HIC1 Modulates Prostate Cancer Progression by Epigenetic Modification
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Molecular Profiling of Peripheral Blood Is Associated with Circulating Tumor Cells Content and Poor Survival in Metastatic Castration-Resistant Prostate Cancer
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No. 12 Molecular profiling of peripheral blood is associated with circulating tumor cells content and poor survival in metastatic castration-resistant prostate cancer Mercedes Marín-Aguilera1, Òscar Reig1,2, Juan José Lozano3, Natalia Jiménez1, Susana García-Recio1,4, Nadina Erill5, Lydia Gaba2, Andrea Tagliapietra2, Vanesa Ortega2, Gemma Carrera6, Anna Colomer5, Pedro Gascón4 and Begoña Mellado1,2 1 Translational Genomics Group and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain 2 Medical Oncology Department, Hospital Clínic, Barcelona, Spain 3 Bioinformatics Platform Department, Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain 4 Laboratory of Translational Oncology, Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain 5 Althia, Barcelona, Spain 6 Medical Oncology Department, Hospital Plató, Barcelona, Spain Correspondence to: Begoña Mellado, email: [email protected] Keywords: circulating tumor cells, peripheral blood, microarrays, cell search system Received: January 22, 2015 Accepted: February 14, 2015 Published: March 12, 2015 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The enumeration of circulating -
Methods in and Applications of the Sequencing of Short Non-Coding Rnas" (2013)
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Methods in and Applications of the Sequencing of Short Non- Coding RNAs Paul Ryvkin University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ryvkin, Paul, "Methods in and Applications of the Sequencing of Short Non-Coding RNAs" (2013). Publicly Accessible Penn Dissertations. 922. https://repository.upenn.edu/edissertations/922 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/922 For more information, please contact [email protected]. Methods in and Applications of the Sequencing of Short Non-Coding RNAs Abstract Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields angingr from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non- coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications ot RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. -
Mechanisms Underlying Phenotypic Heterogeneity in Simplex Autism Spectrum Disorders
Mechanisms Underlying Phenotypic Heterogeneity in Simplex Autism Spectrum Disorders Andrew H. Chiang Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2021 © 2021 Andrew H. Chiang All Rights Reserved Abstract Mechanisms Underlying Phenotypic Heterogeneity in Simplex Autism Spectrum Disorders Andrew H. Chiang Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity. Despite recent progress in ASD genetics, the nature of phenotypic heterogeneity across probands is not well understood. Notably, likely gene- disrupting (LGD) de novo mutations affecting the same gene often result in substantially different ASD phenotypes. We find that truncating mutations in a gene can result in a range of relatively mild decreases (15-30%) in gene expression due to nonsense-mediated decay (NMD), and show that more severe autism phenotypes are associated with greater decreases in expression. We also find that each gene with recurrent ASD mutations can be described by a parameter, phenotype dosage sensitivity (PDS), which characteriZes the relationship between changes in a gene’s dosage and changes in a given phenotype. Using simple linear models, we show that changes in gene dosage account for a substantial fraction of phenotypic variability in ASD. We further observe that LGD mutations affecting the same exon frequently lead to strikingly similar phenotypes in unrelated ASD probands. These patterns are observed for two independent proband cohorts and multiple important ASD-associated phenotypes. The observed phenotypic similarities are likely mediated by similar changes in gene dosage and similar perturbations to the relative expression of splicing isoforms. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
Expression and Functional Characterization of LRRC4, a Novel Brain-Specific Member of the LRR Superfamily
