DOCSLIB.ORG

Frequent Downregulation of LRRC26 by Epigenetic Alterations Is Involved in the Malignant Progression of Triple-Negative Breast Cancer

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Frequent Downregulation of LRRC26 by Epigenetic Alterations Is Involved in the Malignant Progression of Triple-Negative Breast Cancer INTERNATIONAL JOURNAL OF ONCOLOGY 52: 1539-1558, 2018 Frequent downregulation of LRRC26 by epigenetic alterations is involved in the malignant progression of triple-negative breast cancer YOSHIMASA MIYAGAWA1,2*, YOSUKE MATSUSHITA1*, HIROMU SUZUKI3, MASATO KOMATSU1, TETSURO YOSHIMARU1, RYUICHIRO KIMURA1, AYAKO YANAI1,2, JUNKO HONDA4, AKIRA TANGOKU5, MITSUNORI SASA6, YASUO MIYOSHI2 and TOYOMASA KATAGIRI1 1Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima 770-8503; 2Department of Surgery, Division of Breast and Endocrine Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501; 3Department of Molecular Biology, Sapporo Medical University, Sapporo, Hokkaido 060-8556; 4Department of Surgery, National Hospital Organization Higashitokushima Medical Center, Tokushima 779-0193; 5Department of Thoracic and Endocrine Surgery and Oncology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503; 6Department of Surgery, Tokushima Breast Care Clinic, Tokushima 770-0052, Japan Received September 13, 2017; Accepted February 21, 2018 DOI: 10.3892/ijo.2018.4301 Abstract. Triple-negative breast cancer (TNBC), defined as absence of tumor necrosis factor-α (TNF-α) stimulation. breast cancer lacking estrogen- and progesterone-receptor Meanwhile, overexpression of LRRC26 caused the reduction of expression and human epidermal growth factor receptor 2 TNF-α-mediated NF-κB luciferase reporter activity, whereas (HER2) amplification, is a heterogeneous disease. depleting LRRC26 expression resulted in the upregulation of RNA-sequencing analysis of 15 TNBC specimens and The TNF-α-mediated NF-κB downstream genes [interleukin-6 Cancer Genome Atlas-TNBC dataset analysis identified the (IL-6), IL-8 and C-X-C motif chemokine ligand-1]. Taken frequent downregulation of leucine-rich repeat- together, these findings demonstrate that LRRC26 is frequently containing 26 (LRRC26), which negatively regulates nuclear downregulated in TNBC due to DNA methylation and that it factor-κB (NF-κB) signaling, in TNBC tissues. Quantitative suppresses the TNF-α-independent anchorage-independent polymerase chain reaction and bisulfite pyrosequencing analyses growth, invasion and migration of TNBC cells. Loss of LRRC26 revealed that LRRC26 was frequently silenced in TNBC tissues function may be a critical event in the aggressiveness of TNBC and cell lines as a result of promoter methylation. LRRC26 cells through a TNF-α/NF-κB-independent mechanism. expression was restored by 5-aza-2'-deoxycytidine (5'-aza-dC) treatment in HCC1937 TNBC cells, which lack LRRC26 expres- Introduction sion. Notably, small interfering RNA-mediated knockdown of LRRC26 expression significantly enhanced the anchorage-inde- Triple-negative breast cancer (TNBC), defined as a pendent growth, invasion and migration of HCC70 cells, whereas clinical breast cancer subtype that is negative for estrogen ectopic overexpression of LRRC26 in BT20 cells suppressed receptor (ER) and progesterone receptor (PgR) expression their invasion and migration. Conversely, neither knockdown nor and human epidermal growth factor receptor 2 (HER2) gene overexpression of LRRC26 had an effect on cell viability in the amplification, accounts for 15% of all invasive breast cancer cases. TNBC comprises a heterogeneous group of tumors with different histological and molecular characteristics. Clinically, as TNBC patients do not benefit from endocrine therapies (selective estrogen receptor modulators, selective estrogen Correspondence to: Dr Toyomasa Katagiri, Division of Genome receptor downregulators and aromatase inhibitors) (1-3) Medicine, Institute for Genome Research, Tokushima University, or anti-HER2 drugs (trastuzumab, lapatinib, pertuzumab 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan E-mail: [email protected] and trastuzumab emtansine) (4) due to a lack of targeted thera- peutic receptors (5,6), these therapies are not recommended *Contributed equally in National Comprehensive Cancer Network guidelines (7). Therefore, chemotherapy using conventional cytotoxic agents, Key words: LRRC26, triple-negative breast cancer, tumor including