PDK1 Regulates the Maintenance of Cell Body and the Development of Dendrites of Purkinje Cells by Ps6 and Pkcc
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Supplemental Information to Mammadova-Bach Et Al., “Laminin Α1 Orchestrates VEGFA Functions in the Ecosystem of Colorectal Carcinogenesis”
Supplemental information to Mammadova-Bach et al., “Laminin α1 orchestrates VEGFA functions in the ecosystem of colorectal carcinogenesis” Supplemental material and methods Cloning of the villin-LMα1 vector The plasmid pBS-villin-promoter containing the 3.5 Kb of the murine villin promoter, the first non coding exon, 5.5 kb of the first intron and 15 nucleotides of the second villin exon, was generated by S. Robine (Institut Curie, Paris, France). The EcoRI site in the multi cloning site was destroyed by fill in ligation with T4 polymerase according to the manufacturer`s instructions (New England Biolabs, Ozyme, Saint Quentin en Yvelines, France). Site directed mutagenesis (GeneEditor in vitro Site-Directed Mutagenesis system, Promega, Charbonnières-les-Bains, France) was then used to introduce a BsiWI site before the start codon of the villin coding sequence using the 5’ phosphorylated primer: 5’CCTTCTCCTCTAGGCTCGCGTACGATGACGTCGGACTTGCGG3’. A double strand annealed oligonucleotide, 5’GGCCGGACGCGTGAATTCGTCGACGC3’ and 5’GGCCGCGTCGACGAATTCACGC GTCC3’ containing restriction site for MluI, EcoRI and SalI were inserted in the NotI site (present in the multi cloning site), generating the plasmid pBS-villin-promoter-MES. The SV40 polyA region of the pEGFP plasmid (Clontech, Ozyme, Saint Quentin Yvelines, France) was amplified by PCR using primers 5’GGCGCCTCTAGATCATAATCAGCCATA3’ and 5’GGCGCCCTTAAGATACATTGATGAGTT3’ before subcloning into the pGEMTeasy vector (Promega, Charbonnières-les-Bains, France). After EcoRI digestion, the SV40 polyA fragment was purified with the NucleoSpin Extract II kit (Machery-Nagel, Hoerdt, France) and then subcloned into the EcoRI site of the plasmid pBS-villin-promoter-MES. Site directed mutagenesis was used to introduce a BsiWI site (5’ phosphorylated AGCGCAGGGAGCGGCGGCCGTACGATGCGCGGCAGCGGCACG3’) before the initiation codon and a MluI site (5’ phosphorylated 1 CCCGGGCCTGAGCCCTAAACGCGTGCCAGCCTCTGCCCTTGG3’) after the stop codon in the full length cDNA coding for the mouse LMα1 in the pCIS vector (kindly provided by P. -
HCC and Cancer Mutated Genes Summarized in the Literature Gene Symbol Gene Name References*
HCC and cancer mutated genes summarized in the literature Gene symbol Gene name References* A2M Alpha-2-macroglobulin (4) ABL1 c-abl oncogene 1, receptor tyrosine kinase (4,5,22) ACBD7 Acyl-Coenzyme A binding domain containing 7 (23) ACTL6A Actin-like 6A (4,5) ACTL6B Actin-like 6B (4) ACVR1B Activin A receptor, type IB (21,22) ACVR2A Activin A receptor, type IIA (4,21) ADAM10 ADAM metallopeptidase domain 10 (5) ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif, 9 (4) ADCY2 Adenylate cyclase 2 (brain) (26) AJUBA Ajuba LIM protein (21) AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 (4) Akt AKT serine/threonine kinase (28) AKT1 v-akt murine thymoma viral oncogene homolog 1 (5,21,22) AKT2 v-akt murine thymoma viral oncogene homolog 2 (4) ALB Albumin (4) ALK Anaplastic lymphoma receptor tyrosine kinase (22) AMPH Amphiphysin (24) ANK3 Ankyrin 3, node of Ranvier (ankyrin G) (4) ANKRD12 Ankyrin repeat domain 12 (4) ANO1 Anoctamin 1, calcium activated chloride channel (4) APC Adenomatous polyposis coli (4,5,21,22,25,28) APOB Apolipoprotein B [including Ag(x) antigen] (4) AR Androgen receptor (5,21-23) ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 (4) ARHGAP35 Rho GTPase activating protein 35 (21) ARID1A AT rich interactive domain 1A (SWI-like) (4,5,21,22,24,25,27,28) ARID1B AT rich interactive domain 1B (SWI1-like) (4,5,22) ARID2 AT rich interactive domain 2 (ARID, RFX-like) (4,5,22,24,25,27,28) ARID4A AT rich interactive domain 4A (RBP1-like) (28) ARID5B AT rich interactive domain 5B (MRF1-like) (21) ASPM Asp (abnormal -
PRODUCTS and SERVICES Target List
