Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential
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Supplementary Data
Figure 2S 4 7 A - C 080125 CSCs 080418 CSCs - + IFN-a 48 h + IFN-a 48 h + IFN-a 72 h 6 + IFN-a 72 h 3 5 MRFI 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 7 B 13 080125 FBS - D 080418 FBS - + IFN-a 48 h 12 + IFN-a 48 h + IFN-a 72 h + IFN-a 72 h 6 080125 FBS 11 10 5 9 8 4 7 6 3 MRFI 5 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 Molecule Molecule FIGURE 4S FIGURE 5S Panel A Panel B FIGURE 6S A B C D Supplemental Results Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines. Molecule * Cell line IFN-α‡ HLA β2-m# HLA LMP TAP1 TAP2 class II A A HC§ 2 7 10 080125 CSCs - 1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3) + 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68) 080125 FBS - 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75) + 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87) 080418 CSCs - 2 (51) 1 (1) 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3) + 2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2) 080418 FBS - 1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2) + 2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2) 070104 CSCs - 1 (2) 1 (3) 1 (3) 2 (78) 1 (3) 1 (2) 1 (3) 1 (3) 1 (2) + 2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79) * expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # β-2 microglobulin; § β-2 microglobulin-free HLA-A heavy chain; ∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). -
The Regulation of Transcriptional Repression in Hypoxia
Author’s Accepted Manuscript The regulation of transcriptional repression in hypoxia Miguel A.S. Cavadas, Alex Cheong, Cormac T. Taylor PII: S0014-4827(17)30076-9 DOI: http://dx.doi.org/10.1016/j.yexcr.2017.02.024 Reference: YEXCR10481 To appear in: Experimental Cell Research Received date: 10 January 2017 Revised date: 14 February 2017 Accepted date: 15 February 2017 Cite this article as: Miguel A.S. Cavadas, Alex Cheong and Cormac T. Taylor, The regulation of transcriptional repression in hypoxia, Experimental Cell Research, http://dx.doi.org/10.1016/j.yexcr.2017.02.024 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. The regulation of transcriptional repression in hypoxia Miguel A. S. Cavadas1, Alex Cheong2, Cormac T. Taylor3,4 1 Instituto Gulbenkian de ua da Quinta Grande, 2780-156 Oeiras, Portugal. 2 Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK. 3 Systems Biology Ireland, University College Dublin, Dublin 4, Ireland. 4 Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences and Systems Biology Ireland, University College Dublin, Dublin 4, Ireland. Abstract A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. -
Crystal Structure of the Primary Pirna Biogenesis Factor Zucchini Reveals Similarity to the Bacterial PLD Endonuclease Nuc
Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press LETTER TO THE EDITOR Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc FRANKA VOIGT,1 MICHAEL REUTER,2,3 ANISA KASARUHO,2,3 EIKE C. SCHULZ,1 RAMESH S. PILLAI,2,3,4 and ORSOLYA BARABAS1,4 1European Molecular Biology Laboratory, 69117 Heidelberg, Germany 2European Molecular Biology Laboratory, 38042 Grenoble, France 3CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI), 38042 Grenoble, France ABSTRACT Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the double- stranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conforma- tional changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini’s activity. Keywords: Zucchini; piRNA; Piwi; nuclease; phospholipase; PLD6; MitoPLD INTRODUCTION stranded (ss) RNAs (Brennecke et al. -
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. -
Microrna Pharmacoepigenetics: Posttranscriptional Regulation Mechanisms Behind Variable Drug Disposition and Strategy to Develop More Effective Therapy
1521-009X/44/3/308–319$25.00 http://dx.doi.org/10.1124/dmd.115.067470 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 44:308–319, March 2016 Copyright ª 2016 by The American Society for Pharmacology and Experimental Therapeutics Minireview MicroRNA Pharmacoepigenetics: Posttranscriptional Regulation Mechanisms behind Variable Drug Disposition and Strategy to Develop More Effective Therapy Ai-Ming Yu, Ye Tian, Mei-Juan Tu, Pui Yan Ho, and Joseph L. Jilek Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California Received September 30, 2015; accepted November 12, 2015 Downloaded from ABSTRACT Knowledge of drug absorption, distribution, metabolism, and excre- we review the advances in miRNA pharmacoepigenetics including tion (ADME) or pharmacokinetics properties is essential for drug the mechanistic actions of miRNAs in the modulation of Phase I and development and safe use of medicine. Varied or altered ADME may II drug-metabolizing enzymes, efflux and uptake transporters, and lead to a loss of efficacy or adverse drug effects. Understanding the xenobiotic receptors or transcription factors after briefly introducing causes of variations in drug disposition and response has proven the characteristics of miRNA-mediated posttranscriptional gene dmd.aspetjournals.org critical for the practice of personalized or precision medicine. The regulation. Consequently, miRNAs may have significant influence rise of noncoding microRNA (miRNA) pharmacoepigenetics and on drug disposition and response. Therefore, research on miRNA pharmacoepigenomics has come with accumulating evidence sup- pharmacoepigenetics shall not only improve mechanistic under- porting the role of miRNAs in the modulation of ADME gene standing of variations in pharmacotherapy but also provide novel expression and then drug disposition and response. -