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 579 (2005) 3674–3682 FEBS 29683 Expression and functional characterization of LRRC4, a novel brain-specific member of the LRR superfamily Qiuhong Zhanga,1, Jieru Wanga,b,1, Songqing Fana, Lili Wanga, Li Caoa, Ke Tanga, Cong Penga, Zheng Lia, Weifang Lia, Kai Gana, Zhongqi Liua, Xiaoling Lia, Shourong Shenc, Guiyuan Lia,* a Cancer Research Institute, Central South University, Changsha 410078, Hunan, PeopleÕs Republic of China b School of Public Health, Central South University, Changsha 410078, Hunan, PeopleÕs Republic of China c The Third Affiliated Hospital of Xiang Ya School of Medicine, Central South University, Changsha 410078, Hunan, PeopleÕs Republic of China Received 28 February 2005; revised 20 April 2005; accepted 9 May 2005 Available online 13 June 2005 Edited by Lukas Huber sias. Loss of heterozygosity (LOH) of markers on human chro- Abstract LRRC4, a novel member of LRR superfamily thought to be involved in development and tumorigenesis of the mosome 7q are frequently encountered in malignant myeloid nervous tissue, has the potential to suppress tumorigenesis and disorders as well as in head and neck, breast, prostate, ovarian, cell proliferation of U251MG cells. This study aimed at reveal- colon, gastric, pancreatic, and renal cell carcinomas [1,2]. Our ing the correlation between expression of LRRC4 and the main- previous studies demonstrate there is the LOH on chromo- tenance of normal function and tumorigenesis suppression within some 7q31-ter in nasopharyngeal carcinoma [3,4]. Introduc- the central nervous system. -
Implication of LRRC4C and DPP6 in Neurodevelopmental Disorders Gilles Maussion,1 Cristiana Cruceanu,1,2 Jill A
ORIGINAL ARTICLE Implication of LRRC4C and DPP6 in Neurodevelopmental Disorders Gilles Maussion,1 Cristiana Cruceanu,1,2 Jill A. Rosenfeld,3 Scott C. Bell,1 Fabrice Jollant,1,4 Jin Szatkiewicz,5 Ryan L. Collins,6,7 Carrie Hanscom,6 Ilaria Kolobova,1 Nicolas Menjot de Champfleur,8 Ian Blumenthal,6 Colby Chiang,9,10 Vanessa Ota,1 Christina Hultman,11 Colm O’Dushlaine,7 Steve McCarroll,7,12 Martin Alda,13 Sebastien Jacquemont,14 Zehra Ordulu,15,16 Christian R. Marshall,17 Melissa T. Carter,18 Lisa G. Shaffer,3 Pamela Sklar,19 Santhosh Girirajan,20 Cynthia C. Morton,7,21,22 James F. Gusella,6,7,12 Gustavo Turecki,1,2 Dimitri J. Stavropoulos,23 Patrick F. Sullivan,5 Stephen W. Scherer,17,24 Michael E. Talkowski,6,7,25 and Carl Ernst1,2* 1Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada 2Department of Human Genetics, McGill University, Montreal, Canada 3Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington 4Nıˆmes Academic Hospital (CHU), Nıˆmes, France 5Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 6Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 7Broad Institute of MIT and Harvard, Cambridge, Massachusetts 8Department of Neuroradiology, University Hospital Center of Montpellier, Montpellier, France 9Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 10McDonnell Genome Institute, Washington University School -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. -
Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumo
cancers Article Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma Thomas Mohr 1,2 , Sonja Katz 1 , Verena Paulitschke 3 , Nadim Aizarani 4 and Alexander Tolios 5,6,7,∗ 1 ScienceConsult—DI Thomas Mohr KG, Enzianweg 10a, A-2353 Guntramsdorf, Austria; [email protected] or [email protected] (T.M.); [email protected] (S.K.) 2 Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, A-1090 Vienna, Austria 3 Department of Dermatology, Medical University of Vienna, A-1090 Vienna, Austria; [email protected] 4 Max-Planck-Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany; [email protected] 5 Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, A-1090 Vienna, Austria 6 Center of Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, A-1090 Vienna, Austria 7 Section of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics and Citation: Mohr, T.; Katz, S.; Intelligent Systems, Medical University of Vienna, A-1090 Vienna, Austria Paulitschke, V.; Aizarani, N.; Tolios, * Correspondence: [email protected] A. Systematic Analysis of the Transcriptome Profiles and Simple Summary: Endothelial cells, the innermost layer of blood vessels, play an essential role in the Co-Expression Networks of Tumour progression of cancer, particularly liver cancer. To develop cancer therapies targeting those cells, the Endothelial Cells Identifies Several investigation of gene co-expression networks is of great importance. -
Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein -
Identification of Circrna-Lncrna-Mirna-Mrna Competitive Endogenous RNA Network As Novel Prognostic Markers for Acute Myeloid Leukemia
