Protein Is a Substrate of the Kinase Interacting Stathmin (KIS)
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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. -
UHMK1 Dependent Phosphorylation of Cajal Body Protein Coilin Altered 5-FU Sensitivity in Colon Cancer Cells
UHMK1 Dependent Phosphorylation of Cajal Body Protein Coilin Altered 5-FU Sensitivity in Colon Cancer Cells Huan Niu Capital Medical University Meng Zhao Capital Medical University Jing Huang Capital Medical University Jing Wang Capital Medical University Yang Si Capital Medical University Shan Cheng ( [email protected] ) Capital Medical University https://orcid.org/0000-0002-8658-6916 Wei Ding Capital Medical University Research Keywords: Cajal body, coilin, UHMK1, 5-FU resistance, colon cancer Posted Date: August 2nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-753268/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/23 Abstract Background: Resistance to 5-uorouracil (5-FU) in chemotherapy and recurrence of colorectal tumors is a serious problem to be resolved for the improvement of clinical outcomes. Methods: In the present study, the effects of conditioned medium (CM) derived from 5-FU-resistant HCT- 8/FU on cell functions were evaluated. The methods of immunouorescence and RNA-seq analyses were used to investigate the molecular mechanism underlining the roles of CM from resistant cells. Results: we found that CM derived from 5-FU-resistant HCT-8/FU was able to reduce 5-FU chemosensitivity of HCT-8 colon cancer cells, with correlating changes in the number and morphology of the Cajal bodies (CBs) as observable nuclear structures. We identied UHMK1 was able to change the disassembly and reassembly of CBs regulated by the phosphorylation of coilin, a major component of CBs, and subsequently resulted in a large number of variations of RNA alternative splicing, affecting the cell survival following 5-FU treatment through changes in intracellular phenotype and transmitted preadaptive signals to adjacent cells in tumor microenvironment (TME). -
UHMK1) Is Upregulated Upon Hematopoietic Cell Differentiation
bioRxiv preprint doi: https://doi.org/10.1101/187385; this version posted September 11, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The U2AF homology motif kinase 1 (UHMK1) is upregulated upon hematopoietic cell differentiation Isabella Barbutti a, João Agostinho Machado-Neto b, Vanessa Cristina Arfelli c, Paula de Melo Campos a, Fabiola Traina b, Sara Teresinha Olalla Saad a, Leticia Fröhlich Archangelo a,c * a Hematology and Transfusion Medicine Center, State University of Campinas (UNICAMP), Carlos Chagas 480, 13083-878 Campinas-SP, Brazil. b Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil. c Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil. * Corresponding author: Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes 3900, 14049-900 Ribeirão Preto-SP, Brazil. Tel: +55 (16) 33153118; fax: + 55 (16) 3315 0728 E-mail: [email protected] (L.F. Archangelo) 1 bioRxiv preprint doi: https://doi.org/10.1101/187385; this version posted September 11, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Analysis of Alternative Splicing Associated with Aging and Neurodegeneration in the Human Brain
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Research Analysis of alternative splicing associated with aging and neurodegeneration in the human brain James R. Tollervey,1 Zhen Wang,1 Tibor Hortoba´gyi,2 Joshua T. Witten,1 Kathi Zarnack,3 Melis Kayikci,1 Tyson A. Clark,4 Anthony C. Schweitzer,4 Gregor Rot,5 Tomazˇ Curk,5 Blazˇ Zupan,5 Boris Rogelj,2 Christopher E. Shaw,2 and Jernej Ule1,6 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom; 2MRC Centre for Neurodegeneration Research, King’s College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom; 3EMBL–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 4Expression Research, Affymetrix, Inc., Santa Clara, California 95051, USA; 5Faculty of Computer and Information Science, University of Ljubljana, Trzˇasˇka 25, SI-1000 Ljubljana, Slovenia Age is the most important risk factor for neurodegeneration; however, the effects of aging and neurodegeneration on gene expression in the human brain have most often been studied separately. Here, we analyzed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages who were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer’s disease (AD). We identified age-related splicing changes in cognitively normal individuals and found that these were present also in 95% of individuals with FTLD or AD, independent of their age. These changes were consistent with increased polypyrimidine tract binding protein (PTB)– dependent splicing activity. We also identified disease-specific splicing changes that were present in individuals with FTLD or AD, but not in cognitively normal individuals. -
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 Scale-Free Approach for False Discovery Rate Control in Generalized Linear Models
