Foxk1 Promotes Cell Proliferation and Represses Myogenic Differentiation
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The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
Integrated and Functional Genomic Approaches to Elucidate Differential Genetic Dependencies in Melanoma
Integrated and Functional Genomic Approaches to Elucidate Differential Genetic Dependencies in Melanoma The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Wong, Terence. 2018. Integrated and Functional Genomic Approaches to Elucidate Differential Genetic Dependencies in Melanoma. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42014990 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Integrated and Functional Genomic Approaches to Elucidate Differential Genetic Dependencies in Melanoma A dissertation presented by Terence Cheng Wong to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts November 2017 © 2017 Terence Cheng Wong All rights reserved. Dissertation Advisor: Levi Garraway Terence Cheng Wong Integrated and Functional Genomic Approaches to Elucidate Differential Genetic Dependencies in Melanoma ABSTRACT Genomic characterization of human cancers over the past decade has generated comprehensive catalogues of genetic alterations in cancer genomes. Many of these genetic events result in molecular or cellular changes that drive cancer cell phenotypes. In melanoma, a majority of tumors harbor mutations in the BRAF gene, leading to activation of the MAPK pathway and tumor initiation. The development and use of drugs that target the mutant BRAF protein and the MAPK pathway have produced significant clinical benefit in melanoma patients. -
Mediator of DNA Damage Checkpoint 1 (MDC1) Is a Novel Estrogen Receptor Co-Regulator in Invasive 6 Lobular Carcinoma of the Breast 7 8 Evelyn K
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.16.423142; this version posted December 16, 2020. 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 4.0 International license. 1 Running Title: MDC1 co-regulates ER in ILC 2 3 Research article 4 5 Mediator of DNA damage checkpoint 1 (MDC1) is a novel estrogen receptor co-regulator in invasive 6 lobular carcinoma of the breast 7 8 Evelyn K. Bordeaux1+, Joseph L. Sottnik1+, Sanjana Mehrotra1, Sarah E. Ferrara2, Andrew E. Goodspeed2,3, James 9 C. Costello2,3, Matthew J. Sikora1 10 11 +EKB and JLS contributed equally to this project. 12 13 Affiliations 14 1Dept. of Pathology, University of Colorado Anschutz Medical Campus 15 2Biostatistics and Bioinformatics Shared Resource, University of Colorado Comprehensive Cancer Center 16 3Dept. of Pharmacology, University of Colorado Anschutz Medical Campus 17 18 Corresponding author 19 Matthew J. Sikora, PhD.; Mail Stop 8104, Research Complex 1 South, Room 5117, 12801 E. 17th Ave.; Aurora, 20 CO 80045. Tel: (303)724-4301; Fax: (303)724-3712; email: [email protected]. Twitter: 21 @mjsikora 22 23 Authors' contributions 24 MJS conceived of the project. MJS, EKB, and JLS designed and performed experiments. JLS developed models 25 for the project. EKB, JLS, SM, and AEG contributed to data analysis and interpretation. SEF, AEG, and JCC 26 developed and performed informatics analyses. MJS wrote the draft manuscript; all authors read and revised the 27 manuscript and have read and approved of this version of the manuscript. -
Identification and Characterization of the Forkhead Box
IDENTIFICATION AND CHARACTERIZATION OF THE FORKHEAD BOX FAMILY OF TRANSCRIPTIONAL REGULATORS IN PARASITIC SCHISTOSOMES by MELISSA M. VARRECCHIA Submitted in partial fulfillment of the requirements for the degree of Doctor of philosophy Department of Biology CASE WESTERN RESERVE UNIVERSITY August 2017 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of Melissa M. Varrecchia candidate for the degree of Doctor of Philosophy Committee Chair Michael F. Benard Committee Member Emmitt R. Jolly Committee Member Christopher A. Cullis Committee Member Claudia M. Mizutani Committee Member Brian M. McDermott Date of Defense June 6, 2017 *We also certify that written approval has been obtained for any proprietary material contained therein. ii Dedication I would like to dedicate this dissertation to my Mom and Dad. Mom, thank you for your endless love, support and encouragement throughout the years. Dad, I miss you and I know that you are with me always, cheering me on in spirit. iii Table of Contents Table of Contents………………………………………………………………………...1 List of Tables……………………………………………………………………………..6 List of Figures…………………………………………………………………………....8 Acknowledgements…………………………………………………………………..…11 List of Abbreviations…………………………………………………………………...13 Abstract…………………………………………………………………………………15 Chapter 1: Introduction………………………………………………………………..17 1.1 Schistosomiasis………………………………………………………………17 1.2 Pathogenesis and treatment…………………………………………………..18 1.3 Schistosome life cycle………………………………………………………..20 1.4 Schistosome morphology -