PRODUCTS AND SERVICES Target list Kinase Products P.1-11 Kinase Products Biochemical Assays P.12 "QuickScout Screening Assist™ Kits" Kinase Protein Assay Kits P.13 "QuickScout Custom Profiling & Panel Profiling Series" Targets P.14 "QuickScout Custom Profiling Series" Preincubation Targets Cell-Based Assays P.15 NanoBRET™ TE Intracellular Kinase Cell-Based Assay Service Targets P.16 Tyrosine Kinase Ba/F3 Cell-Based Assay Service Targets P.17 Kinase HEK293 Cell-Based Assay Service ~ClariCELL™ ~ Targets P.18 Detection of Protein-Protein Interactions ~ProbeX™~ Stable Cell Lines Crystallization Services P.19 FastLane™ Structures ~Premium~ P.20-21 FastLane™ Structures ~Standard~ Kinase Products For details of products, please see "PRODUCTS AND SERVICES" on page 1~3. Tyrosine Kinases Note: Please contact us for availability or further information. Information may be changed without notice. Expression Protein Kinase Tag Carna Product Name Catalog No. Construct Sequence Accession Number Tag Location System HIS ABL(ABL1) 08-001 Full-length 2-1130 NP_005148.2 N-terminal His Insect (sf21) ABL(ABL1) BTN BTN-ABL(ABL1) 08-401-20N Full-length 2-1130 NP_005148.2 N-terminal DYKDDDDK Insect (sf21) ABL(ABL1) [E255K] HIS ABL(ABL1)[E255K] 08-094 Full-length 2-1130 NP_005148.2 N-terminal His Insect (sf21) HIS ABL(ABL1)[T315I] 08-093 Full-length 2-1130 NP_005148.2 N-terminal His Insect (sf21) ABL(ABL1) [T315I] BTN BTN-ABL(ABL1)[T315I] 08-493-20N Full-length 2-1130 NP_005148.2 N-terminal DYKDDDDK Insect (sf21) ACK(TNK2) GST ACK(TNK2) 08-196 Catalytic domain -
Differences in Gene Expression Profiles and Carcinogenesis Pathways Involved in Cisplatin Resistance of Four Types of Cancer
596 ONCOLOGY REPORTS 30: 596-614, 2013 Differences in gene expression profiles and carcinogenesis pathways involved in cisplatin resistance of four types of cancer YONG YANG1,2, HUI LI1,2, SHENGCAI HOU1,2, BIN HU1,2, JIE LIU1,3 and JUN WANG1,3 1Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Capital Medical University, Beijing 100069; 2Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020; 3Department of Physiology, Capital Medical University, Beijing 100069, P.R. China Received December 23, 2012; Accepted March 4, 2013 DOI: 10.3892/or.2013.2514 Abstract. Cisplatin-based chemotherapy is the standard Introduction therapy used for the treatment of several types of cancer. However, its efficacy is largely limited by the acquired drug Cisplatin is primarily effective through DNA damage and is resistance. To date, little is known about the RNA expression widely used for the treatment of several types of cancer, such changes in cisplatin-resistant cancers. Identification of the as testicular, lung and ovarian cancer. However, the ability RNAs related to cisplatin resistance may provide specific of cancer cells to become resistant to cisplatin remains a insight into cancer therapy. In the present study, expression significant impediment to successful chemotherapy. Although profiling of 7 cancer cell lines was performed using oligo- previous studies have identified numerous mechanisms in nucleotide microarray analysis data obtained from the GEO cisplatin resistance, it remains a major problem that severely database. Bioinformatic analyses such as the Gene Ontology limits the usefulness of this chemotherapeutic agent. Therefore, (GO) and KEGG pathway were used to identify genes and it is crucial to examine more elaborate mechanisms of cisplatin pathways specifically associated with cisplatin resistance. -
Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib
Supplementary Online Content Chen G, McQuade JL, Panka DJ, et al. Clinical, molecular and immune analysis of dabrafenib-trametinib combination treatment for metastatic melanoma that progressed during BRAF inhibitor monotherapy: a phase 2 clinical trial. JAMA Oncology. Published online April 28, 2016. doi:10.1001/jamaoncol.2016.0509. eMethods. eReferences. eTable 1. Clinical efficacy eTable 2. Adverse events eTable 3. Correlation of baseline patient characteristics with treatment outcomes eTable 4. Patient responses and baseline IHC results eFigure 1. Kaplan-Meier analysis of overall survival eFigure 2. Correlation between IHC and RNAseq results eFigure 3. pPRAS40 expression and PFS eFigure 4. Baseline and treatment-induced changes in immune infiltrates eFigure 5. PD-L1 expression eTable 5. Nonsynonymous mutations detected by WES in baseline tumors This supplementary material has been provided by the authors to give readers additional information about their work. © 2016 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/30/2021 eMethods Whole exome sequencing Whole exome capture libraries for both tumor and normal samples were constructed using 100ng genomic DNA input and following the protocol as described by Fisher et al.,3 with the following adapter modification: Illumina paired end adapters were replaced with palindromic forked adapters with unique 8 base index sequences embedded within the adapter. In-solution hybrid selection was performed using the Illumina Rapid Capture Exome enrichment kit with 38Mb target territory (29Mb baited). The targeted region includes 98.3% of the intervals in the Refseq exome database. Dual-indexed libraries were pooled into groups of up to 96 samples prior to hybridization. -