A Scale-free Approach for False Discovery Rate Control in Generalized Linear Models Chenguang Dai,∗ Buyu Lin∗, Xin Xing, and Jun S. Liu Department of Statistics, Harvard University July 3, 2020 Abstract The generalized linear models (GLM) have been widely used in practice to model non- Gaussian response variables. When the number of explanatory features is relatively large, sci- entific researchers are of interest to perform controlled feature selection in order to simplify the downstream analysis. This paper introduces a new framework for feature selection in GLMs that can achieve false discovery rate (FDR) control in two asymptotic regimes. The key step is to construct a mirror statistic to measure the importance of each feature, which is based upon two (asymptotically) independent estimates of the corresponding true coefficient obtained via either the data-splitting method or the Gaussian mirror method. The FDR control is achieved by taking advantage of the mirror statistics property that, for any null feature, its sampling dis- tribution is (asymptotically) symmetric about 0. In the moderate-dimensional setting in which the ratio between the dimension (number of features) p and the sample size n converges to a fixed value, i.e., p=n ! κ 2 (0; 1), we construct the mirror statistic based on the maximum likelihood estimation. In the high-dimensional setting where p n, we use the debiased Lasso to build the mirror statistic. Compared to the Benjamini-Hochberg procedure, which crucially relies on the asymptotic normality of the Z statistic, the proposed methodology is scale free as it only hinges on the symmetric property, thus is expected to be more robust in finite-sample cases. -
A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: -
Experience Alterations in White Matter Structure and Myelin-Related Gene Expression in Adult Rats
bioRxiv preprint doi: https://doi.org/10.1101/532572; this version posted May 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Experience alterations in white matter structure and myelin-related gene expression in adult rats Cassandra Sampaio-Baptista1,8,*, Astrid Vallès2,3,8, Alexandre A. Khrapitchev4, Guus Akkermans2, Anderson M. Winkler1, Sean Foxley1, Nicola R. Sibson4, Mark Roberts3, Karla Miller1, Mathew E. Diamond7, Gerard J.M. Martens2, Peter De Weerd3,5,6,9 Heidi Johansen- Berg1,9 1 Wellcome Centre For Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK 2 Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands 3 Department of Neurocognition, Faculty of Psychology and Neurosciences, Maastricht University, 6200 MD Maastricht, The Netherlands 4 Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK 5 Department of Cognitive Neuroscience, Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands 6 Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands 7 Tactile Perception and Learning Lab, International School for Advanced Studies (SISSA), Trieste, Italy 8 Joint first author 9 Joint senior author * Correspondence: [email protected] ACKNOWLEDGEMENTS The authors would like to thank Riejanne Seigers for her valuable help with the behavioural training, and Ivica Granic for his technical support with the tissue dissections. -
CREB-Dependent Transcription in Astrocytes: Signalling Pathways, Gene Profiles and Neuroprotective Role in Brain Injury
CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Tesis doctoral Luis Pardo Fernández Bellaterra, Septiembre 2015 Instituto de Neurociencias Departamento de Bioquímica i Biologia Molecular Unidad de Bioquímica y Biologia Molecular Facultad de Medicina CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Memoria del trabajo experimental para optar al grado de doctor, correspondiente al Programa de Doctorado en Neurociencias del Instituto de Neurociencias de la Universidad Autónoma de Barcelona, llevado a cabo por Luis Pardo Fernández bajo la dirección de la Dra. Elena Galea Rodríguez de Velasco y la Dra. Roser Masgrau Juanola, en el Instituto de Neurociencias de la Universidad Autónoma de Barcelona. Doctorando Directoras de tesis Luis Pardo Fernández Dra. Elena Galea Dra. Roser Masgrau In memoriam María Dolores Álvarez Durán Abuela, eres la culpable de que haya decidido recorrer el camino de la ciencia. Que estas líneas ayuden a conservar tu recuerdo. A mis padres y hermanos, A Meri INDEX I Summary 1 II Introduction 3 1 Astrocytes: physiology and pathology 5 1.1 Anatomical organization 6 1.2 Origins and heterogeneity 6 1.3 Astrocyte functions 8 1.3.1 Developmental functions 8 1.3.2 Neurovascular functions 9 1.3.3 Metabolic support 11 1.3.4 Homeostatic functions 13 1.3.5 Antioxidant functions 15 1.3.6 Signalling functions 15 1.4 Astrocytes in brain pathology 20 1.5 Reactive astrogliosis 22 2 The transcription -
COX5B-Mediated Bioenergetic Alteration Regulates Tumor Growth and Migration by Modulating AMPK-UHMK1-ERK Cascade in Hepatoma