anthracyclines, cyclophosphamides, taxanes, suppressor, hypermethylation platinum agents and eribulin (8,9), is currently the mainstay of systemic treatment, although patients with TNBC have worse outcomes following chemotherapy than patients with breast 1540 MIYAGAWA et al: FREQUENT HYPERMETHYLATION-MEDIATED DOWNREGULATION OF LRRC26 IN TNBC cancer of other subtypes, including hormone receptor-positive (Takara Bio, Inc., Otsu, Japan). A total of 26 TNBC samples and HER2-positive breast cancer (5,6,10). Thus, since there and 26 normal mammary tissues were surgically resected is no optimized standard chemotherapy protocol for TNBC, with informed consent from patients who were treated at the detailed subtyping of TNBC is necessary to identify more Tokushima Breast Care Clinic (Tokushima, Japan), as previ- effective molecular-targeted therapies. ously described (20) (Table II). Samples were immediately Current omics-based studies, such as genomics and embedded in TissueTek OCT compound (Sakura, Tokyo, transcriptomics, can provide data that can be used to catego- Japan), frozen and stored at -80˚C. rize TNBC. Recent gene expression profiling-based cluster The present study, as well as the use of all clinical mate- analysis using a dataset consisting of 587 TNBC cases from rials aforementioned, was approved by the Ethics Committee 21 independent datasets identified six subtypes, including of Tokushima University (Tokushima, Japan). two basal-like subtypes, as well as an immunomodulatory, a mesenchymal, a mesenchymal stem-like and a luminal RNA-seq analysis. Total RNA was extracted from frozen androgen receptor subtype (11). Moreover, next generation tumors and adjacent normal breast tissues from the 15 out of 26 sequencing (NGS)-based studies detected tumor protein TNBC samples that could produce a large enough amount of p53 and phosphatidylinositol-4,5-bisphosphate 3-kinase RNA for RNA seq analysis using the Nucleospin RNA II system catalytic subunit α mutations in 80 and 9% of TNBC cases, (Takara Bio, Inc.) according to the manufacturer's protocols. respectively (12), highlighting these gene mutations as key Whole-transcriptome RNAs seq analysis was performed genetic events in this subtype. Notably, additional NGS using the SureSelect strand-specific RNA library prepara- studies led to the identification of actionable molecular tion kit (Agilent Technologies, Inc., Santa Clara, CA, USA) characteristics, including ‘BRCAness’, defined as a defect in according to the manufacturer's protocols, followed by paired- homologous recombination repair due to BRCA1 DNA repair end 100-bp sequencing on an Illumina HiSeq 1500 platform associated (BRCA1) or BRCA2 mutation, in TNBC (13,14). (Illumina, Inc., San Diego, CA, USA). All primary sequence Recently, poly(ADP-ribose) polymerase inhibitors were data files are deposited in the DNA Data Bank of Japan (acces- shown to take advantage of synthetic lethality in targeting sion no. JGAS00000000116; http://www.ddbj.nig.ac.jp/). Data TNBC with BRCAness (15,16). Furthermore, the nuclear were analyzed using CLC Biomedical Genomics Workbench factor-κB (NF-κB) signaling pathway is constitutively acti- version 4.0 (Qiagen GmbH, Hilden, Germany) with default vated in the basal-like subtype of breast cancer cells, ~80% parameters. Transcript abundance was calculated as transcript of which include TNBC (17). However, the underlying causes per million. of NF-κB signaling activation have remained poorly under- stood. Quantitative PCR (qPCR) and semi-quantitative PCR. To characterize the molecular features of TNBC, Total RNA extracted from clinical breast cancer samples and RNA-sequencing (RNA-seq) analysis was performed in breast cancer cell lines using the NucleoSpin RNA II system the present study and it was found that leucine-rich repeat (Takara Bio, Inc.) and the poly A-RNAs of a normal human (LRR)-containing 26 (LRRC26), a member of the LRR super- mammary gland (Clontech Laboratories, Inc., Mountainview, family, was frequently downregulated in patients with TNBC. CA, USA) were reverse transcribed using SuperScript II (Life LRRC26, also known as CAPC, is reported to act as a negative Technologies; Thermo Fisher Scientific, Inc., Waltham, MA, regulator of NF-κB activity, and to inhibit cancer cell prolif- USA). qPCR analysis using the ABI PRISM 7500 Real-Time eration and migration (18). However, the pathophysiological PCR system was performed with SYBR® Premix Ex Taq (both role of LRRC26 in carcinogenesis and TNBC progression, from Applied Biosystems; Thermo Fisher Scientific, Inc.). The particularly the mechanisms regulating LRRC26 expression, thermocycling conditions were 10 min at 94˚C, followed by has not yet been elucidated. 