The Pyrazolyl-Urea Gege3 Inhibits Tumor Angiogenesis and Reveals Dystrophia Myotonica Protein Kinase (DMPK)1 As a Novel Angiogenesis Target
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 64), pp: 108195-108212 Research Paper The pyrazolyl-urea GeGe3 inhibits tumor angiogenesis and reveals dystrophia myotonica protein kinase (DMPK)1 as a novel angiogenesis target Elda Meta1, Beat A. Imhof2, Patricia Ropraz2, Richard J. Fish3, Chiara Brullo1, Olga Bruno1 and Adama Sidibé2 1Department of Pharmacy, Medicinal Chemistry Section, University of Genoa, 16132 Genoa, Italy 2Department of Pathology and Immunology, University of Geneva, 1211 Genève, Switzerland 3Department of Genetic Medicine and Development, University of Geneva, 1211 Genève, Switzerland Correspondence to: Adama Sidibé, email: [email protected] Keywords: angiogenesis; novel target; pyrazolyl-urea; kinase inhibitors; DMPK Received: May 04, 2017 Accepted: July 26, 2017 Published: November 21, 2017 Copyright: Meta et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The limitation of targeting VEGF/VEGFR2 signalling to stop angiogenesis in cancer therapy has been blamed on re-activation of alternative receptor tyrosine kinases by compensatory angiogenic factors. Targeting MAPK and PI3K signaling pathways in endothelial cells may be an alternative or complementary approach. Herein we aimed to evaluate the antitumor and antiangiogenic potential of a novel pyrazolyl-urea kinase inhibitor, GeGe3, and to identify its kinase targets. We found GeGe3 to inhibit the proliferation of HUVEC and endothelial tube formation. GeGe3 impaired inter-segmental angiogenesis during development of zebrafish embryos. In mice, GeGe3 blocked angiogenesis and tumor growth in transplanted subcutaneous Lewis Lung Carcinomas. -
SUPPLEMENTARY APPENDIX Exome Sequencing Reveals Heterogeneous Clonal Dynamics in Donor Cell Myeloid Neoplasms After Stem Cell Transplantation
SUPPLEMENTARY APPENDIX Exome sequencing reveals heterogeneous clonal dynamics in donor cell myeloid neoplasms after stem cell transplantation Julia Suárez-González, 1,2 Juan Carlos Triviño, 3 Guiomar Bautista, 4 José Antonio García-Marco, 4 Ángela Figuera, 5 Antonio Balas, 6 José Luis Vicario, 6 Francisco José Ortuño, 7 Raúl Teruel, 7 José María Álamo, 8 Diego Carbonell, 2,9 Cristina Andrés-Zayas, 1,2 Nieves Dorado, 2,9 Gabriela Rodríguez-Macías, 9 Mi Kwon, 2,9 José Luis Díez-Martín, 2,9,10 Carolina Martínez-Laperche 2,9* and Ismael Buño 1,2,9,11* on behalf of the Spanish Group for Hematopoietic Transplantation (GETH) 1Genomics Unit, Gregorio Marañón General University Hospital, Gregorio Marañón Health Research Institute (IiSGM), Madrid; 2Gregorio Marañón Health Research Institute (IiSGM), Madrid; 3Sistemas Genómicos, Valencia; 4Department of Hematology, Puerta de Hierro General University Hospital, Madrid; 5Department of Hematology, La Princesa University Hospital, Madrid; 6Department of Histocompatibility, Madrid Blood Centre, Madrid; 7Department of Hematology and Medical Oncology Unit, IMIB-Arrixaca, Morales Meseguer General University Hospital, Murcia; 8Centro Inmunológico de Alicante - CIALAB, Alicante; 9Department of Hematology, Gregorio Marañón General University Hospital, Madrid; 10 Department of Medicine, School of Medicine, Com - plutense University of Madrid, Madrid and 11 Department of Cell Biology, School of Medicine, Complutense University of Madrid, Madrid, Spain *CM-L and IB contributed equally as co-senior authors. Correspondence: -
Targeting CDK4 Overcomes EMT-Mediated Tumor Heterogeneity and Therapeutic Resistance in KRAS Mutant Lung Cancer