Regulatory Micrornas in Brown, Brite and White Adipose Tissue
cells Review Regulatory microRNAs in Brown, Brite and White Adipose Tissue Seley Gharanei 1,2, Kiran Shabir 3 , James E. Brown 3,4, Martin O. Weickert 1,2,5 , 1,2 1,2,3, 1,2,3, , Thomas M. Barber , Ioannis Kyrou y and Harpal S. Randeva * y 1 Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry CV2 2DX, UK; [email protected] (S.G.); [email protected] (M.O.W.); [email protected] (T.M.B.); [email protected] (I.K.) 2 Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK 3 Aston Medical Research Institute, Aston Medical School, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK; [email protected] (K.S.); [email protected] (J.E.B.) 4 School of Biosciences, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK 5 Centre of Applied Biological & Exercise Sciences, Faculty of Health & Life Sciences, Coventry University, Coventry CV1 5FB, UK * Correspondence: [email protected] Joint senior authors; contributed equally to the manuscript. y Received: 30 September 2020; Accepted: 13 November 2020; Published: 16 November 2020 Abstract: MicroRNAs (miRNAs) constitute a class of short noncoding RNAs which regulate gene expression by targeting messenger RNA, inducing translational repression and messenger RNA degradation. This regulation of gene expression by miRNAs in adipose tissue (AT) can impact on the regulation of metabolism and energy homeostasis, particularly considering the different types of adipocytes which exist in mammals, i.e., white adipocytes (white AT; WAT), brown adipocytes (brown AT; BAT), and inducible brown adipocytes in WAT (beige or brite or brown-in-white adipocytes). -
A Flexible Microfluidic System for Single-Cell Transcriptome Profiling
www.nature.com/scientificreports OPEN A fexible microfuidic system for single‑cell transcriptome profling elucidates phased transcriptional regulators of cell cycle Karen Davey1,7, Daniel Wong2,7, Filip Konopacki2, Eugene Kwa1, Tony Ly3, Heike Fiegler2 & Christopher R. Sibley 1,4,5,6* Single cell transcriptome profling has emerged as a breakthrough technology for the high‑resolution understanding of complex cellular systems. Here we report a fexible, cost‑efective and user‑ friendly droplet‑based microfuidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure‑based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efciencies that compare favorably in the feld. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of diferent bufers and barcoded bead confgurations to facilitate diverse applications. Finally, by 3′ mRNA profling asynchronous human and mouse cells at diferent phases of the cell cycle, we demonstrate the system’s ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and fexible technology for future transcriptomic studies, and other related applications, at cell resolution. Single cell transcriptome profling has recently emerged as a breakthrough technology for understanding how cellular heterogeneity contributes to complex biological systems. Indeed, cultured cells, microorganisms, biopsies, blood and other tissues can be rapidly profled for quantifcation of gene expression at cell resolution. -
Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response To
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) BMJ Open Diab Res Care SUPPLEMEMTARY DATA Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response to Glucagon-like Peptide-1 Analogue Therapy in Type 2 Diabetes Mellitus Chia-Hung Lin, Yun-Shien Lee, Yu-Yao Huang, Chi-Neu Tsai List of supplemental Tables Supplemental Table S1 Demographic variables of 10 participants (training group) applied for DNA methylation chip at baselines Supplement Table S2 Demographic variables of participants (validation group) enrolled in this study Supplemental Table S3 Primers used for bisulfite sequencing primers (BSP), pyrosequencing reaction and centromeric CTCF polymorphism Supplemental Table S4 Differentially methylated regions (DMRs) in human genome and association with glycemic response of GLP-1 treatment in training group List of supplemental Figures Supplement Figure S1: A gender difference was identified in Infinium® MethylationEPIC BeadChip analysis in the training group of this study through volcano and heatmap plot. Supplemental Fig. S2: The volcano plots of the differentially methylation comparing responsive and non-responsive groups before and after GLP-1 analogue treatment. Supplemental Fig. S3: Serum level of TGF-1 as a predictor of a glycemic response to GLP-1 analogue treatment and the correlation of VTRNA2-1 RNA expression versus its promoter methylation status. Supplement Figure S4: The association between change in A1C and (A) VTRNA 2-1 methylation level, (B) TGF-beta1 levels, and (C) mRNA levels of VTRNA 2-1 Lin C-H, et al. -
