(Errγ) Is a Regulator of Skeletogenesis
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I LITERATURE-BASED DISCOVERY of KNOWN and POTENTIAL NEW
LITERATURE-BASED DISCOVERY OF KNOWN AND POTENTIAL NEW MECHANISMS FOR RELATING THE STATUS OF CHOLESTEROL TO THE PROGRESSION OF BREAST CANCER BY YU WANG THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Bioinformatics with a concentration in Library and Information Science in the Graduate College of the University of Illinois at Urbana-Champaign, 2019 Urbana, Illinois Adviser: Professor Vetle I. Torvik Professor Erik Russell Nelson i ABSTRACT Breast cancer has been studied for a long period of time and from a variety of perspectives in order to understand its pathogeny. The pathogeny of breast cancer can be classified into two groups: hereditary and spontaneous. Although cancer in general is considered a genetic disease, spontaneous factors are responsible for most of the pathogeny of breast cancer. In other words, breast cancer is more likely to be caused and deteriorated by the dysfunction of a physical molecule than be caused by germline mutation directly. Interestingly, cholesterol, as one of those molecules, has been discovered to correlate with breast cancer risk. However, the mechanisms of how cholesterol helps breast cancer progression are not thoroughly understood. As a result, this study aims to study known and discover potential new mechanisms regarding to the correlation of cholesterol and breast cancer progression using literature review and literature-based discovery. The known mechanisms are further classified into four groups: cholesterol membrane content, transport of cholesterol, cholesterol metabolites, and other. The potential mechanisms, which are intended to provide potential new treatments, have been identified and checked for feasibility by an expert. -
Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart
RESEARCH ARTICLE Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart Chung-Il An1☯*, Yasunori Ichihashi2☯¤a¤b*, Jie Peng3, Neelima R. Sinha2, Nobuko Hagiwara1* 1 Division of Cardiovascular Medicine, Department of Internal Medicine, University of California Davis, Davis, California, United States of America, 2 Department of Plant Biology, University of California Davis, Davis, California, United States of America, 3 Department of Statistics, University of California Davis, Davis, California, United States of America ☯ These authors contributed equally to this work. a11111 ¤a Current address: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan ¤b Current address: JST, PRESTO, Kawaguchi, Saitama, Japan * [email protected] (CA); [email protected] (YI); [email protected] (NH) Abstract OPEN ACCESS The postnatal heart undergoes highly coordinated developmental processes culminating in Citation: An C-I, Ichihashi Y, Peng J, Sinha NR, the complex physiologic properties of the adult heart. The molecular mechanisms of postna- Hagiwara N (2016) Transcriptome Dynamics and tal heart development remain largely unexplored despite their important clinical implications. Potential Roles of Sox6 in the Postnatal Heart. To gain an integrated view of the dynamic changes in gene expression during postnatal PLoS ONE 11(11): e0166574. doi:10.1371/journal. heart development at the organ level, time-series transcriptome analyses of the postnatal pone.0166574 hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a Editor: Katherine Yutzey, Cincinnati Children's newly developed bioinformatics pipeline. We identified functional gene clusters by principal Hospital Medical Center, UNITED STATES component analysis with self-organizing map clustering which revealed organized, discrete Received: July 16, 2016 gene expression patterns corresponding to biological functions associated with the neona- Accepted: October 31, 2016 tal, juvenile and adult stages of postnatal heart development. -
Prox1regulates the Subtype-Specific Development of Caudal Ganglionic