The Forkhead-Box Family of Transcription Factors: Key Molecular Players in Colorectal Cancer Pathogenesis Paul Laissue
Laissue Molecular Cancer (2019) 18:5 https://doi.org/10.1186/s12943-019-0938-x REVIEW Open Access The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis Paul Laissue Abstract Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide and the fourth most frequent cause of death having an oncological origin. It has been found that transcription factors (TF) dysregulation, leading to the significant expression modifications of genes, is a widely distributed phenomenon regarding human malignant neoplasias. These changes are key determinants regarding tumour’s behaviour as they contribute to cell differentiation/proliferation, migration and metastasis, as well as resistance to chemotherapeutic agents. The forkhead box (FOX) transcription factor family consists of an evolutionarily conserved group of transcriptional regulators engaged in numerous functions during development and adult life. Their dysfunction has been associated with human diseases. Several FOX gene subgroup transcriptional disturbances, affecting numerous complex molecular cascades, have been linked to a wide range of cancer types highlighting their potential usefulness as molecular biomarkers. At least 14 FOX subgroups have been related to CRC pathogenesis, thereby underlining their role for diagnosis, prognosis and treatment purposes. This manuscript aims to provide, for the first time, a comprehensive review of FOX genes’ roles during CRC pathogenesis. The molecular and functional characteristics of most relevant FOX molecules (FOXO, FOXM1, FOXP3) have been described within the context of CRC biology, including their usefulness regarding diagnosis and prognosis. Potential CRC therapeutics (including genome-editing approaches) involving FOX regulation have also been included. Taken together, the information provided here should enable a better understanding of FOX genes’ function in CRC pathogenesis for basic science researchers and clinicians. -
FOXK Transcription Factors Regulation and Critical Role in Cancer
Cancer Letters 458 (2019) 1–12 Contents lists available at ScienceDirect Cancer Letters journal homepage: www.elsevier.com/locate/canlet Mini-review FOXK transcription factors: Regulation and critical role in cancer T Ying Liua, Wei Dingb,HuGea,d, Murugavel Ponnusamya, Qiong Wangd, Xiaodan Haoa, Wei Wua, ∗∗ ∗ Yuan Zhanga, Wanpeng Yua, Xiang Aoa, , Jianxun Wanga,c, a Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao 266021, China b Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, Qingdao 266003, China c School of Basic Medical Sciences, Qingdao University, Qingdao 266071, China d Molecular Informatics Department, Hengrui Pharmaceutical Co., Ltd., Shanghai 200245, China ARTICLE INFO ABSTRACT Keywords: Growing evidence suggests that alterations of gene expression including expression and activities of transcription FOXK1 factors are closely associated with carcinogenesis. Forkhead Box Class K (FOXK) proteins, FOXK1 and FOXK2, FOXK2 are a family of evolutionarily conserved transcriptional factors, which have recently been recognized as key ncRNAs transcriptional regulators involved in many types of cancer. Members of the FOXK family mediate a wide Biomarker spectrum of biological processes, including cell proliferation, differentiation, apoptosis, autophagy, cell cycle Therapeutic target progression, DNA damage and tumorigenesis. Therefore, the deregulation of FOXKs can affect the cell fate and they promote tumorigenesis as well as cancer progression. The mechanisms of FOXKs regulation including post- translational modifications (PTMs), microRNAs (miRNAs) and protein–protein interactions are well demon- strated. However, the detailed mechanisms of FOXKs activation and deregulation in cancer progression are still inconclusive. In this review, we summarize the regulatory mechanisms of FOXKs expression and activity, and their role in the development and progression of cancer. -
Molecular Cloning and Characterization of a Human PAX-7 Cdna Expressed in Normal and Neoplastic Myocytes
4574-4582 Nucleic Acids Research, 1994, Vol. 22, No. 22 .:/ 1994 Oxford University Press Molecular cloning and characterization of a human PAX-7 cDNA expressed in normal and neoplastic myocytes Beat W.Schafer*, Thomas Czerny1, Michele Bernasconi, Michele Genini and Meinrad Busslinger1 University of Zurich, Department of Pediatrics, Division of Clinical Chemistry, Steinwiesstrasse 75, 8032 Zurich, Switzerland and 'Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria Received August 25, 1994; Revised and Accepted October 11, 1994 EMBL accession no. Z35141 ABSTRACT The myogenic basic helix-loop-helix proteins are MRF4 (myf6) of the myogenic basic helix-loop-helix (bHLH) essential components of the regulatory network con- protein