NCOA5 Promotes Proliferation, Migration and Invasion of Colorectal Cancer Cells Via Activation of PI3K/AKT Pathway
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
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. -
The Tumor Suppressor Notch Inhibits Head and Neck Squamous Cell
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2015 THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) Shhyam Moorthy Shhyam Moorthy Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biochemistry, Biophysics, and Structural Biology Commons, Cancer Biology Commons, Cell Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Moorthy, Shhyam and Moorthy, Shhyam, "THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN)" (2015). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 638. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/638 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) by Shhyam Moorthy, B.S. -
The Viral Oncoproteins Tax and HBZ Reprogram the Cellular Mrna Splicing Landscape
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape Charlotte Vandermeulen1,2,3, Tina O’Grady3, Bartimee Galvan3, Majid Cherkaoui1, Alice Desbuleux1,2,4,5, Georges Coppin1,2,4,5, Julien Olivet1,2,4,5, Lamya Ben Ameur6, Keisuke Kataoka7, Seishi Ogawa7, Marc Thiry8, Franck Mortreux6, Michael A. Calderwood2,4,5, David E. Hill2,4,5, Johan Van Weyenbergh9, Benoit Charloteaux2,4,5,10, Marc Vidal2,4*, Franck Dequiedt3*, and Jean-Claude Twizere1,2,11* 1Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.2Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.3Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.4Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 5Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.6Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France.7Department of Pathology and Tumor Biology, Kyoto University, Japan.8Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium.9Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium.10Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium.11Lead Contact. *Correspondence: [email protected]; [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. -
Vascular Histone Deacetylation by Pharmacological HDAC Inhibition
Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Research Vascular histone deacetylation by pharmacological HDAC inhibition Haloom Rafehi,1,2 Aneta Balcerczyk,1,4 Sebastian Lunke,1,5 Antony Kaspi,1 Mark Ziemann,1 Harikrishnan KN,1 Jun Okabe,1,3 Ishant Khurana,1 Jenny Ooi,1 Abdul Waheed Khan,1 Xiao-Jun Du,1,3 Lisa Chang,1 Izhak Haviv,1,4 Samuel T. Keating,1 Tom C. Karagiannis,1 and Assam El-Osta1,2,3 1Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; 2Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia; 3Faculty of Medicine, Monash University, Victoria 3800, Australia HDAC inhibitors can regulate gene expression by post-translational modification of histone as well as nonhistone pro- teins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action. However, little is known of the extent of genome-wide changes in cells stimulated by the hydroxamic acids, TSA and SAHA. In this article, we map vascular chromatin modifications including histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chro- matin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation-mediated gene expression is often associated with modification of other lysine residues, we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). RNA sequencing indicates the differential expression of ~30% of genes, with almost equal numbers being up- and down-regulated. We observed broad deacetylation and gene expression changes conferred by TSA and SAHA mediated by the loss of EP300/CREBBP binding at multiple gene promoters. -
Genetic and Genomics Laboratory Tools and Approaches
Genetic and Genomics Laboratory Tools and Approaches Meredith Yeager, PhD Cancer Genomics Research Laboratory Division of Cancer Epidemiology and Genetics [email protected] DCEG Radiation Epidemiology and Dosimetry Course 2019 www.dceg.cancer.gov/RadEpiCourse (Recent) history of genetics 2 Sequencing of the Human Genome Science 291, 1304-1351 (2001) 3 The Human Genome – 2019 • ~3.3 billion bases (A, C, G, T) • ~20,000 protein-coding genes, many non-coding RNAs (~2% of the genome) • Annotation ongoing – the initial sequencing in 2001 is still being refined, assembled and annotated, even now – hg38 • Variation (polymorphism) present within humans – Population-specific – Cosmopolitan 4 Types of polymorphisms . Single nucleotide polymorphisms (SNPs) . Common SNPs are defined as > 5% in at least one population . Abundant in genome (~50 million and counting) ATGGAACGA(G/C)AGGATA(T/A)TACGCACTATGAAG(C/A)CGGTGAGAGG . Repeats of DNA (long, short, complex, simple), insertions/deletions . A small fraction of SNPs and other types of variation are very or slightly deleterious and may contribute by themselves or with other genetic or environmental factors to a phenotype or disease 5 Different mutation rates at the nucleotide level Mutation type Mutation rate (per generation) Transition on a CpG 1.6X10-7 Transversion on a CpG 4.4X10-8 Transition: purine to purine Transition out of CpG 1.2X10-8 Transversion: purine to pyrimidine Transversion out of CpG 5.5X10-9 Substitution (average) 2.3X10-8 A and G are purines Insertion/deletion (average) 2.3X10-9 C and T are pyrimidines Mutation rate (average) 2.4X10-8 . Size of haploid genome : 3.3X109 nucleotides . -