Teaching an Old Dog New Tricks: Reactivated Developmental Signaling Pathways Regulate ABCB1 and Chemoresistance in Cancer
Lee et al. Cancer Drug Resist 2021;4:424-52 Cancer DOI: 10.20517/cdr.2020.114 Drug Resistance Review Open Access Teaching an old dog new tricks: reactivated developmental signaling pathways regulate ABCB1 and chemoresistance in cancer Wing-Kee Lee, Frank Thévenod Institute for Physiology, Pathophysiology and Toxicology, ZBAF, Witten/Herdecke University, Witten 58453, Germany. Correspondence to: Prof. Wing-Kee Lee, Institute for Physiology, Pathophysiology and Toxicology, Witten/Herdecke University, Stockumer Strasse 12, Witten 58453, Germany. E-mail: [email protected] How to cite this article: Lee WK, Thévenod F. Teaching an old dog new tricks: reactivated developmental signaling pathways regulate ABCB1 and chemoresistance in cancer. Cancer Drug Resist 2021;4:424-52. http://dx.doi.org/10.20517/cdr.2020.114 Received: 11 Dec 2020 First Decision: 27 Jan 2021 Revised: 6 Feb 2021 Accepted: 20 Feb 2021 Available online: 19 Jun 2021 Academic Editor: Godefridus J. Peters Copy Editor: Yue-Yue Zhang Production Editor: Yue-Yue Zhang Abstract Oncogenic multidrug resistance (MDR) is a multifactorial phenotype intimately linked to deregulated expression of detoxification transporters. Drug efflux transporters, particularly the MDR P-glycoprotein ABCB1, represent a central mechanism by which not only chemotherapeutic drugs are extruded or sequestered to prevent drug delivery to their intracellular targets, but also for inhibiting apoptotic cell death cues, such as removal of proapoptotic signals. Several cell populations exhibiting the MDR phenotype co-exist within a tumor, such as cells forming the bulk tumor cell mass, cancer stem cells, and cancer persister cells. The key to regulation of ABCB1 expression is the cellular transcriptional machinery. -
Accompanies CD8 T Cell Effector Function Global DNA Methylation
Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer, Benjamin G. Barwick, Benjamin A. Youngblood, Rafi Ahmed and Jeremy M. Boss This information is current as of October 1, 2021. J Immunol 2013; 191:3419-3429; Prepublished online 16 August 2013; doi: 10.4049/jimmunol.1301395 http://www.jimmunol.org/content/191/6/3419 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130139 Material 5.DC1 References This article cites 81 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/191/6/3419.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer,* Benjamin G. Barwick,* Benjamin A. Youngblood,*,† Rafi Ahmed,*,† and Jeremy M. -
Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002) -
Gastroprotective Peptide Trefoil Factor Family 2 Gene Is Activated By
685 GASTROINTESTINAL CANCER Gut: first published as 10.1136/gut.51.5.685 on 1 November 2002. Downloaded from Gastroprotective peptide trefoil factor family 2 gene is activated by upstream stimulating factor but not by c-Myc in gastrointestinal cancer cells E Al-azzeh, O Dittrich, J Vervoorts, N Blin, P Gött, B Lüscher ............................................................................................................................. Gut 2002;51:685–690 Background: Damage to the gastrointestinal mucosa results in the acute up-regulation of the trefoil factor family peptides TFF1, TFF2, and TFF3. They possess protective, healing, and tumour suppressive functions. Little is known about the regulation of TFF gene expression. The promoters of all three TFF genes contain binding sites (E box) for upstream stimulating factor (USF) and Myc/Max/Mad network proteins. Aims: To determine the nature and function of transcription factors that bind to these E boxes and to See end of article for understand their role for TFF gene expression. authors’ affiliations Methods: TFF promoter activities were determined by reporter gene assays. DNA binding was moni- ....................... tored by electromobility shift assays and by chromatin immunoprecipitation analyses. Expression of Correspondence to: endogenous TFF was determined by multiplex RT-PCR. Dr B Lüscher, Abt. Results: It was observed that the TFF2 promoter is specifically and efficiently activated by USF Biochemie und transcription factors but not by c-Myc. USF displayed comparable binding to a high affinity Myc/Max Molekularbiologie, Institut binding site compared with the three TFF E boxes, while c-Myc exhibited lower affinity to the TFF E für Biochemie, Klinikum der boxes. In contrast, pronounced binding differences were observed in cells with a strong preference for RWTH, Pauwelsstrasse 30, D-52057 Aachen, USF to interact specifically with the TFF2 E box, while Myc was not above background.