family (for review, see ref. 1,2). Recent gene targeting trolling vertebrate myogenesis. However, determined experiments in mice demonstrated that mice lacking either both myoblasts appear in the limb buds which do not initially myoD and myf5, or myogenin alone display severe skeletal express any member of this transcription factor family. muscle deficiencies (3-5) which underscores the importance of In a search for potential novel regulators of myogene- this family of transcription factors for myogenesis. In addition, sis, a human PAX-7 cDNA was isolated from primary these experiments placed myoD and myf5 upstream of myogenin myoblasts. Analysis of the DNA-binding properties of in a possible transcriptional hierarchy (6). The myogenic bHLH the Pax-7 paired domain revealed that it binds DNA in factors have furthermore the potential to convert several non- a sequence-specific manner indistinguishable from that muscle cell types to the muscle phenotype upon ectopic expression of the paralogous Pax-3 protein. -
Pflugers Final
CORE Metadata, citation and similar papers at core.ac.uk Provided by Serveur académique lausannois A comprehensive analysis of gene expression profiles in distal parts of the mouse renal tubule. Sylvain Pradervand2, Annie Mercier Zuber1, Gabriel Centeno1, Olivier Bonny1,3,4 and Dmitri Firsov1,4 1 - Department of Pharmacology and Toxicology, University of Lausanne, 1005 Lausanne, Switzerland 2 - DNA Array Facility, University of Lausanne, 1015 Lausanne, Switzerland 3 - Service of Nephrology, Lausanne University Hospital, 1005 Lausanne, Switzerland 4 – these two authors have equally contributed to the study to whom correspondence should be addressed: Dmitri FIRSOV Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925406 Fax: ++ 41-216925355 e-mail: [email protected] and Olivier BONNY Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925417 Fax: ++ 41-216925355 e-mail: [email protected] 1 Abstract The distal parts of the renal tubule play a critical role in maintaining homeostasis of extracellular fluids. In this review, we present an in-depth analysis of microarray-based gene expression profiles available for microdissected mouse distal nephron segments, i.e., the distal convoluted tubule (DCT) and the connecting tubule (CNT), and for the cortical portion of the collecting duct (CCD) (Zuber et al., 2009). Classification of expressed transcripts in 14 major functional gene categories demonstrated that all principal proteins involved in maintaining of salt and water balance are represented by highly abundant transcripts. However, a significant number of transcripts belonging, for instance, to categories of G protein-coupled receptors (GPCR) or serine-threonine kinases exhibit high expression levels but remain unassigned to a specific renal function. -
FOXK1 Promotes Malignant Progression of Breast Cancer by Activating PI3K/AKT/Mtor Signaling Pathway
European Review for Medical and Pharmacological Sciences 2019; 23: 9978-9987 FOXK1 promotes malignant progression of breast cancer by activating PI3K/AKT/mTOR signaling pathway Z.-Q. LI1, M. QU2, H.-X. WAN1, H. WANG3, Q. DENG4, Y. ZHANG5 1Department of Oncology, Sanya People’s Hospital, Sanya, China 2Special Care Unit, Sanya People’s Hospital, Sanya, China 3Department of Pathology, Sanya People’s Hospital, Sanya, China 4Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China 5Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China Zhiqiang Li and Miao Qu contributed equally to this work Abstract. – OBJECTIVE: The aim of this the PI3K/AKT/mTOR signaling pathway, thereby study was to investigate the expression charac- promoting the malignant progression of BCa. teristics of forkhead box K1 (FOXK1) in breast Finally, PI3Kα/mTOR-IN-1, which was the inhib- cancer (BCa). Meanwhile, its relationship with itor of the PI3K/AKT/mTOR signaling pathway, clinicopathology and prognosis of patients with significantly reversed the proliferative capacity BCa was also explored. of cells in FOXK1 overexpression group, as well PATIENTS AND METHODS: The expression as enhanced anti-apoptotic ability. level of FOXK1 in 65 paired BCa tissues and pa- CONCLUSIONS: FOXK1 expression was re- ra-cancerous tissues was detected by quan- markably increased both in BCa tissues and titative Real Time-Polymerase Chain Reaction cells. Meanwhile, it was markedly associated (qRT-PCR). The relationship between FOXK1 ex- with pathological stage and poor prognosis of pression and BCa pathological parameters as patients. Besides, FOXK1 might promote the well as the prognosis of patients was analyzed. -
A High-Density Map for Navigating the Human Polycomb Complexome