And Nfkb1-Mediated Gene Expression in Inflammation and Carcinogenesis
British Journal of Cancer (2008) 99, 2070 – 2082 & 2008 Cancer Research UK All rights reserved 0007 – 0920/08 $32.00 www.bjcancer.com Regulatory potential for concerted modulation of Nrf2- and Nfkb1-mediated gene expression in inflammation and carcinogenesis 1,4 2 3 1 *,2 S Nair ,STDoh, JY Chan , A-N Kong and L Cai 1 2 Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biomedical Engineering, 3 Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Pathology, University of California, Irvine, CA 92697, USA Many studies have implicated nuclear factor E2-related factor 2 (Nrf2) and nuclear factor-kB1 (Nfkb1) in inflammation and cancer. However, the regulatory potential for crosstalk between these two important transcription factors in inflammation and carcinogenesis has not been explored. To delineate conserved transcription factor-binding site signatures, we performed bioinformatic analyses on the promoter regions of human and murine Nrf2 and Nfkb1. We performed multiple sequence alignment of Nrf2 and Nfkb1 genes in five mammalian species – human, chimpanzee, dog, mouse and rat – to explore conserved biological features. We constructed a canonical regulatory network for concerted modulation of Nrf2 and Nfkb1 involving several members of the mitogen-activated protein kinase (MAPK) family and present a putative model for concerted modulation of Nrf2 and Nfkb1 in inflammation/ carcinogenesis. Our results reflect potential for putative crosstalk between Nrf2 and Nfkb1 modulated through the MAPK cascade that may influence inflammation-associated etiopathogenesis of cancer. Taken together, the elucidation of potential relationships between Nrf2 and Nfkb1 may help to better understand transcriptional regulation, as well as transcription factor networks, associated with the etiopathogenesis of inflammation and cancer. -
The Landscape of Ahr Regulators and Coregulators to Fine-Tune Ahr Functions
International Journal of Molecular Sciences Review The Landscape of AhR Regulators and Coregulators to Fine-Tune AhR Functions Marco Gargaro †, Giulia Scalisi † , Giorgia Manni, Giada Mondanelli , Ursula Grohmann *,‡ and Francesca Fallarino *,‡ Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; [email protected] (M.G.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (G.M.) * Correspondence: [email protected] (U.G.); [email protected] (F.F.) † These authors contributed equally to this work. ‡ These authors share senior authorship. Abstract: The aryl-hydrocarbon receptor (AhR) is a ligand-activated transcription factor that me- diates numerous cellular responses. Originally investigated in toxicology because of its ability to bind environmental contaminants, AhR has attracted enormous attention in the field of immunology in the last 20 years. In addition, the discovery of endogenous and plant-derived ligands points to AhR also having a crucial role in normal cell physiology. Thus, AhR is emerging as a promiscuous receptor that can mediate either toxic or physiologic effects upon sensing multiple exogenous and endogenous molecules. Within this scenario, several factors appear to contribute to the outcome of gene transcriptional regulation by AhR, including the nature of the ligand as such and its further metabolism by AhR-induced enzymes, the local tissue microenvironment, and the presence of coregu- lators or specific transcription factors in the cell. Here, we review the current knowledge on the array of transcription factors and coregulators that, by interacting with AhR, tune its transcriptional activity in response to endogenous and exogenous ligands. -
Transcriptional Regulators Are Upregulated in the Substantia Nigra
Journal of Emerging Investigators Transcriptional Regulators are Upregulated in the Substantia Nigra of Parkinson’s Disease Patients Marianne Cowherd1 and Inhan Lee2 1Community High School, Ann Arbor, MI 2miRcore, Ann Arbor, MI Summary neurological conditions is an established practice (3). Parkinson’s disease (PD) affects approximately 10 Significant gene expression dysregulation in the SN and million people worldwide with tremors, bradykinesia, in the striatum has been described, particularly decreased apathy, memory loss, and language issues. Though such expression in PD synapses. Protein degradation has symptoms are due to the loss of the substantia nigra (SN) been found to be upregulated (4). Mutations in SNCA brain region, the ultimate causes and complete pathology are unknown. To understand the global gene expression (5), LRRK2 (6), and GBA (6) have also been identified changes in SN, microarray expression data from the SN as familial markers of PD. SNCA encodes alpha- tissue of 9 controls and 16 PD patients were compared, synuclein, a protein found in presynaptic terminals that and significantly upregulated and downregulated may regulate vesicle presence and dopamine release. genes were identified. Among the upregulated genes, Eighteen SNCA mutations have been associated with a network of 33 interacting genes centered around the PD and, although the exact pathogenic mechanism is cAMP-response element binding protein (CREBBP) was not confirmed, mutated alpha-synuclein is the major found. The downstream effects of increased CREBBP- component of protein aggregates, called Lewy bodies, related transcription and the resulting protein levels that are often found in PD brains and may contribute may result in PD symptoms, making CREBBP a potential therapeutic target due to its central role in the interactive to cell death. -
