive SNARE complexes (10) but Munc18 could addi- teins functioning in synaptic vesicle exocytosis at the presynaptic tionally participate in loading Stx onto kinesin. -
Oncoscore: a Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes
www.nature.com/scientificreports OPEN OncoScore: a novel, Internet- based tool to assess the oncogenic potential of genes Received: 06 July 2016 Rocco Piazza1, Daniele Ramazzotti2, Roberta Spinelli1, Alessandra Pirola3, Luca De Sano4, Accepted: 15 March 2017 Pierangelo Ferrari3, Vera Magistroni1, Nicoletta Cordani1, Nitesh Sharma5 & Published: 07 April 2017 Carlo Gambacorti-Passerini1 The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating capability of OncoScore (OncoScore cut-off threshold = 21.09; AUC = 90.3%, 95% CI: 88.1–92.5%), indicating that OncoScore provides useful results in cases where an efficient prioritization of cancer-associated genes is needed. The huge amount of data emerging from NGS projects is bringing a revolution in molecular medicine, leading to the discovery of a large number of new somatic alterations that are associated with the onset and/or progression of cancer. However, researchers are facing a formidable challenge in prioritizing cancer genes among the variants generated by NGS experiments. Despite the development of a significant number of tools devoted to cancer driver prediction, limited effort has been dedicated to tools able to generate a gene-centered Oncogenic Score based on the evidence already available in the scientific literature. -
Concordance of Copy Number Loss and Down-Regulation of Tumor Suppressor Genes: a Pan-Cancer Study Min Zhao1 and Zhongming Zhao2,3,4,5*
The Author(s) BMC Genomics 2016, 17(Suppl 7):532 DOI 10.1186/s12864-016-2904-y RESEARCH Open Access Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study Min Zhao1 and Zhongming Zhao2,3,4,5* From The International Conference on Intelligent Biology and Medicine (ICIBM) 2015 Indianapolis, IN, USA. 13-15 November 2015 Abstract Background: Tumor suppressor genes (TSGs) encode the guardian molecules to control cell growth. The genomic alteration of TSGs may cause tumorigenesis and promote cancer progression. So far, investigators have mainly studied the functional effects of somatic single nucleotide variants in TSGs. Copy number variation (CNV) is another important form of genetic variation, and is often involved in cancer biology and drug treatment, but studies of CNV in TSGs are less represented in literature. In addition, there is a lack of a combinatory analysis of gene expression and CNV in this important gene set. Such a study may provide more insights into the relationship between gene dosage and tumorigenesis. To meet this demand, we performed a systematic analysis of CNVs and gene expression in TSGs to provide a systematic view of CNV and gene expression change in TSGs in pan-cancer. Results: We identified 1170 TSGs with copy number gain or loss in 5846 tumor samples. Among them, 207 TSGs tended to have copy number loss (CNL), from which fifteen CNL hotspot regions were identified. The functional enrichment analysis revealed that the 207 TSGs were enriched in cancer-related pathways such as P53 signaling pathway and the P53 interactome. -
Supplementary Tables S1-S3
Supplementary Table S1: Real time RT-PCR primers COX-2 Forward 5’- CCACTTCAAGGGAGTCTGGA -3’ Reverse 5’- AAGGGCCCTGGTGTAGTAGG -3’ Wnt5a Forward 5’- TGAATAACCCTGTTCAGATGTCA -3’ Reverse 5’- TGTACTGCATGTGGTCCTGA -3’ Spp1 Forward 5'- GACCCATCTCAGAAGCAGAA -3' Reverse 5'- TTCGTCAGATTCATCCGAGT -3' CUGBP2 Forward 5’- ATGCAACAGCTCAACACTGC -3’ Reverse 5’- CAGCGTTGCCAGATTCTGTA -3’ Supplementary Table S2: Genes synergistically regulated by oncogenic Ras and TGF-β AU-rich probe_id Gene Name Gene Symbol element Fold change RasV12 + TGF-β RasV12 TGF-β 1368519_at serine (or cysteine) peptidase inhibitor, clade E, member 1 Serpine1 ARE 42.22 5.53 75.28 1373000_at sushi-repeat-containing protein, X-linked 2 (predicted) Srpx2 19.24 25.59 73.63 1383486_at Transcribed locus --- ARE 5.93 27.94 52.85 1367581_a_at secreted phosphoprotein 1 Spp1 2.46 19.28 49.76 1368359_a_at VGF nerve growth factor inducible Vgf 3.11 4.61 48.10 1392618_at Transcribed locus --- ARE 3.48 24.30 45.76 1398302_at prolactin-like protein F Prlpf ARE 1.39 3.29 45.23 1392264_s_at serine (or cysteine) peptidase inhibitor, clade E, member 1 Serpine1 ARE 24.92 3.67 40.09 1391022_at laminin, beta 3 Lamb3 2.13 3.31 38.15 1384605_at Transcribed locus --- 2.94 14.57 37.91 1367973_at chemokine (C-C motif) ligand 2 Ccl2 ARE 5.47 17.28 37.90 1369249_at progressive ankylosis homolog (mouse) Ank ARE 3.12 8.33 33.58 1398479_at ryanodine receptor 3 Ryr3 ARE 1.42 9.28 29.65 1371194_at tumor necrosis factor alpha induced protein 6 Tnfaip6 ARE 2.95 7.90 29.24 1386344_at Progressive ankylosis homolog (mouse)