DOCSLIB.ORG

Production in Human NK Cells PRDM1/Blimp-1 Controls Effector

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Production in Human NK Cells PRDM1/Blimp-1 Controls Effector PRDM1/Blimp-1 Controls Effector Cytokine Production in Human NK Cells Matthew A. Smith, Michelle Maurin, Hyun Il Cho, Brian Becknell, Aharon G. Freud, Jianhua Yu, Sheng Wei, Julie This information is current as Djeu, Esteban Celis, Michael A. Caligiuri and Kenneth L. of September 23, 2021. Wright J Immunol 2010; 185:6058-6067; Prepublished online 13 October 2010; doi: 10.4049/jimmunol.1001682 Downloaded from http://www.jimmunol.org/content/185/10/6058 Supplementary http://www.jimmunol.org/content/suppl/2010/10/14/jimmunol.100168 Material 2.DC1 http://www.jimmunol.org/ References This article cites 51 articles, 28 of which you can access for free at: http://www.jimmunol.org/content/185/10/6058.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 23, 2021 • No Triage! Every submission reviewed by practicing scientists • 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 © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology PRDM1/Blimp-1 Controls Effector Cytokine Production in Human NK Cells Matthew A. Smith,*,† Michelle Maurin,* Hyun Il Cho,* Brian Becknell,‡ Aharon G. Freud,‡ Jianhua Yu,‡ Sheng Wei,* Julie Djeu,* Esteban Celis,* Michael A. Caligiuri,‡ and Kenneth L. Wright*,† NK cells are major effectors of the innate immune response through cytolysis and bridge to the adaptive immune response through cytokine release. The mediators of activation are well studied; however, little is known about the mechanisms that re- strain activation. In this report, we demonstrate that the transcriptional repressor PRDM1 (also known as Blimp-1 or PRDI-BF1) is a critical negative regulator of NK function. Three distinct PRDM1 isoforms are selectively induced in the CD56dim NK population in response to activation. PRDM1 coordinately suppresses the release of IFN-g, TNF-a, and TNF-b through direct binding to multiple conserved regulatory regions. Ablation of PRDM1 expression leads to enhanced production of IFN-g and Downloaded from TNF-a but does not alter cytotoxicity, whereas overexpression blocks cytokine production. PRDM1 response elements are defined at the IFNG and TNF loci. Collectively, these data demonstrate a key role for PRDM1 in the negative regulation of NK activation and position PRDM1 as a common regulator of the adaptive and innate immune response. The Journal of Immunology, 2010, 185: 6058–6067. http://www.jimmunol.org/ atural killer cells play critical functions in innate and IFN-g production and increased cytotoxicity (9). IL-18 induces nu- adaptive immunity. Although these lymphocytes were clear localization of NF-kB p50/p65 which, cooperatively with N initially identified by their ability to lyse leukemia cells AP-1, increases IFN-g and cytotoxicity (10). Furthermore, NFAT in a non-MHC–restricted manner, subsequent studies highlighted induces transcription of GM-CSF and TNF-a in NK cells (11). their role in cytokine production. In response to activating stimuli, Conversely, relatively few negative regulators of activation-induced NK cells proliferate, increase cytotoxicity, and produce cytokines, transcription have been identified in NK cells. ATF3 was recently such as IFN-g, TNF-a, and GM-CSF (1). IL-2 upregulates the ex- shown to downregulate IFN-g levels, and ATF2/2 mice exhibit in- pression of effector molecules and enhances natural cytotoxicity creased resistance to murine CMV infection (12). The transcription against a variety of targets. Furthermore, IL-2 and IL-15 signal factor H2.0-like homeobox negatively regulates IFN-g production, by guest on September 23, 2021 through the common gcR to control proliferation, with IL-15 be- primarily through degradation of phosphorylated STAT4 not ing uniquely required for survival in vivo (2). IL-12 and IL-18 direct DNA-binding activity (13). signal through distinct heterodimeric receptor complexes to elicit PRDM1 (also known as Blimp-1 or PRDI-BF1) is a transcrip- increases in IFN-g via several mechanisms, including increased tional repressor encoded by the PRDM1 gene on chromosome transcription, message stability, and nuclear retention (3–5). Syn- 6q21. It was originally identified as a postinduction suppressor of ergistic increases in cytotoxicity and IFN-g production are ob- IFNB in virally infected osteosarcoma cells (14). Subsequent served in response to costimulation with IL-12 and IL-18 (6, 7). work revealed a pivotal role in the terminal differentiation of Ab- Cytokine-mediated activation of NK cells proceeds through producing plasma cells (15). We and other investigators previously several well-characterized nuclear transcription factors, many of showed that PRDM1 exerts its repressive functions through re- which are functionally conserved between T