45 cycles of denaturation at 94˚C for 15 sec, 1 min annealing The present study aimed to characterize the molecular and extension at 60˚C, and reading of the fluorescence. Following mechanism of LRRC26 downregulation in TNBC. threshold-dependent cycling, melting curve analysis was performed from 60 to 94˚C. The quantitative calculation was Materials and methods analyzed using 2-∆∆Cq (21). Semi-quantitative PCR analysis was performed as described previously (22,23). Gene-specific Cell lines and clinical specimens. The human breast cancer primers used for qPCR and semi-quantitative PCR were as cell lines, MDA-MB-231, HCC1143, BT-20, BT-549, HCC1395,
Load more

Recommended publications
  • Clinical Utility Gene Card For: 3-M Syndrome – Update 2013
    European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.156 & 2014 Macmillan Publishers Limited All rights reserved 1018-4813/14 www.nature.com/ejhg CLINICAL UTILITY GENE CARD UPDATE Clinical utility gene card for: 3-M syndrome – Update 2013 Muriel Holder-Espinasse*,1, Melita Irving1 and Vale´rie Cormier-Daire2 European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.156; published online 31 July 2013 Update to: European Journal of Human Genetics (2011) 19, doi:10.1038/ejhg.2011.32; published online 2 March 2011 1. DISEASE CHARACTERISTICS nonsense and missense mutations c.4333C4T (p.Arg1445*) and 1.1 Name of the disease (synonyms) c.4391A4C (p.His1464Pro), respectively, render CUL7 deficient 3-M syndrome (gloomy face syndrome, dolichospondylic dysplasia). in recruiting ROC1, leading to impaired ubiquitination. OBSL1: microsatellites analysis of the locus (2q35-36.1) in con- 1.2 OMIM# of the disease sanguineous families. OBSL1: microsatellites analysis of the locus 273750. (2q35-36.1) in consanguineous families. Mutations induce non- sense mediated decay. Knockdown of OBSL1 in HEK293 cells 1.3 Name of the analysed genes or DNA/chromosome segments shows the role of this gene in the maintenance of normal levels of CUL7, OBSL1 and CCDC8.1–5 CUL7. Abnormal IGFBP2 andIGFBP5 mRNA levels in two patients with OBSL1 mutations, suggesting that OBSL1 modulates the 1.4 OMIM# of the gene(s) expression of IGFBP proteins. CCDC8: microsatellites analysis 609577 (CUL7), 610991 (OBSL1) and 614145 (CCDC8). at the locus (19q13.2-q13.32). CCDC8, 1-BP DUP, 612G and CCDC8, 1-BP.
    [Show full text]
  • Analysis of Trans Esnps Infers Regulatory Network Architecture
    Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation.
    [Show full text]
  • Title a New Centrosomal Protein Regulates Neurogenesis By
    Title A new centrosomal protein regulates neurogenesis by microtubule organization Authors: Germán Camargo Ortega1-3†, Sven Falk1,2†, Pia A. Johansson1,2†, Elise Peyre4, Sanjeeb Kumar Sahu5, Loïc Broic4, Camino De Juan Romero6, Kalina Draganova1,2, Stanislav Vinopal7, Kaviya Chinnappa1‡, Anna Gavranovic1, Tugay Karakaya1, Juliane Merl-Pham8, Arie Geerlof9, Regina Feederle10,11, Wei Shao12,13, Song-Hai Shi12,13, Stefanie M. Hauck8, Frank Bradke7, Victor Borrell6, Vijay K. Tiwari§, Wieland B. Huttner14, Michaela Wilsch- Bräuninger14, Laurent Nguyen4 and Magdalena Götz1,2,11* Affiliations: 1. Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany. 2. Physiological Genomics, Biomedical Center, Ludwig-Maximilian University Munich, Germany. 3. Graduate School of Systemic Neurosciences, Biocenter, Ludwig-Maximilian University Munich, Germany. 4. GIGA-Neurosciences, Molecular regulation of neurogenesis, University of Liège, Belgium 5. Institute of Molecular Biology (IMB), Mainz, Germany. 6. Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d’Alacant, Spain. 7. Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. 8. Research Unit Protein Science, Helmholtz Centre Munich, German Research Center for Environmental Health, Munich, Germany. 9. Protein Expression and Purification Facility, Institute of Structural Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany. 10. Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany. 11. SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig- Maximilian University Munich, Germany. 12. Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA 13.
