Autocrine Endothelin-3/Endothelin Receptor B Signaling Maintains Cellular and Molecular Properties of Glioblastoma Stem Cells
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Differential Gene Expression Profile in Endometrioid And
[CANCER RESEARCH 63, 5697–5702, September 15, 2003] Advances in Brief Differential Gene Expression Profile in Endometrioid and Nonendometrioid Endometrial Carcinoma: STK15 Is Frequently Overexpressed and Amplified in Nonendometrioid Carcinomas1 Gema Moreno-Bueno, Carolina Sa´nchez-Este´vez, Rau´l Cassia, Sandra Rodrı´guez-Perales, Ramo´n Dı´az-Uriarte, Orlando Domı´nguez, David Hardisson, Miguel Andujar, Jaime Prat, Xavier Matias-Guiu, Juan C. Cigudosa, and Jose´Palacios2 Laboratory of Breast and Gynaecological Cancer, Molecular Pathology Programme [G. M-B., C. S-E., R. C., J. Pa.] and Biotechnology Programme [S. R-P., R. D-U., O. D., J. C. C.], Centro Nacional de Investigaciones Oncologicas, Madrid; Department of Pathology, Hospital Universitario La Paz, Madrid [D. H.]; Department of Pathology, Hospital Materno Infantil, Las Palmas [M. A.]; Department of Pathology, Hospital Sant Pau y Sant Creu, Barcelona [J. Pr.]; and Department of Pathology, Hospital Arnau de Villanova, Lleida [X. M-G.], Spain Abstract tiated endometrioid carcinomas that usually develop in pre- and perimenopausal women. They are associated with estrogen stimula- Endometrial carcinoma (EC) comprises at least two types of cancer: tion, coexist with, or are preceded by atypical endometrial hyperplasia endometrioid carcinomas (EECs) are estrogen-related tumors, which are and are associated with ER positivity and with K-RAS, PTEN, and frequently euploid and have a good prognosis. Nonendometrioid carcino-  mas (NEECs; serous and clear cell forms) are not estrogen related, are -catenin mutations, and microsatellite instability. Conversely, type II frequently aneuploid, and are clinically aggressive. We used cDNA mi- tumors are NEECs (papillary serous and clear cell carcinomas) that croarrays containing 6386 different genes to analyze gene expression occur in older women. -
Myosin Myth4-FERM Structures Highlight Important Principles of Convergent Evolution
Myosin MyTH4-FERM structures highlight important principles of convergent evolution Vicente José Planelles-Herreroa,b, Florian Blanca,c, Serena Sirigua, Helena Sirkiaa, Jeffrey Clausea, Yannick Souriguesa, Daniel O. Johnsrudd, Beatrice Amiguesa, Marco Cecchinic, Susan P. Gilberte, Anne Houdussea,1,2, and Margaret A. Titusd,1,2 aStructural Motility, Institut Curie, CNRS, UMR 144, PSL Research University, F-75005 Paris, France; bUPMC Université de Paris 6, Institut de Formation Doctorale, Sorbonne Universités, 75252 Paris Cedex 05, France; cLaboratoire d’Ingénierie des Fonctions Moléculaires, Institut de Science et d’Ingénierie Supramoléculaires, UMR 7006 CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France; dDepartment of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455; and eDepartment of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 Edited by James A. Spudich, Stanford University School of Medicine, Stanford, CA, and approved March 31, 2016 (received for review January 15, 2016) Myosins containing MyTH4-FERM (myosin tail homology 4-band (Fig. 1). These MF myosins are widespread and likely quite an- 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found cient because they are found in many different branches of the in a wide range of phylogenetically divergent organisms, such as phylogenetic tree (5, 6), including Opisthokonts (which includes humans and the social amoeba Dictyostelium (Dd). Interestingly, Metazoa, unicellular Holozoa, and Fungi), Amoebozoa, and the evolutionarily distant MF myosins have similar roles in the exten- SAR (Stramenopiles, Alveolates, and Rhizaria) (Fig. 1 A and B). sion of actin-filled membrane protrusions such as filopodia and Over the course of hundreds of millions years of parallel evolution bind to microtubules (MT), suggesting that the core functions of the MF myosins have acquired or maintained roles in the formation these MF myosins have been highly conserved over evolution. -
