Critical Physiological and Pathological Functions of Forkhead Box O Tumor Suppressors
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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. -
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. -
Introduction to Nutrigenetics, Nutrigenomics and Epigenetics
Medicine, Nursing and Health Sciences Introduction to Nutrigenetics, Nutrigenomics and Epigenetics Australia n China n India n Italy n Malaysia n South Africa Introduction to Nutrigenetics, Nutrigenomics and Epigenetics The Nutrition Society of Australia (Melbourne), Monash University and MyGene are pleased to invite you to our upcoming ‘Introduction to Nutrigenetics, Nutrigenomics and Epigenetics’ symposium. Please note, numbers will be capped at 100, and delegates need to sign up for their preferred workshop sessions using the link below. Where: Level 5 of The Alfred Centre, Monash University (Go to the 1.00pm Networking coffee/tea Foyer of Lecture Theatre ‘B’ set of lifts in the The Alfred Centre), 99 Commercial Road, 1.30pm Introduction to Nutrigenetics, Michael Fenech (CSIRO) Melbourne. Nutrigenomics and Epigenetics Jeff Craig (MCRI) When: 1-5.15pm, 2.30pm Global trends in genetics: research, Graeme Smith (MyGene) Tuesday 27 August 2013 technology and practice Melissa Adamski (MyGene) RSVP: Brianna McFarlane, [email protected] 3.10pm Tea/coffee break Foyer of Lecture Theatre (by 13 August 2013) 3.30pm Workshop 1 Level 5 breakout room The workshops are a choice of two 4.15pm Changeover time from following topics (click link below to sign up): 4.30pm Workshop 2 Level 5 breakout room Workshop preference: 5.15pm Close http://www.mygene.com.au/nsa- symposium/ 1. Designing genetic research projects (including considering the data, Biographies In 2003-05, Dr Fenech proposed a novel interpreting the data and validation) disease prevention strategy based on Michael Fenech 2. Adding genetic testing to your personalised diagnosis and prevention of current research project Professor Michael Fenech is recognised DNA damage by appropriate diet/life-style internationally for his research in nutritional intervention, which has led to the Genome 3. -
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. -
6615 Sofiva Genomics
6615 SOFIVA GENOMICS Chairman Yi-Ning Su 2017.01.04 Company Profile SOFIVA GENOMICS Founded in July, 2012, SOFIVA GENOMICS focuses on clinical needs to develop next-generation testing models in genomic medicine Maternal-Fetal Medicine Genomic Medicine Clinical Medicine We have Asia’s leading genetic testing laboratory to provide comprehensive services to those in need Our Orientation ■ Mothers and fetuses Targets ■ Individuals with genetic diseases ■ Individuals with cancer ■ Healthy individuals ■ Mothers and fetuses: Helping mothers successfully conceive and safely give birth to healthy babies ■ Individuals with genetic diseases: Helping doctors in giving patients swift and accurate diagnoses and treatments Service Orientation ■ Individuals with cancer: Facilitating the detection, prognosis, and tracking of cancer so that doctors can treat and monitor their patients more accurately ■ Healthy individuals: Grasping their genetic health and risk of contracting disease and early planning for health promotion ■ Now: Technology and platform combining biochemical detection + gene chip Technical + next-generation sequencing to provide customers with comprehensive Development testing services ■Future: Development of comprehensive and customized testing using a single sample and a single platform ■ Business promotion: Joint promotion and hospitals, introduction to medical personnel, onsite recommendations, promotion at foreign Marketing and domestic conferences/expos Channels ■ PR promotion: online/Facebook marketing, literature and posters to -
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 -
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. -
A Murine Atlas of Age-Related Changes in Intercellular Communication Inferred with the Package Scdiffcom
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.13.456238; this version posted August 15, 2021. 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. scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom Cyril Lagger 1,*, Eugen Ursu 2,*, Anaïs Equey 3, Roberto A. Avelar 1, Angela O. Pisco 4, Robi Tacutu 2, João Pedro de Magalhães 1,# 1. Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK 2. Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania 3. Department of Medicine, Karolinska Institutet, Stockholm, Sweden 4. Chan Zuckerberg Biohub, San Francisco, California, USA *These authors contributed equally #Corresponding author’s email: [email protected] Abstract Dysregulation of intercellular communication is a well-established hallmark of aging. To better understand how this process contributes to the aging phenotype, we built scAgeCom, a comprehensive atlas presenting how cell-type to cell-type interactions vary with age in 23 mouse tissues. We first created an R package, scDiffCom, designed to perform differential intercellular communication analysis between two conditions of interest in any mouse or human single-cell RNA-seq dataset. The package relies on its own list of curated ligand-receptor interactions compiled from seven established studies. We applied this tool to single-cell transcriptomics data from the Tabula Muris Senis consortium and the Calico murine aging cell atlas. -
Lncrna WT1-AS Attenuates Hypoxia/Ischemia Induced Neuronal Injury in Cerebral Ischemic Stroke Via Mir-186-5P/XIAP Axis
LncRNA WT1-AS Attenuates hypoxia/ischemia Induced Neuronal Injury in Cerebral Ischemic Stroke via miR-186-5p/XIAP Axis Jianquan You Jiangsu Taizhou People's Hospital Fei Qian Jiangsu Taizhou People's Hospital Yu Huang Jiangsu Taizhou People's Hospital Yingxuan Guo Jiangsu Taizhou People's Hospital Yaqian Lv Jiangsu Taizhou People's Hospital Yuqi Yang Jiangsu Taizhou People's Hospital Xiupan Lu Jiangsu Taizhou People's Hospital Ting Guo Jiangsu Taizhou People's Hospital Jun Wang ( [email protected] ) Jiangsu Taizhou People's Hospital https://orcid.org/0000-0002-5511-7914 Bin Gu Jiangsu Taizhou People's Hospital Research Article Keywords: WT1-AS, Cerebral ischemic stroke, MiR-186-5p, XIAP, Oxygen glucose deprivation Posted Date: August 20th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-818657/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background Cerebral ischemic stroke was a nervous system disease with high occurrence rate and mortality rate. This study aimed to investigate the role and mechanism of lncRNA WT1-AS in cerebral ischemic stroke. Materials and methods Starbase and dual luciferase reporter gene assay were used to analyze the target relationship between lncRNA WT1-AS and miR-186-5p. qRT-PCR analysis was used to detect lncRNA WT1-AS and miR-186-5p expression. OGD-induced SH-SY5Y cells injury model was conducted, and cell viability and cell apoptosis were determined by MTT and ow cytometer assay. Caspase3 ability was determined using Caspase3 activity detection kit. Results miR-186-5p was a target of lncRNA-WT1-AS.