The Journal of Neuroscience, September 16, 2015 • 35(37):12869–12889 • 12869 Development/Plasticity/Repair Prox1 Regulates the Subtype-Specific Development of Caudal Ganglionic Eminence-Derived GABAergic Cortical Interneurons X Goichi Miyoshi,1 Allison Young,1 Timothy Petros,1 Theofanis Karayannis,1 Melissa McKenzie Chang,1 Alfonso Lavado,2 Tomohiko Iwano,3 Miho Nakajima,4 Hiroki Taniguchi,5 Z. Josh Huang,5 XNathaniel Heintz,4 Guillermo Oliver,2 Fumio Matsuzaki,3 Robert P. Machold,1 and Gord Fishell1 1Department of Neuroscience and Physiology, NYU Neuroscience Institute, Smilow Research Center, New York University School of Medicine, New York, New York 10016, 2Department of Genetics & Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, 3Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan, 4Laboratory of Molecular Biology, Howard Hughes Medical Institute, GENSAT Project, The Rockefeller University, New York, New York 10065, and 5Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Neurogliaform (RELNϩ) and bipolar (VIPϩ) GABAergic interneurons of the mammalian cerebral cortex provide critical inhibition locally within the superficial layers. While these subtypes are known to originate from the embryonic caudal ganglionic eminence (CGE), the specific genetic programs that direct their positioning, maturation, and integration into the cortical network have not been eluci- dated. Here, we report that in mice expression of the transcription factor Prox1 is selectively maintained in postmitotic CGE-derived cortical interneuron precursors and that loss of Prox1 impairs the integration of these cells into superficial layers. Moreover, Prox1 differentially regulates the postnatal maturation of each specific subtype originating from the CGE (RELN, Calb2/VIP, and VIP). -
Supplemental Tables4.Pdf
Yano_Supplemental_Table_S4 Gene ontology – Biological process 1 of 9 Fold List Pop Pop GO Term Count % PValue Bonferroni Benjamini FDR Genes Total Hits Total Enrichment DLC1, CADM1, NELL2, CLSTN1, PCDHGA8, CTNNB1, NRCAM, APP, CNTNAP2, FERT2, RAPGEF1, PTPRM, MPDZ, SDK1, PCDH9, PTPRS, VEZT, NRXN1, MYH9, GO:0007155~cell CTNNA2, NCAM1, NCAM2, DDR1, LSAMP, CNTN1, 50 5.61 2.14E-08 510 311 7436 2.34 4.50E-05 4.50E-05 3.70E-05 adhesion ROR2, VCAN, DST, LIMS1, TNC, ASTN1, CTNND2, CTNND1, CDH2, NEO1, CDH4, CD24A, FAT3, PVRL3, TRO, TTYH1, MLLT4, LPP, NLGN1, PCDH19, LAMA1, ITGA9, CDH13, CDON, PSPC1 DLC1, CADM1, NELL2, CLSTN1, PCDHGA8, CTNNB1, NRCAM, APP, CNTNAP2, FERT2, RAPGEF1, PTPRM, MPDZ, SDK1, PCDH9, PTPRS, VEZT, NRXN1, MYH9, GO:0022610~biological CTNNA2, NCAM1, NCAM2, DDR1, LSAMP, CNTN1, 50 5.61 2.14E-08 510 311 7436 2.34 4.50E-05 4.50E-05 3.70E-05 adhesion ROR2, VCAN, DST, LIMS1, TNC, ASTN1, CTNND2, CTNND1, CDH2, NEO1, CDH4, CD24A, FAT3, PVRL3, TRO, TTYH1, MLLT4, LPP, NLGN1, PCDH19, LAMA1, ITGA9, CDH13, CDON, PSPC1 DCC, ENAH, PLXNA2, CAPZA2, ATP5B, ASTN1, PAX6, ZEB2, CDH2, CDH4, GLI3, CD24A, EPHB1, NRCAM, GO:0006928~cell CTTNBP2, EDNRB, APP, PTK2, ETV1, CLASP2, STRBP, 36 4.04 3.46E-07 510 205 7436 2.56 7.28E-04 3.64E-04 5.98E-04 motion NRG1, DCLK1, PLAT, SGPL1, TGFBR1, EVL, MYH9, YWHAE, NCKAP1, CTNNA2, SEMA6A, EPHA4, NDEL1, FYN, LRP6 PLXNA2, ADCY5, PAX6, GLI3, CTNNB1, LPHN2, EDNRB, LPHN3, APP, CSNK2A1, GPR45, NRG1, RAPGEF1, WWOX, SGPL1, TLE4, SPEN, NCAM1, DDR1, GRB10, GRM3, GNAQ, HIPK1, GNB1, HIPK2, PYGO1, GO:0007166~cell RNF138, ROR2, CNTN1, -
Accompanies CD8 T Cell Effector Function Global DNA Methylation
Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer, Benjamin G. Barwick, Benjamin A. Youngblood, Rafi Ahmed and Jeremy M. Boss This information is current as of October 1, 2021. J Immunol 2013; 191:3419-3429; Prepublished online 16 August 2013; doi: 10.4049/jimmunol.1301395 http://www.jimmunol.org/content/191/6/3419 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130139 Material 5.DC1 References This article cites 81 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/191/6/3419.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer,* Benjamin G. Barwick,* Benjamin A. Youngblood,*,† Rafi Ahmed,*,† and Jeremy M. -
Biomedicines