Detection of H3k4me3 Identifies Neurohiv Signatures, Genomic
viruses Article Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis Liana Basova 1, Alexander Lindsey 1, Anne Marie McGovern 1, Ronald J. Ellis 2 and Maria Cecilia Garibaldi Marcondes 1,* 1 San Diego Biomedical Research Institute, San Diego, CA 92121, USA; [email protected] (L.B.); [email protected] (A.L.); [email protected] (A.M.M.) 2 Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA; [email protected] * Correspondence: [email protected] Abstract: Human postmortem specimens are extremely valuable resources for investigating trans- lational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic Citation: Basova, L.; Lindsey, A.; signatures would be more stable than RNA for assessing global changes associated with outcomes McGovern, A.M.; Ellis, R.J.; of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Marcondes, M.C.G. Detection of H3K4me3 Identifies NeuroHIV Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was Signatures, Genomic Effects of abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human Methamphetamine and Addiction prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not Pathways in Postmortem HIV+ Brain (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling. -
Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6 Atish D
Published OnlineFirst November 29, 2016; DOI: 10.1158/0008-5472.CAN-16-0455 Cancer Tumor and Stem Cell Biology Research Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6 Atish D. Choudhury1,2,3, Anna C. Schinzel1,3, Maura B. Cotter1, Rosina T. Lis1,4, Katherine Labella1, Ying Jie Lock1, Francesca Izzo1,3, Isil Guney1,2, Michaela Bowden1, Yvonne Y. Li1, Jinal Patel3, Emily Hartman3, Steven A. Carr3, Monica Schenone3, Jacob D. Jaffe3, Philip W. Kantoff1,2, Peter S. Hammerman1,2,3, and William C. Hahn1,2,3 Abstract In prostate cancer, the development of castration resistance castration in a mouse xenograft model system. Tumors in is pivotal in progression to aggressive disease. However, which castration resistance was conferred by NEK6 were understanding of the pathways involved remains incomplete. predominantly squamous in histology with no evidence of In this study, we performed a high-throughput genetic screen AR signaling. Gene expression profiling suggested that NEK6 to identify kinases that enable tumor formation by androgen- overexpression stimulated cytoskeletal, differentiation, and dependent prostate epithelial (LHSR-AR) cells under andro- immune signaling pathways and maintained gene expression gen-deprived conditions. In addition to the identification of patterns normally decreased by castration. Phosphoproteome known mediators of castration resistance, which served to profiling revealed the transcription factor FOXJ2 as a novel validate the screen, we identified a mitotic-related serine/ NEK6 substrate, with FOXJ2 phosphorylation associated with threonine kinase, NEK6, as a mediator of androgen-indepen- increased expression of newly identified NEK6 transcriptional dent tumor growth. NEK6 was overexpressed in a subset targets. -
ZNF384-Related Fusion Genes Define a Subgroup of Childhood B-Cell
Acute Lymphoblastic Leukemia SUPPLEMENTARY APPENDIX ZNF384 -related fusion genes define a subgroup of childhood B-cell precursor acute lymphoblastic leukemia with a characteristic immunotype Shinsuke Hirabayashi, 1,2 Kentaro Ohki, 1 Kazuhiko Nakabayashi, 3 Hitoshi Ichikawa, 4 Yukihide Momozawa, 5 Kohji Oka - mura, 6 Akinori Yaguchi, 1,7 Kazuki Terada, 1 Yuya Saito, 1,8 Ai Yoshimi, 1,9 Hiroko Ogata-Kawata, 3 Hiromi Sakamoto, 4 Moto - hiro Kato, 1,10 Junya Fujimura, 7 Moeko Hino, 11 Akitoshi Kinoshita, 12 Harumi Kakuda, 13 Hidemitsu Kurosawa, 14 Keisuke Kato, 9 Ryosuke Kajiwara, 15 Koichi Moriwaki, 16 Tsuyoshi Morimoto, 17 Kozue Nakamura, 18 Yasushi Noguchi, 19 Tomoo Osumi, 1,20 Kazuo Sakashita, 21 Junko Takita, 22 Yuki Yuza, 8 Koich Matsuda, 23 Teruhiko Yoshida, 4 Kenji Matsumoto, 24 Kenichiro Hata, 3 Michiaki Kubo, 5 Yoichi Matsubara, 25 Takashi Fukushima, 26 Katsuyoshi Koh, 27 Atsushi Manabe, 2 Akira Ohara 28 and Nobutaka Kiyokawa 1 for the Tokyo Children’s Cancer Study Group (TCCSG) 1Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Seta - gaya-ku, Tokyo; 2Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo; 3Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo; 4Division of Genetics, National Cancer Center Re - search Institute, Chuo-ku, Tokyo; 5Laboratory for Genotyping Development, Center for Integrative Medical Sciences (IMS), RIKEN, Yoko - hama-shi, Kanagawa; 6Department