Resource A High-Density Map for Navigating the Human Polycomb Complexome Graphical Abstract Authors Simon Hauri, Federico Comoglio, Makiko Seimiya, ..., Renato Paro, Matthias Gstaiger, Christian Beisel Correspondence [email protected] (M.G.), [email protected] (C.B.) In Brief Polycomb group (PcG) proteins mediate gene silencing and epigenetic memory in higher eukaryotes. By systematically mapping the human PcG complexome, Hauri et al. resolve Polycomb subcomplexes at high resolution and identify two human PRC2 and two PR- DUB complexes. Furthermore, genomic profiling reveals segregation of PRC1 and PR-DUB target genes. Highlights Accession Numbers d 1,400 high-confidence interactions reveal the modular GSE51673 organization of human PcG proteins d Detailed dissection of PRC1 and PRC2 subcomplexes d Two human PR-DUB complexes contain the glycosyltransferase OGT1 d PR-DUB and PRC1 bind largely distinct sets of target genes Hauri et al., 2016, Cell Reports 17, 583–595 October 4, 2016 ª 2016 The Authors. http://dx.doi.org/10.1016/j.celrep.2016.08.096 Cell Reports Resource A High-Density Map for Navigating the Human Polycomb Complexome Simon Hauri,1,2,7,8 Federico Comoglio,3,7,9 Makiko Seimiya,3 Moritz Gerstung,3,10 Timo Glatter,1,11 Klaus Hansen,4 Ruedi Aebersold,1,5 Renato Paro,3,6 Matthias Gstaiger,1,2,* and Christian Beisel3,12,* 1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich,€ 8093 Zurich,€ Switzerland 2Competence Center Personalized Medicine UZH/ETH, 8044 Zurich,€ Switzerland 3Department -
Tissue-Specific Metabolic Regulation of FOXO-Binding Protein
cells Review Tissue-Specific Metabolic Regulation of FOXO-Binding Protein: FOXO Does Not Act Alone Noriko Kodani 1 and Jun Nakae 2,* 1 Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; [email protected] 2 Department of Physiology, International University of Health and Welfare School of Medicine, Narita 286-8686, Japan * Correspondence: [email protected]; Tel.: +81-476-20-7701 Received: 17 January 2020; Accepted: 10 March 2020; Published: 13 March 2020 Abstract: The transcription factor forkhead box (FOXO) controls important biological responses, including proliferation, apoptosis, differentiation, metabolism, and oxidative stress resistance. The transcriptional activity of FOXO is tightly regulated in a variety of cellular processes. FOXO can convert the external stimuli of insulin, growth factors, nutrients, cytokines, and oxidative stress into cell-specific biological responses by regulating the transcriptional activity of target genes. However, how a single transcription factor regulates a large set of target genes in various tissues in response to a variety of external stimuli remains to be clarified. Evidence indicates that FOXO-binding proteins synergistically function to achieve tightly controlled processes. Here, we review the elaborate mechanism of FOXO-binding proteins, focusing on adipogenesis, glucose homeostasis, and other metabolic regulations in order to deepen our understanding and to identify a novel therapeutic target for the prevention and treatment of metabolic disorders. Keywords: FOXO; transcription factor; FOXO-binding protein 1. Introduction Forkhead box (FOXO) transcription factors play important roles in apoptosis, the cell cycle, DNA damage repair, oxidative stress, cell differentiation, glucose metabolism, and other cellular functions [1]. -
Transcriptomic Profiling Identifies Differentially Expressed Genes In
G C A T T A C G G C A T genes Article Transcriptomic Profiling Identifies Differentially Expressed Genes in Palbociclib-Resistant ER+ MCF7 Breast Cancer Cells Lilibeth Lanceta 1, Conor O’Neill 2, Nadiia Lypova 1 , Xiahong Li 3, Eric Rouchka 4, Sabine Waigel 1, Jorge G. Gomez-Gutierrez 5,6 , Jason Chesney 1,6 and Yoannis Imbert-Fernandez 1,6,* 1 Department of Medicine, School of Medicine, University of Louisville, Louisville, KY 40202, USA; [email protected] (L.L.); [email protected] (N.L.); [email protected] (S.W.); [email protected] (J.C.) 2 College of Medicine, University of Kentucky, Lexington, KY 40506, USA; [email protected] 3 Department of Anatomical Sciences and Neurobiology, Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA; [email protected] 4 Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA; [email protected] 5 Department of Surgery, School of Medicine, University of Louisville, Louisville, KY 40202, USA; [email protected] 6 James Graham Brown Cancer Center School of Medicine, University of Louisville, Louisville, KY 40202, USA * Correspondence: [email protected]; Tel.: +1-502-852-6570 Received: 20 March 2020; Accepted: 18 April 2020; Published: 24 April 2020 Abstract: Acquired resistance to cyclin-dependent kinases 4 and 6 (CDK4/6) inhibition in estrogen receptor-positive (ER+) breast cancer remains a significant clinical challenge. Efforts to uncover the mechanisms underlying resistance are needed to establish clinically actionable targets effective against resistant tumors. In this study, we sought to identify differentially expressed genes (DEGs) associated with acquired resistance to palbociclib in ER+ breast cancer.