biomedicines Article The Fabp4-Cre-Model is Insufficient to Study Hoxc9 Function in Adipose Tissue Sebastian Dommel 1,*, Claudia Berger 1 , Anne Kunath 1, Matthias Kern 1, Martin Gericke 2,3, Peter Kovacs 1 , Esther Guiu-Jurado 1, Nora Klöting 1,4 and Matthias Blüher 1,4,* 1 Medical Department III—Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, D-04103 Leipzig, Germany; [email protected] (C.B.); [email protected] (A.K.); [email protected] (M.K.); [email protected] (P.K.); [email protected] (E.G.-J.); [email protected] (N.K.) 2 Institute of Anatomy, Leipzig University, D-04103 Leipzig, Germany; [email protected] 3 Institute of Anatomy and Cell Biology, Martin-Luther-University, D-06108 Halle (Saale), Germany 4 Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig University, D-04103 Leipzig, Germany * Correspondence: [email protected] (S.D.); [email protected] (M.B.); Tel.: +49-341-9713400 (S.D.); +49-341-9715984 (M.B.) Received: 18 May 2020; Accepted: 26 June 2020; Published: 29 June 2020 Abstract: Developmental genes are important regulators of fat distribution and adipose tissue (AT) function. In humans, the expression of homeobox c9 (HOXC9) is significantly higher in subcutaneous compared to omental AT and correlates with body fat mass. To gain more mechanistic insights into the role of Hoxc9 in AT, we generated Fabp4-Cre-mediated Hoxc9 knockout mice (ATHoxc9-/-). -
Supplemental Materials and Methods
Supplemental Material for: Transcriptional silencing of γ-globin by BCL11A involves long-range interactions and cooperation with SOX6 Jian Xu, Vijay G. Sankaran, Min Ni, Tobias F. Menne, Rishi V. Puram, Woojin Kim, Stuart H. Orkin* *To whom correspondence should be addressed. E-mail: [email protected] Supplemental Materials and Methods Flow cytometry Cells at various stages of differentiation were analyzed by flow cytometry using FACSCalibur (BD Biosciences, San Jose, CA). Live cells were identified and gated by exclusion of 7-amino-actinomycin D (7-AAD; BD Pharmingen). The cells were analyzed for expression of cell surface receptors with antibodies specific for CD34, CD45, CD71, CD235, and CD36 conjugated to phycoerythrin (PE), fluorescein isothiocyanate (FITC), or allophycocyanin (APC; BD Pharmingen). Data were analyzed using FlowJo software (Ashland, OR). Cytology Cytocentrifuge preparations were stained with May-Grunwald-Giemsa as previously described (Sankaran et al. 2008). Real-time RT-PCR Real-time quantitative RT-PCR was performed using the iQ SYBR Green Supermix (Bio- Rad). The following primers were used for real-time RT-PCR: human and mouse BCL11A-XL (forward, 5’-ATGCGAGCTGTGCAACTATG-3’; reverse, 5’- GTAAACGTCCTTCCCCACCT-3’), human and mouse BCL11A-L (forward, 5’- CAGCTCAAAAGAGGGCAGAC-3’; reverse, 5’-GAGCTTCCATCCGAAAACTG-3’), and human BCL11A exon 1 and 2 (common between all known isoforms; forward, 5’- AACCCCAGCACTTAAGCAAA-3’; reverse, 5’-GGAGGTCATGATCCCCTTCT-3’). Supplemental Figure Legends Supplemental Figure 1. Expression of BCL11A isoforms in human and mouse erythroid cells. (A) Schematic diagram of human BCL11A isoforms (Liu et al. 2006). The antibodies used for ChIP experiments and their corresponding epitopes are indicated. Locations of primers used for RT-PCR analysis of all BCL11A isoforms (forward and reverse primers indicated by arrowheads), XL and L isoforms are indicated. -
Association Between Non-Coding Polymorphisms of HOPX Gene and Syncope in Hypertrophic Cardiomyopathy
Original Investigation 617 Association between non-coding polymorphisms of HOPX gene and syncope in hypertrophic cardiomyopathy Çağrı Güleç, Neslihan Abacı, Fatih Bayrak1, Evrim Kömürcü Bayrak, Gökhan Kahveci2, Celal Güven3, Nihan Erginel Ünaltuna Department of Genetics Institute for Experimental Medicine (DETAE), İstanbul University; İstanbul-Turkey 1Department of Cardiology, Faculty of Medicine, Acıbadem University; İstanbul-Turkey 2Clinic of Cardiology, Koşuyolu Kartal Heart Training and Research Hospital; İstanbul-Turkey 3Department of Biophysics, Faculty of Medicine, Adıyaman University; Adıyaman-Turkey ABSTRACT Objective: Homeodomain Only Protein X (HOPX) is an unusual homeodomain protein which regulates Serum Response Factor (SRF) dependent gene expression. Due to the regulatory role of HOPX on