DOCSLIB.ORG

Science Journals

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Science Journals SCIENCE IMMUNOLOGY | RESEARCH RESOURCE IMMUNOGENOMICS 2017 © The Authors, some rights reserved; exclusive licensee Epigenomics of human CD8 T cell differentiation American Association for the Advancement and aging of Science. David M. Moskowitz,1,2* David W. Zhang,1,3,4* Bin Hu,3,4 Sabine Le Saux,3,4 Rolando E. Yanes,3,4 Zhongde Ye,3,4 Jason D. Buenrostro,1,5 Cornelia M. Weyand,3,4 William J. Greenleaf,1†‡ Jörg J. Goronzy 3,4†‡ The efficacy of the adaptive immune response declines markedly with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using the assay for transposase-accessible chromatin using sequencing, we inferred that the transcription factor binding activities cor- related with naïve and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA sequencing, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles impli- Downloaded from cated for BATF, ETS1, Eomes, and Sp1. Extending our analysis to aged humans, we found that the differences between the memory and naïve CD8 T cell subsets were largely preserved across age but that naïve and central memory cells from older individuals exhibited a shift toward more differentiated patterns of chromatin openness. In addition, aged naïve cells displayed a loss in chromatin accessibility at gene promoters, largely associated with a decrease in nuclear respiratory factor 1 (NRF1) binding. This shift was implicated in a marked drop-off in the ability of the aged naïve cells to transcribe respiratory chain genes, which may explain the reduced capacity of oxidative phosphorylation in older naïve cells. Our findings identify BATF- and NRF1-driven gene regulation as potential targets for delaying CD8 T cell http://immunology.sciencemag.org/ aging and restoring function. INTRODUCTION respond to antigenic stimulation (12). Limited genome-wide epigene- Aging is a ubiquitous biological process that drastically alters phys- tic studies have been performed on human CD8 T cell subsets; they iological function. Correspondingly, immune competency erodes have not comprehensively profiled chromatin accessibility in naïve, with age, leading to higher incidences of malignancies and increased EM, and CM compartments, nor have they examined the baseline morbidity and mortality from infections (1, 2). Much of this decline regulatory landscape for age-related dysfunction (13–15). has been attributed to a breakdown in T cell homeostasis, degrading Here, we report the genome-wide maps of chromatin accessibil- the competence of the central mediator of adaptive immunity (3, 4). ity in purified CD8 T cell subsets from age-segregated human donors. In the absence of thymic production, T cell renewal in humans is These data enabled us to define the changes across differentiation by entirely driven by the proliferation of peripheral naïve T cells (5). comparing naïve, EM, and CM cells and then to determine how those by guest on March 1, 2017 This homeostatic proliferation is similar across naïve CD4 and CD8 regulatory programs, as well as the subsets’ baseline chromatin land- T cells, independent of age (6), and maintains a diverse naïve T cell scapes, differ with age. Our results describe immune aging of CD8 repertoire in aged individuals (7). However, although the CD4 T cell naïve and CM T cells as a shift toward a more differentiated state, compartment is stable, age drastically affects the distribution of CD8 coupled with an erosion of chromatin accessibility at key promoters, subsets, causing a diminution of naïve and central memory (CM) in part mediated by a loss of nuclear respiratory factor 1 (NRF1) cells and an expansion of effector memory (EM) cells (8). In addi- binding. tion, naïve T cells develop functional defects with age that may relate to replicative stress induced by homeostatic turnover (9). Characterizing these cell-intrinsic drivers of T cell aging and their relationship to dif- RESULTS ferentiation is critical in identifying and combating immune aging. Genome-wide mapping of chromatin accessibility in CD8 Changes to the epigenetic landscape are hallmarks of both aging T cell subsets and differentiation and encompass chromatin remodeling, histone Using the assay for transposase-accessible chromatin using se- modifications, and DNA methylation (10, 11). Substantial revisions quencing (ATAC-seq) (16, 17), we generated genome-wide maps of to the epigenetic landscape are required for naïve T cells to lose their chromatin accessibility in three human CD8 T cell subsets, purified stem cell–like attributes and develop into memory cells that rapidly by sorting peripheral blood mononuclear cells (PBMCs): naïve (CD28hiCD45RAhiCD62Lhi), CM (CD45RAloCD62Lhi), and EM lo lo 1Department of Genetics, Stanford University School of Medicine, Stanford, CA (CD45RA CD62L ; Fig. 1A and fig. S1). The PBMCs were isolated 94305, USA. 2Biomedical Informatics Training Program, Stanford University School from 10 healthy individuals, comprising 5 donors under age 35 years of Medicine, Stanford, CA 94305, USA. 3Division of Immunology and Rheumatology, 4 (“young”; 2 males and 3 females) and 5 over age 60 years (“old”; 3 males Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department lo hi of Medicine, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94306, USA. and 2 females). We excluded terminally differentiated CD28 CD45RA 5Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford effector T cells, which mostly contain oligoclonally expanded herpes University School of Medicine, Stanford, CA 94305, USA. virus–specific cells, to focus on age-related chromatin changes rather *These authors contributed equally to this work. than changes induced by chronic viral stimulation. To support the †Corresponding author. Email: [email protected] (J.J.G.); wjg@stanford. edu (W.J.G.) functional relevance of the chromatin openness patterns we identified, we ‡These authors contributed equally to this work. also performed RNA sequencing (RNA-seq) in each of the T cell subsets. Moskowitz et al., Sci. Immunol. 2, eaag0192 (2017) 17 February 2017 1 of 13 SCIENCE IMMUNOLOGY | RESEARCH RESOURCE A CD8 näive CD8 central memory CD8 effector memory CD45RA+/CD62L+/CD28+ CD45RA–/CD62L+ CD45RA–/CD62L– CD45RA CD62L chr2:87,040 kb 87,010 kb chr12:6,900 kb 6,930 kb chr12:68,554 kb 68,548 kb chr14:25,104 kb 25,098 kb B Downloaded from 45.9 45.9 17.9 17.9 CD8 näive 0 0 0 0 45.9 45.9 17.9 17.9 CD8 CM 0 0 0 0 45.9 45.9 17.9 17.9 http://immunology.sciencemag.org/ CD8 EM 0 0 0 0 RefSeq genes CD8A CD4 IFNG GZMB CD 100 150 Na Na Na Count 0 Na 0.5 0.9 Na Naïve Na Class Na 75 Na Repetitive Na Na Heterochromatin/ CM repressed CM by guest on March 1, 2017 CM Transcribed CM 50 CM CM Enhancer CM CM CM Poised CM EM Promoter CM 25 EM EM EM ChromHMM annotation (percentage) EM EM EM EM EM 0 EM Naive CD8 T cells, ATAC−seq EM genome-wide peaks Fig. 1. ATAC-seq open chromatin maps capture characteristic signatures that correlate with phenotypically defined CD8 T cell subsets. (A) T cells were sorted into naïve (CD28hiCD45RAhiCD62Lhi), CM (CD45RAloCD62Lhi), and EM (CD45RAloCD62Llo) CD8 T cell subsets, as shown in fig. S1. Contour plots show purity of sorted popula- tions. (B) ATAC-seq signal tracks in naïve, CM, and EM subsets at selected functionally relevant genes (CD8, CD4, IFNG, and GZMB). Small boxes in gene diagrams (bottom) represent exons. Each subset’s count is aggregated across the 10 constituent donors. The y axes are in units of reads per million reads in peaks. (C) Proportion of chroma- tin states in naïve CD8 T cells, genome-wide (left), and for ATAC-seq peaks (right). Chromatin states were called by the Roadmap Epigenomics Project using ChromHMM, and we aggregated the state calls over functionally related subclasses. Percentages are as fractions of base pairs. (D) Heat map of Spearman correlation coefficients of openness between naïve (Na), CM, and EM samples. Dendrograms indicate results from consensus clustering. Sequencing read density at phenotype-defining genes confirmed Across all three subsets, we identified a total of 64,089 distinct chro- successful transposition in each subset, with accessible chromatin at the matin accessibility peaks. Using predictions of chromatin states in CD8A locus and minimal accessibility at the CD4 locus (Fig. 1B). IFNG naïve CD8 T cells from the Roadmap Epigenomics Project (18), we ob - and GZMB, which are more rapidly inducible in memory T cells after served that the peaks were concentrated at promoters and enhancers, activation, were more open in CM and EM than naïve cells. and depleted at heterochromatic regions (Fig. 1C). Hierarchical clustering Moskowitz et al., Sci. Immunol. 2, eaag0192 (2017) 17 February 2017 2 of 13 SCIENCE IMMUNOLOGY | RESEARCH RESOURCE of the peaks segregated the three T cell subsets (Fig. 1D), with the two for several members of the bZIP, T-box, and RUNT TF families among memory populations clustering more closely with each other than the most significantly enriched (table S1). Our top hits encompassed with the naïve population. To mitigate the impact of donor heteroge- known regulators of T cell differentiation and development, such as neity, we excluded sex chromosomes, which have been shown to be a Eomes and TBX21 (T-bet) (P < 10−66) (24). The TF family with the major site of interindividual variation in chromatin accessibility (19). greatest representation was bZIP, which includes Jun-AP1 and BATF, To uncover the chromatin accessibility landscapes underlying both critical to T cell differentiation (25). These TFs were also more naïve and memory cell identity in the young, we identified loci of dif- expressed in EM than naïve.