    [Show full text]
  • Disruption of the Neuronal PAS3 Gene in a Family Affected with Schizophrenia D Kamnasaran, W J Muir, M a Ferguson-Smith,Dwcox
    325 ORIGINAL ARTICLE J Med Genet: first published as 10.1136/jmg.40.5.325 on 1 May 2003. Downloaded from Disruption of the neuronal PAS3 gene in a family affected with schizophrenia D Kamnasaran, W J Muir, M A Ferguson-Smith,DWCox ............................................................................................................................. J Med Genet 2003;40:325–332 Schizophrenia and its subtypes are part of a complex brain disorder with multiple postulated aetiolo- gies. There is evidence that this common disease is genetically heterogeneous, with many loci involved. See end of article for In this report, we describe a mother and daughter affected with schizophrenia, who are carriers of a authors’ affiliations t(9;14)(q34;q13) chromosome. By mapping on flow sorted aberrant chromosomes isolated from lym- ....................... phoblast cell lines, both subjects were found to have a translocation breakpoint junction between the Correspondence to: markers D14S730 and D14S70, a 683 kb interval on chromosome 14q13. This interval was found to Dr D W Cox, 8-39 Medical contain the neuronal PAS3 gene (NPAS3), by annotating the genomic sequence for ESTs and perform- Sciences Building, ing RACE and cDNA library screenings. The NPAS3 gene was characterised with respect to the University of Alberta, genomic structure, human expression profile, and protein cellular localisation to gain insight into gene Edmonton, Alberta T6G function. The translocation breakpoint junction lies within the third intron of NPAS3, resulting in the dis- 2H7, Canada; [email protected] ruption of the coding potential. The fact that the bHLH and PAS domains are disrupted from the remain- ing parts of the encoded protein suggests that the DNA binding and dimerisation functions of this Revised version received protein are destroyed.
    [Show full text]
  • Transcription Factor P73 Regulates Th1 Differentiation
    ARTICLE https://doi.org/10.1038/s41467-020-15172-5 OPEN Transcription factor p73 regulates Th1 differentiation Min Ren1, Majid Kazemian 1,4, Ming Zheng2, JianPing He3, Peng Li1, Jangsuk Oh1, Wei Liao1, Jessica Li1, ✉ Jonathan Rajaseelan1, Brian L. Kelsall 3, Gary Peltz 2 & Warren J. Leonard1 Inter-individual differences in T helper (Th) cell responses affect susceptibility to infectious, allergic and autoimmune diseases. To identify factors contributing to these response differ- 1234567890():,; ences, here we analyze in vitro differentiated Th1 cells from 16 inbred mouse strains. Haplotype-based computational genetic analysis indicates that the p53 family protein, p73, affects Th1 differentiation. In cells differentiated under Th1 conditions in vitro, p73 negatively regulates IFNγ production. p73 binds within, or upstream of, and modulates the expression of Th1 differentiation-related genes such as Ifng and Il12rb2. Furthermore, in mouse experimental autoimmune encephalitis, p73-deficient mice have increased IFNγ production and less dis- ease severity, whereas in an adoptive transfer model of inflammatory bowel disease, transfer of p73-deficient naïve CD4+ T cells increases Th1 responses and augments disease severity. Our results thus identify p73 as a negative regulator of the Th1 immune response, suggesting that p73 dysregulation may contribute to susceptibility to autoimmune disease. 1 Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892-1674, USA. 2 Department of Anesthesia, Stanford University School of Medicine, Stanford, CA 94305, USA. 3 Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA. 4Present address: Department of Biochemistry and Computer Science, Purdue University, West ✉ Lafayette, IN 37906, USA.