SRF activity and the regulatory role of SRF on cardiac hypertrophy, we aimed to inves- tigate the relationship between HOPX gene variations and hypertrophic cardiomyopathy (HCM). Methods: In this study, designed as a case-control study, we analyzed coding and flanking non-coding regions of the HOPX gene through 67 patients with HCM and 31 healty subjects. Certain regions of the gene were investigated by Single Stranded Conformation Polymorphism (SSCP) and Restriction Fragment Length Polymorphism (RFLP). Statistical analyses of genotypes and their relationship with clinical parameters were performed by chi-square, Kruskal-Wallis and the Fisher’s exact test. Results: In 5’ Untranslated Region (UTR) and intronic region of the HOPX gene, we found a C>T substitution and an 8-bp insertion/deletion (In/ Del) polymorphism, respectively. These two polymorphisms seemed to constitute an haplotype. While the frequency of homozygous genotypes of In/Del and C/T polymorphisms were found significantly lower in the patients with syncope (p=0.014 and p=0.017, respectively), frequency of their heterozygous genotypes were found significantly higher in the patients with syncope (p=0.048 and p=0.030, respectively). -
Accepted Manuscript
The role of sex and sex Hormones in Neurodegenerative Diseases Elisabetta Vegeto, Alessandro Villa, Sara Della Torre, Valeria Crippa, Paola Rusmini, Riccardo Cristofani, Mariarita Galbiati, Adriana Maggi*, Angelo Poletti* Downloaded from https://academic.oup.com/edrv/advance-article-abstract/doi/10.1210/endrev/bnz005/5572525 by guest on 22 October 2019 Department of Excellence of Pharmacological and Biomolecular Sciences and Center of Excellence on Neurodegenerative Diseases Università degli Studi di Milano, Italy Key terms: Sex Hormones, Alzheimer’s disease, Parkinson’s Disease, Amyotrophic Lateral Sclerosis, Spinal and Bulbar Muscular Atrophy *These Authors equally contributed to this manuscript Corresponding author's contact information: Angelo Poletti, PhD - Dipartimento di Scienze Farmacologiche e Biomolecolari, Center of Excellence on Neurodegenerative Diseases. Università degli Studi di Milano, via Balzaretti 9, 20133, Milan, Italy. Ph. +390250318215; Fax +390250318204; e-mail [email protected] Disclosure statement. The Authors have no item to disclose Grants: National Institute of Health Grant RO1AG027713; European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 278850 (INMiND); Fondazione Cariplo, Italy (2011-0591, 2014-0686 and 2017_0747); Fondazione Telethon, Italy (n. GGP14039, GGP19218); Fondazione AriSLA, Italy (ALS_HSPB8, ALS_Granulopathy, MLOpathy, Target_RAN), Italian Ministry of Health (n. GR-2011-02347198), Agenzia Italiana del Farmaco (AIFA) (Co_ALS), Italian Ministry of University and Research (MIUR), PRIN - Progetti di ricerca di interesse nazionale (n. 2015LFPNMN and 2017F2A2C5), MIUR progetto di eccellenza, Fondo per il Finanziamento delle Attività Base di Ricerca (FFABR-MIUR), Fondazione Regionale per la RicercaAccepted Biomedica (FRRB) (Regione Lombardia, Manuscript TRANS_ALS, project nr. 2015-0023), Università degli Studi di Milano e piano di sviluppo UNIMI - linea B, European Molecular Biology Organization (EMBO) short term fellowship (n. -
Gender Differences in T Cell Regulation and Responses to Sex Hormones
Gender differences in T cell regulation and responses to sex hormones By FARRAH Z. ALI A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Immunity and Infection College of Medical and Dental Sciences The University of Birmingham September 2013 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Conflicting effects of sex hormones on the immune system could potentially explain the increased susceptibility of females to autoimmune diseases. In this study, I wanted to explore the regulation of the response to sex hormones in T cells from male and female donors. We initially investigated the levels of gene expression for sex hormone receptors and sex hormone metabolising enzymes in CD45RA+ /CD4+ T cells from male and female donors at baseline and after in vitro stimulation. I found that expression of 5α-reductase 1, an enzyme which converts testosterone into the more active dihydrotestosterone (DHT), is upregulated both on the mRNA and protein level in T cells from female but not male donors after stimulation. Since androgens are generally thought to have an anti-inflammatory role, this may be a mechanism that regulates the exposure of stimulated T cells to the inhibitory influence of DHT. -