Load more

Recommended publications
  • Detection of Interacting Transcription Factors in Human Tissues Using
    Myšičková and Vingron BMC Genomics 2012, 13(Suppl 1):S2 http://www.biomedcentral.com/1471-2164/13/S1/S2 PROCEEDINGS Open Access Detection of interacting transcription factors in human tissues using predicted DNA binding affinity Alena Myšičková*, Martin Vingron From The Tenth Asia Pacific Bioinformatics Conference (APBC 2012) Melbourne, Australia. 17-19 January 2012 Abstract Background: Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF. Results: We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue.
    [Show full text]
  • Identifying and Mapping Cell-Type-Specific Chromatin PNAS PLUS Programming of Gene Expression
    Identifying and mapping cell-type-specific chromatin PNAS PLUS programming of gene expression Troels T. Marstranda and John D. Storeya,b,1 aLewis-Sigler Institute for Integrative Genomics, and bDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544 Edited by Wing Hung Wong, Stanford University, Stanford, CA, and approved January 2, 2014 (received for review July 2, 2013) A problem of substantial interest is to systematically map variation Relating DHS to gene-expression levels across multiple cell in chromatin structure to gene-expression regulation across con- types is challenging because the DHS represents a continuous ditions, environments, or differentiated cell types. We developed variable along the genome not bound to any specific region, and and applied a quantitative framework for determining the exis- the relationship between DHS and gene expression is largely tence, strength, and type of relationship between high-resolution uncharacterized. To exploit variation across cell types and test chromatin structure in terms of DNaseI hypersensitivity and genome- for cell-type-specific relationships between DHS and gene expres- wide gene-expression levels in 20 diverse human cell types. We sion, the measurement units must be placed on a common scale, show that ∼25% of genes show cell-type-specific expression ex- the continuous DHS measure associated to each gene in a well- plained by alterations in chromatin structure. We find that distal defined manner, and all measurements considered simultaneously. regions of chromatin structure (e.g., ±200 kb) capture more genes Moreover, the chromatin and gene-expression relationship may with this relationship than local regions (e.g., ±2.5 kb), yet the local only manifest in a single cell type, making standard measures of regions show a more pronounced effect.
    [Show full text]
  • REST Mediates Androgen Receptor Actions on Gene Repression And
    Published online 24 October 2013 Nucleic Acids Research, 2014, Vol. 42, No. 2 999–1015 doi:10.1093/nar/gkt921 REST mediates androgen receptor actions on gene repression and predicts early recurrence of prostate cancer Charlotte Svensson1, Jens Ceder2, Diego Iglesias-Gato1, Yin-Choy Chuan1, See Tong Pang3, Anders Bjartell2, Roxana Merino Martinez4, Laura Bott5, Leszek Helczynski6, David Ulmert2,7, Yuzhuo Wang8, Yuanjie Niu9, Colin Collins8 and Amilcar Flores-Morales1,* 1Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Downloaded from DK-2200 Copenhagen, Denmark, 2Division of Urological Cancers, Department of Clinical Sciences, Ska˚ ne University Hospital, Lund University, 20502 Malmo¨ , Sweden, 3Department of Urology, Chang Gung Memorial Hospital, Tao-Yuan 33305, Taiwan, R.O.C., 4Department of Epidemiology, Karolinska Institutet, 171 77 Stockholm, Sweden, 5Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden, 6Regional Laboratories Region Ska˚ ne, Clinical Pathology, 205 80 Malmo¨ , Sweden, 7Department of Surgery (Urology), Memorial Sloan-Kettering Cancer Center, New York, NY 100 65, USA, 8Vancouver Prostate http://nar.oxfordjournals.org/ Centre and The Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada V6H 3Z6 and 9Tianjin Institute of Urology, Tianjin Medical University, Tianjin 300 211, China Received December 19, 2012; Accepted September 20, 2013 ABSTRACT that has previously been implicated in the growth at University of British Columbia on August 12, 2014 The androgen receptor (AR) is a key regulator of NE-like castration-resistant tumors. The of prostate tumorgenesis through actions that are analysis of prostate cancer tissue microarrays not fully understood. We identified the repressor revealed that tumors with reduced expression of element (RE)-1 silencing transcription factor REST have higher probability of early recurrence, (REST) as a mediator of AR actions on gene repres- independently of their Gleason score.