    [Show full text]
  • Immobilization of Firefly Luciferase on PVA-Co-PE Nanofibers Membrane
    Research Article www.acsami.org Immobilization of Firefly Luciferase on PVA-co-PE Nanofibers Membrane as Biosensor for Bioluminescent Detection of ATP † † Wenwen Wang, Qinghua Zhao, Mengying Luo, Mufang Li, Dong Wang,* Yuedan Wang, and Qiongzhen Liu School of Materials Science and Engineering, Wuhan Textile University, Wuhan 430073, China ABSTRACT: The bioluminescent reaction catalyzed by firefly luciferase has become widely established as an outstanding analytical system for assay of adenosine triphosphate (ATP). When in solution, the luciferase is unstable and cannot be reused. The problem can be partially solved by immobilizing the luciferase on solid substrates. The poly(vinyl alcohol-co-ethylene) (PVA-co-PE) nanofibers membrane has abundant active hydroxyl groups on the surface. The PVA-co-PE nanofibers membrane was first activated by cyanuric chloride with triazinyl group. Then the activated PVA-co- PE nanofibers membrane was subsequently reacted with 1,3-propanediamine and biotin. The firefly luciferase was immobilized onto the surface of 1,3-propanediamine- and biotin-functionalized membranes. The surface chemical structure and morphologies of nanofibers membranes were characterized by FTIR-ATR spectra and SEM. The hydrophilicity of membranes was tested by water contact angle measurements. The detection of fluorescence intensity displayed that the firefly-luciferase-immobilized PVA-co-PE nanofibers membranes indicated high catalytic activity and efficiency. Especially, the firefly-luciferase-immobilized nanofiber membrane which was functionalized
    [Show full text]
  • Identification and Validation of Methylation-Driven Genes Prognostic Signature for Recurrence of Laryngeal Squamous Cell Carcino
    Cui et al. Cancer Cell Int (2020) 20:472 https://doi.org/10.1186/s12935-020-01567-3 Cancer Cell International PRIMARY RESEARCH Open Access Identifcation and validation of methylation-driven genes prognostic signature for recurrence of laryngeal squamous cell carcinoma by integrated bioinformatics analysis Jie Cui3†, Liping Wang2†, Waisheng Zhong4†, Zhen Chen5, Jie Chen4*, Hong Yang3* and Genglong Liu1* Abstract Background: Recurrence remains a major obstacle to long-term survival of laryngeal squamous cell carcinoma (LSCC). We conducted a genome-wide integrated analysis of methylation and the transcriptome to establish methyla- tion-driven genes prognostic signature (MDGPS) to precisely predict recurrence probability and optimize therapeutic strategies for LSCC. Methods: LSCC DNA methylation datasets and RNA sequencing (RNA-seq) dataset were acquired from the Cancer Genome Atlas (TCGA). MethylMix was applied to detect DNA methylation-driven genes (MDGs). By univariate and multivariate Cox regression analyses, fve genes of DNA MDGs was developed a recurrence-free survival (RFS)-related MDGPS. The predictive accuracy and clinical value of the MDGPS were evaluated by receiver operating characteristic (ROC) and decision curve analysis (DCA), and compared with TNM stage system. Additionally, prognostic value of MDGPS was validated by external Gene Expression Omnibus (GEO) database. According to 5 MDGs, the candidate small molecules for LSCC were screen out by the CMap database. To strengthen the bioinformatics analysis results, 30 pairs of clinical samples were evaluated by digoxigenin-labeled chromogenic in situ hybridization (CISH). Results: A total of 88 DNA MDGs were identifed, and fve RFS-related MDGs (LINC01354, CCDC8, PHYHD1, MAGEB2 and ZNF732) were chosen to construct a MDGPS.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Evidence for Differential Alternative Splicing in Blood of Young Boys With
    Stamova et al. Molecular Autism 2013, 4:30 http://www.molecularautism.com/content/4/1/30 RESEARCH Open Access Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders Boryana S Stamova1,2,5*, Yingfang Tian1,2,4, Christine W Nordahl1,3, Mark D Shen1,3, Sally Rogers1,3, David G Amaral1,3 and Frank R Sharp1,2 Abstract Background: Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume. Methods: RNA from blood was processed on whole genome exon arrays for 2-4–year-old ASD and TD boys. An ANCOVA with age and batch as covariates was used to predict DAS for ALL ASD (n=30), ASD with normal total cerebral volumes (NTCV), and ASD with large total cerebral volumes (LTCV) compared to TD controls (n=20). Results: A total of 53 genes were predicted to have DAS for ALL ASD versus TD, 169 genes for ASD_NTCV versus TD, 1 gene for ASD_LTCV versus TD, and 27 genes for ASD_LTCV versus ASD_NTCV. These differences were significant at P <0.05 after false discovery rate corrections for multiple comparisons (FDR <5% false positives). A number of the genes predicted to have DAS in ASD are known to regulate DAS (SFPQ, SRPK1, SRSF11, SRSF2IP, FUS, LSM14A). In addition, a number of genes with predicted DAS are involved in pathways implicated in previous ASD studies, such as ROS monocyte/macrophage, Natural Killer Cell, mTOR, and NGF signaling.