The Cardiopulmonary Effects of the Calcitonin Gene- Related Peptide Family Kalsitonin-Geni İle İlişkili Peptit Ailesinin Kardiyopulmoner Etkileri
Turk J Pharm Sci 2020;17(3):349-356 DOI: 10.4274/tjps.galenos.2019.47123 REVIEW The Cardiopulmonary Effects of the Calcitonin Gene- related Peptide Family Kalsitonin-Geni İle İlişkili Peptit Ailesinin Kardiyopulmoner Etkileri Gökçen TELLİ1, Banu Cahide TEL1, Bülent GÜMÜŞEL2* 1Hacettepe University Faculty of Pharmacy, Department of Pharmacology, Ankara, Turkey 2Lokman Hekim University Faculty of Pharmacy, Department of Pharmacology, Ankara, Turkey ABSTRACT Cardiopulmonary diseases are very common among the population. They are high-cost diseases and there are still no definitive treatments. The roles of members of the calcitonin-gene related-peptide (CGRP) family in treating cardiopulmonary diseases have been studied for many years and promising results obtained. Especially in recent years, two important members of the family, adrenomedullin and adrenomedullin2/intermedin, have been considered new treatment targets in cardiopulmonary diseases. In this review, the roles of CGRP family members in cardiopulmonary diseases are investigated based on the studies performed to date. Key words: CGRP family, cardiopulmonary diseases, adrenomedullin, adrenomedullin2/intermedin, pulmonary hypertension ÖZ Kardiyopulmoner hastalıklar toplumda sık görülen, tedavi maliyeti oldukça yüksek ve halen kesin bir tedavisi bulunmayan hastalıklardır. Kalsitonin- geni ile ilişkili peptit (CGRP) ailesinin üyelerinin bir çok kardiyopulmoner hastalıktaki rolleri uzun yıllardır çalışılmakta ve umut vadeden sonuçlar elde edilmektedir. Özellikle son yıllarda CGRP ailesine -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
Circmyo10 Promotes Osteosarcoma Progression by Regulating Mir-370
Chen et al. Molecular Cancer (2019) 18:150 https://doi.org/10.1186/s12943-019-1076-1 RESEARCH Open Access CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/ RUVBL1 axis to enhance the transcriptional activity of β-catenin/LEF1 complex via effects on chromatin remodeling Junxin Chen1†, Gang Liu1†, Yizheng Wu1†, Jianjun Ma1†, Hongfei Wu2, Ziang Xie1, Shuai Chen1, Yute Yang1, Shengyu Wang1, Panyang Shen1, Yifan Fang3, Shunwu Fan1, Shuying Shen1* and Xiangqian Fang1* Abstract Background: CircMYO10 is a circular RNA generated by back-splicing of gene MYO10 and is upregulated in osteosarcoma cell lines, but its functional role in osteosarcoma is still unknown. This study aimed to clarify the mechanism of circMYO10 in osteosarcoma. Methods: CircMYO10 expression in 10 paired osteosarcoma and chondroma tissues was assessed by quantitative reverse transcription polymerase chain reaction (PCR). The function of circMYO10/miR-370-3p/RUVBL1 axis was assessed regarding two key characteristics: proliferation and endothelial–mesenchymal transition (EMT). Bioinformatics analysis, western blotting, real-time PCR, fluorescence in situ hybridization, immunoprecipitation, RNA pull-down assays, luciferase reporter assays, chromatin immunoprecipitation, and rescue experiments were used to evaluate the mechanism. Stably transfected MG63 cells were injected via tail vein or subcutaneously into nude mice to assess the role of circMYO10 in vivo. Results: CircMYO10 was significantly upregulated, while miR-370-3p was downregulated, in osteosarcoma cell lines and human osteosarcoma samples. Silencing circMYO10 inhibited cell proliferation and EMT in vivo and in vitro. Mechanistic investigations revealed that miR-370-3p targets RUVBL1 directly, and inhibits the interaction between RUVBL1 and β-catenin/LEF1 complex while circMYO10 showed a contrary effect via the inhibition of miR-370-3p. -
Supporting Online Material