    [Show full text]
  • 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
    [Show full text]
  • Regulation of Adult Neurogenesis in Mammalian Brain
    International Journal of Molecular Sciences Review Regulation of Adult Neurogenesis in Mammalian Brain 1,2, 3, 3,4 Maria Victoria Niklison-Chirou y, Massimiliano Agostini y, Ivano Amelio and Gerry Melino 3,* 1 Centre for Therapeutic Innovation (CTI-Bath), Department of Pharmacy & Pharmacology, University of Bath, Bath BA2 7AY, UK; [email protected] 2 Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK 3 Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; [email protected] (M.A.); [email protected] (I.A.) 4 School of Life Sciences, University of Nottingham, Nottingham NG7 2HU, UK * Correspondence: [email protected] These authors contributed equally to this work. y Received: 18 May 2020; Accepted: 7 July 2020; Published: 9 July 2020 Abstract: Adult neurogenesis is a multistage process by which neurons are generated and integrated into existing neuronal circuits. In the adult brain, neurogenesis is mainly localized in two specialized niches, the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ) adjacent to the lateral ventricles. Neurogenesis plays a fundamental role in postnatal brain, where it is required for neuronal plasticity. Moreover, perturbation of adult neurogenesis contributes to several human diseases, including cognitive impairment and neurodegenerative diseases. The interplay between extrinsic and intrinsic factors is fundamental in regulating neurogenesis. Over the past decades, several studies on intrinsic pathways, including transcription factors, have highlighted their fundamental role in regulating every stage of neurogenesis. However, it is likely that transcriptional regulation is part of a more sophisticated regulatory network, which includes epigenetic modifications, non-coding RNAs and metabolic pathways.
    [Show full text]
  • Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
    www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1.
    [Show full text]
  • Elucidation of the ELK1 Target Gene Network Reveals a Role in the Coordinate Regulation of Core Components of the Gene Regulation Machinery
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery Joanna Boros,1,5 Ian J. Donaldson,1,5 Amanda O’Donnell,1 Zaneta A. Odrowaz,1 Leo Zeef,1 Mathieu Lupien,2,4 Clifford A. Meyer,3 X. Shirley Liu,3 Myles Brown,2 and Andrew D. Sharrocks1,6 1Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom; 2Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA Transcription factors play an important role in orchestrating the activation of specific networks of genes through targeting their proximal promoter and distal enhancer regions. However, it is unclear how the specificity of downstream responses is maintained by individual members of transcription-factor families and, in most cases, what their target repertoire is. We have used ChIP-chip analysis to identify the target genes of the ETS-domain transcription factor ELK1. Two distinct modes of ELK1 target gene selection are identified; the first involves redundant promoter binding with other ETS-domain family members; the second occurs through combinatorial binding with a second transcription factor SRF, which specifies a unique group of target genes. One of the most prominent groups of genes forming the ELK1 target network includes classes involved in core gene expression control, namely, components of the basal transcriptional machinery, the spliceosome and the ribosome.