    [Show full text]
  • 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,
    [Show full text]
  • Crystal Structure of Firefly Luciferase Throws Light on a Superfamily of Adenylate-Forming Enzymes Elena Conti, Nick P Franks and Peter Brick*
    Research Article 287 Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes Elena Conti, Nick P Franks and Peter Brick* Background: Firefly luciferase is a 62 kDa protein that catalyzes the production Address: Biophysics Section, Blackett Laboratory, of light. In the presence of MgATP and molecular oxygen, the enzyme oxidizes its Imperial College, London SW7 2BZ, UK. substrate, firefly luciferin, emitting yellow-green light. The reaction proceeds *Corresponding author. through activation of the substrate to form an adenylate intermediate. Firefly luciferase shows extensive sequence homology with a number of enzymes that Key words: acyl-coenzyme A ligase, adenylate, utilize ATP in adenylation reactions. firefly luciferase, peptide synthetase, X-ray crystallography Results: We have determined the crystal structure of firefly luciferase at 2.0 Å Received: 30 Nov 1995 resolution. The protein is folded into two compact domains. The large N-terminal Revisions requested: 21 Dec 1995 domain consists of a b-barrel and two b-sheets. The sheets are flanked by Revisions received: 15 Jan 1996 a-helices to form an ababa five-layered structure. The C-terminal portion of the Accepted: 31 Jan 1996 molecule forms a distinct domain, which is separated from the N-terminal domain Structure 15 March 1996, 4:287–298 by a wide cleft. © Current Biology Ltd ISSN 0969-2126 Conclusions: Firefly luciferase is the first member of a superfamily of homologous enzymes, which includes acyl-coenzyme A ligases and peptide synthetases, to have its structure characterized. The residues conserved within the superfamily are located on the surfaces of the two domains on either side of the cleft, but are too far apart to interact simultaneously with the substrates.
    [Show full text]
  • Tepzz¥ 6Z54za T
    (19) TZZ¥ ZZ_T (11) EP 3 260 540 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 27.12.2017 Bulletin 2017/52 C12N 15/113 (2010.01) A61K 9/127 (2006.01) A61K 31/713 (2006.01) C12Q 1/68 (2006.01) (21) Application number: 17000579.7 (22) Date of filing: 12.11.2011 (84) Designated Contracting States: • Sarma, Kavitha AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Philadelphia, PA 19146 (US) GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO • Borowsky, Mark PL PT RO RS SE SI SK SM TR Needham, MA 02494 (US) • Ohsumi, Toshiro Kendrick (30) Priority: 12.11.2010 US 412862 P Cambridge, MA 02141 (US) 20.12.2010 US 201061425174 P 28.07.2011 US 201161512754 P (74) Representative: Clegg, Richard Ian et al Mewburn Ellis LLP (62) Document number(s) of the earlier application(s) in City Tower accordance with Art. 76 EPC: 40 Basinghall Street 11840099.3 / 2 638 163 London EC2V 5DE (GB) (71) Applicant: The General Hospital Corporation Remarks: Boston, MA 02114 (US) •Thecomplete document including Reference Tables and the Sequence Listing can be downloaded from (72) Inventors: the EPO website • Lee, Jeannie T •This application was filed on 05-04-2017 as a Boston, MA 02114 (US) divisional application to the application mentioned • Zhao, Jing under INID code 62. San Diego, CA 92122 (US) •Claims filed after the date of receipt of the divisional application (Rule 68(4) EPC). (54) POLYCOMB-ASSOCIATED NON-CODING RNAS (57) This invention relates to long non-coding RNAs (IncRNAs), libraries of those ncRNAs that bind chromatin modifiers, such as Polycomb Repressive Complex 2, inhibitory nucleic acids and methods and compositions for targeting IncRNAs.
    [Show full text]