1 2 3 4 5 6 7 Supplementary Information for 8 9 Fractalkine-induced microglial vasoregulation occurs within the retina and is altered early in diabetic 10 retinopathy 11 12 *Samuel A. Mills, *Andrew I. Jobling, *Michael A. Dixon, Bang V. Bui, Kirstan A. Vessey, Joanna A. Phipps, 13 Ursula Greferath, Gene Venables, Vickie H.Y. Wong, Connie H.Y. Wong, Zheng He, Flora Hui, James C. 14 Young, Josh Tonc, Elena Ivanova, Botir T. Sagdullaev, Erica L. Fletcher 15 * Joint first authors 16 17 Corresponding author: 18 Prof. Erica L. Fletcher. Department of Anatomy & Neuroscience. The University of Melbourne, Grattan St, 19 Parkville 3010, Victoria, Australia. 20 Email: [email protected] ; Tel: +61-3-8344-3218; Fax: +61-3-9347-5219 21 22 This PDF file includes: 23 24 Supplementary text 25 Figures S1 to S10 26 Tables S1 to S7 27 Legends for Movies S1 to S2 28 SI References 29 30 Other supplementary materials for this manuscript include the following: 31 32 Movies S1 to S2 33 34 35 36 1 1 Supplementary Information Text 2 Materials and Methods 3 Microglial process movement on retinal vessels 4 Dark agouti rats were anaesthetized, injected intraperitoneally with rhodamine B (Sigma-Aldrich) to label blood 5 vessels and retinal explants established as described in the main text. Retinal microglia were labelled with Iba-1 6 and imaging performed on an inverted confocal microscope (Leica SP5). Baseline images were taken for 10 7 minutes, followed by the addition of PBS (10 minutes) and then either fractalkine or fractalkine + candesartan 8 (10 minutes) using concentrations outlined in the main 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. -
Searching for Novel Peptide Hormones in the Human Genome Olivier Mirabeau
Searching for novel peptide hormones in the human genome Olivier Mirabeau To cite this version: Olivier Mirabeau. Searching for novel peptide hormones in the human genome. Life Sciences [q-bio]. Université Montpellier II - Sciences et Techniques du Languedoc, 2008. English. tel-00340710 HAL Id: tel-00340710 https://tel.archives-ouvertes.fr/tel-00340710 Submitted on 21 Nov 2008 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITE MONTPELLIER II SCIENCES ET TECHNIQUES DU LANGUEDOC THESE pour obtenir le grade de DOCTEUR DE L'UNIVERSITE MONTPELLIER II Discipline : Biologie Informatique Ecole Doctorale : Sciences chimiques et biologiques pour la santé Formation doctorale : Biologie-Santé Recherche de nouvelles hormones peptidiques codées par le génome humain par Olivier Mirabeau présentée et soutenue publiquement le 30 janvier 2008 JURY M. Hubert Vaudry Rapporteur M. Jean-Philippe Vert Rapporteur Mme Nadia Rosenthal Examinatrice M. Jean Martinez Président M. Olivier Gascuel Directeur M. Cornelius Gross Examinateur Résumé Résumé Cette thèse porte sur la découverte de gènes humains non caractérisés codant pour des précurseurs à hormones peptidiques. Les hormones peptidiques (PH) ont un rôle important dans la plupart des processus physiologiques du corps humain. -
EDNRB Gene Endothelin Receptor Type B
EDNRB gene endothelin receptor type B Normal Function The EDNRB gene provides instructions for making a protein called endothelin receptor type B. This protein is located on the surface of cells and functions as a signaling mechanism, transmitting information from outside the cell to inside the cell. The receptor interacts with proteins called endothelins to regulate several critical biological processes, including the development and function of blood vessels, the production of certain hormones, and the stimulation of cell growth and division. Endothelin 3 (produced from the EDN3 gene) is one of the proteins that interacts with endothelin receptor type B. During early development before birth (embryonic development), endothelin 3 and endothelin receptor type B together play an important role in neural crest cells. These cells migrate from the developing spinal cord to specific regions in the embryo, where they give rise to many different types of cells. In particular, endothelin 