cancers Article COX5B-Mediated Bioenergetic Alteration Regulates Tumor Growth and Migration by Modulating AMPK-UHMK1-ERK Cascade in Hepatoma 1, 1,2,3, 1 1 3 Yu-De Chu y, Wey-Ran Lin y , Yang-Hsiang Lin , Wen-Hsin Kuo , Chin-Ju Tseng , Siew-Na Lim 3,4, Yen-Lin Huang 5, Shih-Chiang Huang 5, Ting-Jung Wu 1, Kwang-Huei Lin 1 and Chau-Ting Yeh 1,2,3,6,* 1 Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; [email protected] (Y.-D.C.); [email protected] (W.-R.L.); [email protected] (Y.-H.L.); [email protected] (W.-H.K.); [email protected] (T.-J.W.); [email protected] (K.-H.L.) 2 Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan 3 Department of Internal Medicine, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; [email protected] (C.-J.T.); [email protected] (S.-N.L.) 4 Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan 5 Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; [email protected] (Y.-L.H.); [email protected] (S.-C.H.) 6 Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan * Correspondence: [email protected]; Tel.: +886-3-3281200 (ext. 8129) These authors contributed equally to this work. y Received: 11 June 2020; Accepted: 19 June 2020; Published: 22 June 2020 Abstract: The oxidative phosphorylation machinery in mitochondria, which generates the main bioenergy pool in cells, includes four enzyme complexes for electron transport and ATP synthase. -
Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors
University of Cincinnati Date: 12/20/2010 I, Arturo R Maldonado , hereby submit this original work as part of the requirements for the degree of Doctor of Philosophy in Developmental Biology. It is entitled: Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors Student's name: Arturo R Maldonado This work and its defense approved by: Committee chair: Jeffrey Whitsett Committee member: Timothy Crombleholme, MD Committee member: Dan Wiginton, PhD Committee member: Rhonda Cardin, PhD Committee member: Tim Cripe 1297 Last Printed:1/11/2011 Document Of Defense Form Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors A dissertation submitted to the Graduate School of the University of Cincinnati College of Medicine in partial fulfillment of the requirements for the degree of DOCTORATE OF PHILOSOPHY (PH.D.) in the Division of Molecular & Developmental Biology 2010 By Arturo Rafael Maldonado B.A., University of Miami, Coral Gables, Florida June 1993 M.D., New Jersey Medical School, Newark, New Jersey June 1999 Committee Chair: Jeffrey A. Whitsett, M.D. Advisor: Timothy M. Crombleholme, M.D. Timothy P. Cripe, M.D. Ph.D. Dan Wiginton, Ph.D. Rhonda D. Cardin, Ph.D. ABSTRACT Since 1999, cancer has surpassed heart disease as the number one cause of death in the US for people under the age of 85. Malignant Peripheral Nerve Sheath Tumor (MPNST), a common malignancy in patients with Neurofibromatosis, and colorectal cancer are midkine- producing tumors with high mortality rates. In vitro and preclinical xenograft models of MPNST were utilized in this dissertation to study the role of midkine (MDK), a tumor-specific gene over- expressed in these tumors and to test the efficacy of a MDK-transcriptionally targeted oncolytic HSV-1 (oHSV). -
Downloaded from the European Nucleotide Archive (ENA; 126
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 5 September 2018 doi:10.20944/preprints201809.0082.v1 1 Article 2 Transcriptomics as precision medicine to classify in 3 vivo models of dietary-induced atherosclerosis at 4 cellular and molecular levels 5 Alexei Evsikov 1,2, Caralina Marín de Evsikova 1,2* 6 1 Epigenetics & Functional Genomics Laboratory, Department of Molecular Medicine, Morsani College of 7 Medicine, University of South Florida, Tampa, Florida, 33612, USA; 8 2 Department of Research and Development, Bay Pines Veteran Administration Healthcare System, Bay 9 Pines, FL 33744, USA 10 11 * Correspondence: [email protected]; Tel.: +1-813-974-2248 12 13 Abstract: The central promise of personalized medicine is individualized treatments that target 14 molecular mechanisms underlying the physiological changes and symptoms arising from disease. 15 We demonstrate a bioinformatics analysis pipeline as a proof-of-principle to test the feasibility and 16 practicality of comparative transcriptomics to classify two of the most popular in vivo diet-induced 17 models of coronary atherosclerosis, apolipoprotein E null mice and New Zealand White rabbits. 18 Transcriptomics analyses indicate the two models extensively share dysregulated genes albeit with 19 some unique pathways. For instance, while both models have alterations in the mitochondrion, the 20 biochemical pathway analysis revealed, Complex IV in the electron transfer chain is higher in mice, 21 whereas the rest of the electron transfer chain components are higher in the rabbits. Several fatty 22 acids anabolic pathways are expressed higher in mice, whereas fatty acids and lipids degradation 23 pathways are higher in rabbits.