    [Show full text]
  • SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation–Specific Fusion Transcript in Prostate Cancer
    Published OnlineFirst March 17, 2009; DOI: 10.1158/0008-5472.CAN-08-4926 Priority Report SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation–Specific Fusion Transcript in Prostate Cancer David S. Rickman,1 Dorothee Pflueger,1 Benjamin Moss,1 Vanessa E. VanDoren,1 Chen X. Chen,1 Alexandre de la Taille,4,5 Rainer Kuefer,6 Ashutosh K. Tewari,2 Sunita R. Setlur,7 Francesca Demichelis,1,3 and Mark A. Rubin1 Departments of 1Pathology and Laboratory Medicine and 2Urology, and 3Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York; 4Department of Urology, CHU Mondor and 5Institut National de la Sante et de la Recherche Medicale, Unite´841, Cre´teil,France; 6Department of Urology, University Hospital Ulm, Ulm, Germany; and 7Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts Abstract (2, 3), and a specific expression profile (4, 5). Androgen-regulated ¶ Chromosomal rearrangements account for all erythroblast genes account for the majority of the 5 genomic regulatory transformation–specific (ETS) family member gene fusions promoters elements fused with ETS genes in prostate cancer (6). The promoter of the androgen-regulated transmembrane protease, that have been reported in prostate cancer and have clinical, serine 2 TMPRSS2 diagnostic, and prognostic implications. Androgen-regulated ( ) gene is fused to the coding region of members genes account for the majority of the 5¶ genomic regulatory of the ETS family of transcription factors, most commonly v-ets TMPRSS2-ERG, erythroblastosis virus E26 oncogene homologue (avian; ERG; ref. 7). promoter elements fused with ETS genes. Solute carrier family 45, member 3 SLC45A3 TMPRSS2-ETV1, and SLC45A3-ERG rearrangements account ( ), also referred to as for roughly 90% of ETS fusion prostate cancer.
    [Show full text]
  • The Suppressive Effects of 1,25-Dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 8-2014 The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration Carolyn Jeanne Ricciardi University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Molecular, Genetic, and Biochemical Nutrition Commons Recommended Citation Ricciardi, Carolyn Jeanne, "The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration. " Master's Thesis, University of Tennessee, 2014. https://trace.tennessee.edu/utk_gradthes/2876 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Carolyn Jeanne Ricciardi entitled "The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Nutrition.
    [Show full text]
  • Table S1. Complete Gene Expression Data from Human Diabetes RT² Profiler™ PCR Array Receptors, Transporters & Channels* A
    Table S1. Complete gene expression data from Human Diabetes RT² Profiler™ PCR Array Position Unigene GenBank Symbol Description FC Average Ct Receptors, Transporters & Channels* NGT GDM A01 Hs,5447 NM_000352 ABCC8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 0.93 35.00 35.00 A04 0Hs,2549 NM_000025 ADRB3 Adrenergic, beta-3-, receptor 0.88 34.92 35.00 A07 Hs,1307 NM_000486 AQP2 Aquaporin 2 (collecting duct) 0.93 35.00 35.00 A09 30Hs,5117 NM_001123 CCR2 Chemokine (C-C motif) receptor 2 1.00 26.28 26.17 A10 94Hs,5916 396NM_006139 CD28 CD28 molecule 0.81 34.51 34.71 A11 29Hs,5126 NM_001712 CEACAM1 Carcinoembryonic antigen-related cell adhesion molecule 1 1.31 26.08 25.59 B01 82Hs,2478 NM_005214 CTLA4 (biliaryCytotoxic glycoprotein) T-lymphocyte -associated protein 4 0.53 30.90 31.71 B11 24Hs,208 NM_000160 GCGR Glucagon receptor 0.93 35.00 35.00 C01 Hs,3891 NM_002062 GLP1R Glucagon-like peptide 1 receptor 0.93 35.00 35.00 C07 03Hs,6434 NM_000201 ICAM1 Intercellular adhesion molecule 1 0.84 28.74 28.89 D02 47Hs,5134 NM_000418 IL4R Interleukin 4 receptor 0.64 34.22 34.75 D06 57Hs,4657 NM_000208 INSR Insulin receptor 0.93 35.00 35.00 E05 44Hs,4312 NM_006178 NSF N-ethylmaleimide-sensitive factor 0.48 28.42 29.37 F08 79Hs,2961 NM_004578 RAB4A RAB4A, member RAS oncogene family 0.88 20.55 20.63 F10 69Hs,7287 NM_000655 SELL Selectin L 0.97 23.89 23.83 F11 56Hs,3806 NM_001042 SLC2A4 Solute carrier family 2 (facilitated glucose transporter), member 4 0.77 34.72 35.00 F12 91Hs,5111 NM_003825 SNAP23 Synaptosomal-associated protein, 23kDa 3.90