3 and endothelin receptor type B are essential for the formation of nerves in the intestine (enteric nerves) and for the production of specialized cells called melanocytes. Melanocytes produce melanin, a pigment that contributes to skin, hair, and eye color. Melanin is also involved in the normal function of the inner ear. Health Conditions Related to Genetic Changes Hirschsprung disease More than 30 mutations in the EDNRB gene have been found to cause Hirschsprung disease, a disorder that causes severe constipation or blockage of the intestine. Although Hirschsprung disease is a feature of another condition called Waardenburg syndrome type IV (described below), EDNRB gene mutations can also cause Hirschsprung disease in people without Waardenburg syndrome. -
Spectrum of MYO7A Mutations in an Indigenous South African
G C A T T A C G G C A T genes Article Spectrum of MYO7A Mutations in an Indigenous South African Population Further Elucidates the Nonsyndromic Autosomal Recessive Phenotype of DFNB2 to Include Both Homozygous and Compound Heterozygous Mutations Rosemary Ida Kabahuma 1,2,*, Wolf-Dieter Schubert 2, Christiaan Labuschagne 3, Denise Yan 4, Susan Halloran Blanton 4,5 , Michael Sean Pepper 6 and Xue Zhong Liu 4,5,* 1 Department of Otorhinolaryngology, University of Pretoria, Pretoria 0001, South Africa 2 Departments of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0001, South Africa; [email protected] 3 Inqaba Biotechnical Industries, Pretoria 0002, South Africa; [email protected] 4 Department Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; [email protected] (D.Y.); [email protected] (S.H.B.) 5 Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA 6 Department Immunology and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Citation: Kabahuma, R.I.; Pretoria 0001, South Africa; [email protected] Schubert, W.-D.; Labuschagne, C.; * Correspondence: [email protected] (R.I.K.); [email protected] (X.Z.L.) Yan, D.; Blanton, S.H.; Pepper, M.S.; Liu, X.Z. Spectrum of MYO7A Abstract: MYO7A gene encodes unconventional myosin VIIA, which, when mutated, causes a phe- Mutations in an Indigenous South notypic spectrum ranging from recessive hearing loss DFNB2 to deaf-blindness, Usher Type 1B African Population Further (USH1B). -
The Borg Family of Cdc42 Effector Proteins Cdc42ep1–5
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Institute of Cancer Research Repository Biochemical Society Transactions (2016) 0 1–8 DOI: 10.1042/BST20160219 1 2 The Borg family of Cdc42 effector proteins 3 4 Cdc42EP1–5 5 6 Aaron J. Farrugia and Fernando Calvo 7 8 Tumour Microenvironment Team, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW2 6JB, U.K. 9 Correspondence: Fernando Calvo ([email protected]) 10 11 12 13 Despite being discovered more than 15 years ago, the Borg (binder of Rho GTPases) 14 – family of Cdc42 effector proteins (Cdc42EP1 5) remains largely uncharacterised and rela- 15 tively little is known about their structure, regulation and role in development and disease. 16 Recent studies are starting to unravel some of the key functional and mechanistic 17 aspects of the Borg proteins, including their role in cytoskeletal remodelling and signal- 18 ling. In addition, the participation of Borg proteins in important cellular processes such as 19 cell shape, directed migration and differentiation is slowly emerging, directly linking Borgs 20 with important physiological and pathological processes such as angiogenesis, neuro- 21 fi transmission and cancer-associated desmoplasia. Here, we review some of these nd- 22 ings and discuss future prospects. 23 24 25 26 27 28 29 Introduction 30 The Rho GTPase family member Cdc42 regulates a diverse range of cellular functions including cyto- 31 kinesis, cytoskeletal remodelling and cell polarity [1,2]. Like other Rho family members, Cdc42 cycles 32 between two tightly regulated conformational states, a GTP-bound active state and a GDP-bound 33 inactive state [3].