Targeting CDK4 overcomes EMT-mediated tumor heterogeneity and therapeutic resistance in KRAS mutant lung cancer Aparna Padhye1,2, Jessica M. Konen1, B. Leticia Rodriguez1, Jared J. Fradette1, Joshua K. Ochieng1, Lixia Diao3, Jing Wang3, Wei Lu4, Luisa S. Solis4, Harsh Batra4, Maria G. Raso4, Michael D. Peoples5, Rosalba Minelli5, Alessandro Carugo5, Christopher A. Bristow5, Don L. Gibbons1,6* 1. Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 2. University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. 3. Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 4. Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA 5. TRACTION Platform, Division of Therapeutics Development, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 6. Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. *Corresponding author. Email: [email protected] Supplemental Methods Plasmids, Transfections, and Lentiviral Generation and Transduction Transfections of si-RNAs werr performed using the Lipofectamine 2000 Transfection Reagent (Thermo Fisher Scientific). Constitutive Cdkn1a overexpression cell lines were generated by using Cdkn1a mouse Tagged ORF Clone (Origene (NM_007669)). Cdkn1a ORF was also subcloned into dox-inducible pTRIPZ-GFP vector to generate doxycycline inducible cell lines using EcoRI and AgeI restriction cut sites. Constitutive Cdkn1a shRNAs were purchased from Milipore sigma. The sequences used in the experiments are listed in table S11. Dox- inducible shRNAs were expressed in Tet-pLKO-puro vector with a scramble sequence as the non-targeting control. -
The Human Genome Project: Biology, Computers, and Privacy. INSTITUTION Biological Sciences Curriculum Study, Colorado Springs
DOCUMENT RESUME ED 461 499 SE 061 488 AUTHOR Cutter, Mary Ann G.; Drexler, Edward; Gottesman, Kay S.; Goulding, Philip G.; McCullough, Laurence B.; McInerney, Joseph D.; Micikas, Lynda B.; Mural, Richard J.; Murray, Jeffrey C.; Zola, John TITLE The Human Genome Project: Biology, Computers, and Privacy. INSTITUTION Biological Sciences Curriculum Study, Colorado Springs. SPONS AGENCY Department of Energy, Washington, DC. PUB DATE 1996-00-00 NOTE 212p.; Distribution of material supported the U.S. Department of Energy and the University of Iowa Genome Center. Accompanying software not available from ERIC. CONTRACT DE-FG03-93ER61584 AVAILABLE FROM Biological Science and Curriculum Study, Colorado Springs, CO 80918-3842. Tel: 719-531-5550; Fax: 719-531-9104; e-mail: [email protected]; Web site: http://www.bscs.org. For full text: http://www.bscs.org/pdf/projects/HGN2/HGN-II.pdf. PUB TYPE Guides Classroom Learner (051) Guides Classroom Teacher (052) EDRS PRICE MF01/PC09 Plus Postage. DESCRIPTORS *Biology; *Ethics; Evolution; Genetic Engineering; *Genetics; High Schools; *Public Policy; Science Activities; *Science and Society; Science Curriculum; Science Education; Technology IDENTIFIERS Biological Sciences Curriculum Study; *Human Genome Project ABSTRACT This module, for high school teachers, is the second of two modules about the Human Genome Project (HGP) produced by the Biological Sciences Curriculum Study (BSCS). The first section of this module provides background information for teachers about the structure and objectives of the HGP, aspects of the science and technology that underlie the HGP, information science as it relates to the HGP, and ethics and public policy, especially as they concern information science and the HGP. -
The Role of Network Science in Glioblastoma
cancers Review The Role of Network Science in Glioblastoma Marta B. Lopes 1,2,* , Eduarda P. Martins 3,4 , Susana Vinga 5,6 and Bruno M. Costa 3,4 1 Center for Mathematics and Applications (CMA), FCT, UNL, 2829-516 Caparica, Portugal 2 NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), FCT, UNL, 2829-516 Caparica, Portugal 3 Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; [email protected] (E.P.M.); [email protected] (B.M.C.) 4 ICVS/3B’s—PT Government Associate Laboratory, 4710-057/4805-017 Braga/Guimarães, Portugal 5 INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, 1000-029 Lisbon, Portugal; [email protected] 6 IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal * Correspondence: [email protected] Simple Summary: Knowledge extraction from cancer genomic studies is continuously challenged by the fast-growing technological advances generating high-dimensional data. Network science is a promising discipline to cope with the resulting complex and heterogeneous datasets, enabling the disclosure of the molecular networks involved in cancer development and progression. We present a narrative review of the network-based strategies that have been applied to glioblastoma (GBM), a complex and heterogeneous disease, along with a discussion on the relevant findings and open challenges and future research opportunities. Abstract: Network science has long been recognized as a well-established discipline across many Citation: Lopes, M.B.; Martins, E.P.; biological domains. In the particular case of cancer genomics, network discovery is challenged by Vinga, S.; Costa, B.M. -