Transcriptional Silencing of G-Globin by BCL11A Involves Long-Range Interactions and Cooperation with SOX6
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptional silencing of g-globin by BCL11A involves long-range interactions and cooperation with SOX6 Jian Xu,1,2,3 Vijay G. Sankaran,1,2,4 Min Ni,5 Tobias F. Menne,1,2 Rishi V. Puram,4 Woojin Kim,1,2 and Stuart H. Orkin1,2,3,6 1Division of Hematology/Oncology, Children’s Hospital Boston, Boston, Massachusetts 02115, USA; 2Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; 3Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA; 4Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts 02115, USA; 5Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA The developmental switch from human fetal (g) to adult (b) hemoglobin represents a clinically important example of developmental gene regulation. The transcription factor BCL11A is a central mediator of g-globin silencing and hemoglobin switching. Here we determine chromatin occupancy of BCL11A at the human b-globin locus and other genomic regions in vivo by high-resolution chromatin immunoprecipitation (ChIP)–chip analysis. BCL11A binds the upstream locus control region (LCR), e-globin, and the intergenic regions between g-globin and d-globin genes. A chromosome conformation capture (3C) assay shows that BCL11A reconfigures the b-globin cluster by modulating chromosomal loop formation. We also show that BCL11A and the HMG-box-containing transcription factor SOX6 interact physically and functionally during erythroid maturation. BCL11A and SOX6 co-occupy the human b-globin cluster along with GATA1, and cooperate in silencing g-globin transcription in adult human erythroid progenitors. -
Novel Insights on Imaging Sex Hormone-Dependent Tumourigenesis in Vivo
Endocrine-Related Cancer (2011) 18 R41–R51 REVIEW Novel insights on imaging sex hormone-dependent tumourigenesis in vivo Balaji Ramachandran, Alessia Stell, Luca Maravigna, Adriana Maggi and Paolo Ciana Center of Excellence on Neurodegenerative Diseases and Department of Pharmacological Sciences, University of Milan, Via Balzaretti, 9 I-20123 Milan, Italy (Correspondence should be addressed to P Ciana; Email: [email protected]) Abstract Sex hormones modulate proliferation, apoptosis, migration, metastasis and angiogenesis in cancer cells influencing tumourigenesis from the early hyperplastic growth till the end-stage metastasis. Although decades of studies have detailed these effects at the level of molecular pathways, where and when these actions are needed for the growth and progression of hormone- dependent neoplasia is poorly elucidated. Investigation of the hormone influences in carcinogenesis in the spatio-temporal dimension is expected to unravel critical steps in tumour progression and in the onset of resistance to hormone therapies. Non-invasive in vivo imaging represents a powerful tool to follow in time hormone signalling in the whole body during tumour development. This review summarizes the tools currently available to follow hormone action in living organisms. Endocrine-Related Cancer (2011) 18 R41–R51 Introduction (Hanahan & Weinberg 2000). In hormone-related carcinogenesis, endogenous and exogenous hormones Neoplastic transformation is a highly regulated and influence a multiplicity of cell functions. Dysregula- ordered process, where a sequela of biological events tion of sex hormone-receptor signalling occurs in the leads cancer cells to acquire specific phenotypic traits tumourigenesis of breast, endometrial, ovary, prostate necessary to escape the strong selective pressure of and testis, where oestrogens, progestin and androgens the host tumour surveillance (Merlo et al.