G C A T T A C G G C A T genes Article Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia Yaqi Cheng , Yaru Su, Shoubi Wang, Yurun Liu, Lin Jin , Qi Wan, Ying Liu, Chaoyang Li, Xuan Sang, Liu Yang, Chang Liu and Zhichong Wang * State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; [email protected] (Y.C.); [email protected] (Y.S.); [email protected] (S.W.); [email protected] (Y.L.); [email protected] (L.J.); [email protected] (Q.W.); [email protected] (Y.L.); [email protected] (C.L.); [email protected] (X.S.); [email protected] (L.Y.); [email protected] (C.L.) * Correspondence: [email protected]; Tel.: +86-020-8733-0379 Received: 1 July 2020; Accepted: 29 July 2020; Published: 31 July 2020 Abstract: Background: Acute myeloid leukemia (AML) is one of the most common malignant and aggressive hematologic tumors, and its pathogenesis is associated with abnormal post- transcriptional regulation. Unbalanced competitive endogenous RNA (ceRNA) promotes tumorigenesis and progression, and greatly contributes to tumor risk classification and prognosis. However, the comprehensive analysis of the circular RNA (circRNA)-long non-coding RNA (lncRNA)-miRNA-mRNA ceRNA network in the prognosis of AML is still rarely reported. Method: We obtained transcriptome data of AML and normal samples from The Cancer Genome Atlas (TCGA), Genotype-tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases, and identified differentially expressed (DE) mRNAs, lncRNAs, and circRNAs. -
Supplementary Material Peptide-Conjugated Oligonucleotides Evoke Long-Lasting Myotonic Dystrophy Correction in Patient-Derived C
Supplementary material Peptide-conjugated oligonucleotides evoke long-lasting myotonic dystrophy correction in patient-derived cells and mice Arnaud F. Klein1†, Miguel A. Varela2,3,4†, Ludovic Arandel1, Ashling Holland2,3,4, Naira Naouar1, Andrey Arzumanov2,5, David Seoane2,3,4, Lucile Revillod1, Guillaume Bassez1, Arnaud Ferry1,6, Dominic Jauvin7, Genevieve Gourdon1, Jack Puymirat7, Michael J. Gait5, Denis Furling1#* & Matthew J. A. Wood2,3,4#* 1Sorbonne Université, Inserm, Association Institut de Myologie, Centre de Recherche en Myologie, CRM, F-75013 Paris, France 2Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK 3Department of Paediatrics, John Radcliffe Hospital, University of Oxford, Oxford, UK 4MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK 5Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK 6Sorbonne Paris Cité, Université Paris Descartes, F-75005 Paris, France 7Unit of Human Genetics, Hôpital de l'Enfant-Jésus, CHU Research Center, QC, Canada † These authors contributed equally to the work # These authors shared co-last authorship Methods Synthesis of Peptide-PMO Conjugates. Pip6a Ac-(RXRRBRRXRYQFLIRXRBRXRB)-CO OH was synthesized and conjugated to PMO as described previously (1). The PMO sequence targeting CUG expanded repeats (5′-CAGCAGCAGCAGCAGCAGCAG-3′) and PMO control reverse (5′-GACGACGACGACGACGACGAC-3′) were purchased from Gene Tools LLC. Animal model and ASO injections. Experiments were carried out in the “Centre d’études fonctionnelles” (Faculté de Médecine Sorbonne University) according to French legislation and Ethics committee approval (#1760-2015091512001083v6). HSA-LR mice are gift from Pr. Thornton. The intravenous injections were performed by single or multiple administrations via the tail vein in mice of 5 to 8 weeks of age. -
ABSTRACT WON, EUGENE THOME. Cloning and Characterization Of
ABSTRACT WON, EUGENE THOME. Cloning and Characterization of Leptin in a Teleost Fish and its Role in Mediating Appetite and Growth. (Under the direction of Russell J. Borski). Mammalian and clinical studies show that leptin circulates as an endocrine reflection of fat deposition that relays information about energy reserves to the brain and periphery through its ubiquitously expressed receptor (OBR). The leptin system thereby modulates appetite and energy expenditure according to endogenous energy levels in what is referred to as a lipostatic model of energy homeostasis. Due to difficulty in sequencing leptin and OBR genes in lower vertebrates, however, limited information has been gathered about this system in ectotherms generally, including teleost fishes. Upon cloning a putative leptin gene in striped bass (Morone saxatilis), representing the first leptin identified in Perciformes, the largest and most diverse order of fish, we profiled its tissue distribution, measured gene expression during fed, fasted and refed conditions, assessed its effect on appetite and tested its regulatory influence on key elements of the endocrine growth axis. The OBR gene was also cloned and its mRNA measured under similar metabolic states in brain regions associated with appetite regulation. This research portrays a leptin system in Morone that adjusts energy intake and expenditure according to nutritional state. Leptin may thereby influence the shift away from feeding and toward growth during positive energy states, and therefore serve as an anabolic switch for metabolically expensive processes. While genome duplication events have resulted in leptin paralogs in some fish lineages, the single Morone leptin appears to be orthologous to the medaka A-type.