To 11-Year-Old Preterm-Born Children
biomedicines Article Postnatal Expression Profile of MicroRNAs Associated with Cardiovascular Diseases in 3- to 11-Year-Old Preterm-Born Children Ilona Hromadnikova 1,* , Katerina Kotlabova 1, Ladislav Krofta 2 and Jan Sirc 2 1 Department of Molecular Biology and Cell Pathology, Third Faculty of Medicine, Charles University, 100 00 Prague, Czech Republic; [email protected] 2 Third Faculty of Medicine, Institute for the Care of the Mother and Child, Charles University, 147 00 Prague, Czech Republic; [email protected] (L.K.); [email protected] (J.S.) * Correspondence: [email protected]; Tel.: +420-296511336 Abstract: (1) Background: Preterm-born children have an increased cardiovascular risk with the first clinical manifestation during childhood and/or adolescence. (2) Methods: The occurrence of overweight/obesity, prehypertension/hypertension, valve problems or heart defects, and postnatal microRNA expression profiles were examined in preterm-born children at the age of 3 to 11 years descending from preterm prelabor rupture of membranes (PPROM) and spontaneous preterm birth (PTB) pregnancies. The whole peripheral blood gene expression of 29 selected microRNAs associated with cardiovascular diseases was the subject of our interest. (3) Results: Nearly one-third of preterm- born children (32.43%) had valve problems and/or heart defects. The occurrence of systolic and diastolic prehypertension/hypertension was also inconsiderable in a group of preterm-born children (27.03% and 18.92%). The vast majority of children descending from either PPROM (85.45%) or PTB pregnancies (85.71%) had also significantly altered microRNA expression profiles at 90.0% Citation: Hromadnikova, I.; specificity. (4) Conclusions: Postnatal microRNA expression profiles were significantly influenced Kotlabova, K.; Krofta, L.; Sirc, J. -
Identification of New Kinase Clusters Required for Neurite Outgrowth And
Cell Death and Differentiation (2008) 15, 283–298 & 2008 Nature Publishing Group All rights reserved 1350-9047/08 $30.00 www.nature.com/cdd Identification of new kinase clusters required for neurite outgrowth and retraction by a loss-of-function RNA interference screen SHY Loh1, L Francescut1, P Lingor2,3,MBa¨hr2,3 and P Nicotera*,1 Disruption of synaptic integrity, loss of connectivity and axodendritic degeneration are early and essential components of neurodegeneration. Although neuronal cell death mechanisms have been thoroughly investigated, less is known about the signals involved in axodendritic damage and the processes involved in regeneration. Here we conducted a genome-wide RNA interference-based forward genetic screen, using small interfering RNA targeting all human kinases, and identified clusters of kinases families essential for growth cone collapse, neurite retraction and neurite outgrowth. Of 59 kinases identified as positive regulators of neurite outgrowth, almost 50% were in the tyrosine kinase/tyrosine kinase-like (TK/TKL) receptor subgroups, underlining the importance of extracellular ligands in this process. Neurite outgrowth was inhibited by 66 other kinases, none of which were TK/TKL members, whereas 79 kinases inhibited lysophosphatidic acid-induced neurite retraction. Twenty kinases were involved in both inhibitory processes suggesting shared mechanisms. Within this group of 20 kinases, some (ULK1, PDK1, MAP4K4) have been implicated previously in axonal events, but others (MAST2, FASTK, CKM and DGUOK) have not. For a subset of kinases, the effect on neurite outgrowth was validated in rat primary cerebellar cultures. The ability to affect regeneration was further tested in a model of axodendritic lesion using primary rat midbrain cultures.