and NK lineages (8). cruitment of histone-modifying enzymes (HDAC2, G9a, PRMT5, STAT4 is induced in response to IL-12 and is required for optimal and LSD1) and Groucho corepressors (16–18). Through silencing of direct (cMyc, CIITA, Pax5) and indirect targets, PRDM1 is a master regulator of terminal differentiation of B lymphocytes, me- *Immunology Program, H. Lee Moffitt Cancer Center and Research Institute; †Department of Molecular Medicine, University of South Florida, Tampa, FL diating cell cycle exit, repression of early B cell factors, and in- 33612; and ‡Ohio State Comprehensive Cancer Center, Columbus, OH 43210 duction of Ig secretion (19, 20). Received for publication May 20, 2010. Accepted for publication September 11, More recently, a role for PRDM1 in T lymphocytes has emerged. 2010. PRDM1 is expressed in CD4 and CD8 T cell lineages and is critical This work was supported by the James and Ester King Biomedical Research Program for maintenance of homeostasis. Conditional knockout in T lym- (09KT-03). phocytes leads to increased effector populations, resulting in severe The sequences presented in this article have been submitted to the Gene Expression Omnibus under accession number GE22919. colitis (21, 22). Upon activation, an autoregulatory loop exists, whereby IL-2 induces PRDM1 expression, which, in turn, nega- Address correspondence and reprint requests to Dr. Kenneth L. Wright, H. Lee Moffitt Cancer Center, MRC4E, 12902 Magnolia Drive, Tampa, FL 33612. E-mail tively regulates IL-2 transcription (23, 24). During CD4 polariza- address: Ken.Wright@moffitt.org tion, PRDM1 is preferentially expressed in Th2 cells and reinforces The online version of this article contains supplemental material. commitment to this lineage through repression of Ifng, cfos, and Abbreviations used in this paper: ChIP, chromatin immunoprecipitation; Ct, threshold tbx21 (24, 25). Within the CD8 lineage, PRDM1 is expressed at cycle; KD, knockdown; NT, nontargeting; PARP, poly(ADP-ribose) polymerase; higher levels in exhausted subsets and promotes acquisition of poly-IC, polyinosinic-polycytidylic acid; siRNA, small interfering RNA. the effector phenotype through suppression of memory potential Copyright Ó 2010 by The American Association of Immunologists, Inc. 0022-1767/10/$16.00 (26–28). Thus, in addition to well-characterized B cell-specific www.jimmunol.org/cgi/doi/10.4049/jimmunol.1001682 The Journal of Immunology 6059 functions, PRDM1 is a critical regulator of T lymphocytes. In this and counts per minute were determined using a PerkinElmer 1470 auto- report, we provide a functional description of PRDM1 in NK cells. matic gamma counter (PerkinElmer, Wellesley, MA). The percentage of cytotoxicity was calculated using the following formula: (experimental 2 spontaneous release)/(total 2 spontaneous release) 3 100. Materials and Methods Chromatin immunoprecipitation Cells and cytokines A total of 20 3 106 purified NK cells were stimulated for 24 h with IL-2 Primary human NK cells were isolated via negative selection using the (100 U/ml), IL-12 (10 ng/ml), and IL-18 (100 ng/ml). Chromatin EZSep kit (StemCell Technologies, Vancouver, BC, Canada), according to was prepared, as previously described (30). A total of 4.5 3 106 cell the manufacturer’s instructions. Purity was verified by flow cytometry, 2 + + equivalents were used for each immunoprecipitation reaction. Primary and cells were routinely found to be 90–95% CD3 CD56 CD16 . Cells Abs were used at 0.5 mgineach900-ml reaction and were incubated over- were maintained in RPMI 1640 (Life Technologies, Carlsbad, CA), sup- night. Abs used included PRDM1 (PRDI-BF1) (Cell Signaling Tech- plemented with 10% FBS and 1% penicillin-streptomycin. For small in- nology) and normal rabbit IgG (Upstate Biotechnology, Lake Placid, NY). terfering RNA (siRNA) experiments, cells were grown in Accell Delivery Immune complexes were captured with protein A/G beads (Santa Cruz Media (Dharmacon, Chicago, IL), supplemented with 2% FBS. For Biotechnology, Santa Cruz, CA) and washed, as described. Eluted DNA stimulations, the following recombinant human cytokines were used: IL-2 was column purified (Qiagen) after reversal of cross-links (4 h at 65˚C) (100 U/ml; PeproTech, Rocky Hill, NJ), IL-12 (10 ng/ml; PeproTech), IL- and RNase treatment and proteinase K treatment. PCR was performed 18 (100 ng/ml; MBL, Woburn, MA), TNF-a (20–100 ng/ml; eBioscience, using 1.5 mlelutedDNA(∼1/40th) in duplicate. Primers designed against San Diego, CA), and IFN-g (10–50 ng/ml; eBioscience), a-IFN (10 or the second exon of myoglobin B (Diagenode, Liege, Belgium) were used 50ng/ml; Sigma-Aldrich, St. Louis, MO). as a negative control locus. The percentage of input was calculated by 2 Mice linearization of DCt (CtIP Ct1%input) for specific and IgG samples. Downloaded from C57BL/6 mice (n = 4) were immunized i.v.