    [Show full text]
  • Nrf1 and Nrf2 Positively and C-Fos and Fra1 Negatively Regulate the Human Antioxidant Response Element-Mediated Expression of NAD(P)H:Quinone Oxidoreductase1 Gene
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 14960–14965, December 1996 Pharmacology Nrf1 and Nrf2 positively and c-Fos and Fra1 negatively regulate the human antioxidant response element-mediated expression of NAD(P)H:quinone oxidoreductase1 gene RADJENDIRANE VENUGOPAL AND ANIL K. JAISWAL* Department of Pharmacology, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111 Communicated by Y. W. Kan, University of California, San Francisco, CA, August 5, 1996 (received for review February 21, 1996) ABSTRACT Twenty-four base pairs of the human anti- (c-Jun, Jun-D, and Jun-B) form homodimers among them- oxidant response element (hARE) are required for high basal selves and heterodimers with c-Fos and Fra (Fra1 and Fra2) transcription of the NAD(P)H:quinone oxidoreductase1 proteins and bind to the TRE (a single AP1 binding site) and (NQO1) gene and its induction in response to xenobiotics and regulate the expression of target genes (6). Nrf1 and Nrf2 are antioxidants. hARE is a unique cis-element that contains one recently identified NF-E2-related factors that bind to the perfect and one imperfect AP1 element arranged as inverse sequence GCTGAGTCATGATGAGTCA (7, 8). The Nrf1 repeats separated by 3 bp, followed by a ‘‘GC’’ box. We report and Nrf2 contain 742 and 589 amino acids, respectively. Both here that Jun, Fos, Fra, and Nrf nuclear transcription factors these proteins display marked homology to the NF-E2, which bind to the hARE. Overexpression of cDNA derived combi- regulates expression of globin genes in developing erythroid nations of the nuclear proteins Jun and Fos or Jun and Fra1 cells through interaction with upstream AP1-like recognition repressed hARE-mediated chloramphenicol acetyltransferase sites (9).
    [Show full text]
  • Pharmacodynamic Effects of Seliciclib, an Orally Administered
    Cancer Therapy: Clinical Pharmacodynamic Effects of Seliciclib, an Orally Administered Cell Cycle Modulator, in Undifferentiated Nasopharyngeal Cancer Wen-Son Hsieh,4 Ross Soo,1Bee-Keow Peh,2 Thomas Loh,4 Difeng Dong,3 Donny Soh,5 Lim-SoonWong,3,5 Simon Green,6 Judy Chiao,6 Chun-Ying Cui,1Yo k e -F o n g L a i , 4 Soo-Chin Lee,1Benjamin Mow,1 Richie Soong,2 Manuel Salto-Tellez,2 and Boon-Cher Goh1, 2 Abstract Purpose: Cell cycle dysregulation resulting in expression of antiapoptotic genes and uncontrolled proliferation is a feature of undifferentiated nasopharyngeal carcinoma. The pharmacodynamic effects of seliciclib, a cyclin-dependent kinase (CDK) inhibitor, were studied in patients with nasopharyngeal carcinoma. Experimental Design: Patients with treatment-naI«ve locally advanced nasopharyngeal carci- noma received seliciclib at 800 mg or 400 mg twice daily on days1 to 3 and 8 to12.Paired tumor samples obtained at baseline and on day 13 were assessed by light microscopy, immunohisto- chemistry, and transcriptionalprofiling using real-time PCR low-density array consisting of apanel of 380 genes related to cell cycle inhibition, apoptosis, signal transduction, and cell proliferation. Results: At 800 mg bd, one patient experienced grade 3 liver toxicity and another had grade 2 vomiting; no significant toxicities were experienced in 13 patients treated at 400 mg bd. Seven of fourteen evaluable patients had clinical evidence of tumor reduction. Some of these responses were associated with increased tumor apoptosis, necrosis, and decreases in plasma EBV DNA posttreatment. Reduced protein expression of Mcl-1, cyclin D1, phosphorylated retinoblastoma protein pRB (T821), and significant transcriptional down-regulation of genes related to cellular proliferation and survival were shown in some patients posttreatment, indicative of cell cycle modulation by seliciclib, more specifically inhibition of cdk2/cyclin E, cdk7/cyclin H, and cdk9/cyclinT.
    [Show full text]