Load more

Recommended publications
  • Cytogenomic SNP Microarray - Fetal ARUP Test Code 2002366 Maternal Contamination Study Fetal Spec Fetal Cells
    Patient Report |FINAL Client: Example Client ABC123 Patient: Patient, Example 123 Test Drive Salt Lake City, UT 84108 DOB 2/13/1987 UNITED STATES Gender: Female Patient Identifiers: 01234567890ABCD, 012345 Physician: Doctor, Example Visit Number (FIN): 01234567890ABCD Collection Date: 00/00/0000 00:00 Cytogenomic SNP Microarray - Fetal ARUP test code 2002366 Maternal Contamination Study Fetal Spec Fetal Cells Single fetal genotype present; no maternal cells present. Fetal and maternal samples were tested using STR markers to rule out maternal cell contamination. This result has been reviewed and approved by Maternal Specimen Yes Cytogenomic SNP Microarray - Fetal Abnormal * (Ref Interval: Normal) Test Performed: Cytogenomic SNP Microarray- Fetal (ARRAY FE) Specimen Type: Direct (uncultured) villi Indication for Testing: Patient with 46,XX,t(4;13)(p16.3;q12) (Quest: EN935475D) ----------------------------------------------------------------- ----- RESULT SUMMARY Abnormal Microarray Result (Male) Unbalanced Translocation Involving Chromosomes 4 and 13 Classification: Pathogenic 4p Terminal Deletion (Wolf-Hirschhorn syndrome) Copy number change: 4p16.3p16.2 loss Size: 5.1 Mb 13q Proximal Region Deletion Copy number change: 13q11q12.12 loss Size: 6.1 Mb ----------------------------------------------------------------- ----- RESULT DESCRIPTION This analysis showed a terminal deletion (1 copy present) involving chromosome 4 within 4p16.3p16.2 and a proximal interstitial deletion (1 copy present) involving chromosome 13 within 13q11q12.12. This
    [Show full text]
  • 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.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • NIH Public Access Provided by Digital.CSIC Author Manuscript Bioessays
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE NIH Public Access provided by Digital.CSIC Author Manuscript Bioessays. Author manuscript; available in PMC 2007 October 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Bioessays. 2007 April ; 29(4): 356±370. GTP-binding proteins of the Rho/Rac family: regulation, effectors and functions in vivo Xosé R. Bustelo*, Vincent Sauzeau, and Inmaculada M. Berenjeno Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-University of Salamanca, Salamanca, Spain. Summary Rho/Rac proteins constitute a subgroup of the Ras superfamily of GTP hydrolases. Although originally implicated in the control of cytoskeletal events, it is currently known that these GTPases coordinate diverse cellular functions, including cell polarity, vesicular trafficking, the cell cycle and transcriptomal dynamics. In this review, we will provide an overview on the recent advances in this field regarding the mechanism of regulation and signaling, and the roles in vivo of this important GTPase family. Introduction The isolation of rhoA,(1) the first member of the Rho/Rac family ever identified, was achieved by Richard Axel’s group in 1985 during the search for ras -related genes in Aplysia.(1) The subsequent use of conventional cloning techniques and the more-recent characterization of genomes revealed that the original gene is not alone, having numerous family counterparts in other species including, among many others, S. cerevisiae(7 genes), A. taliana(11 genes), C. elegans(9 genes), D. melanogaster(9 genes) and H.
    [Show full text]
  • Genome-Wide Association Study Confirms Extant PD Risk Loci Among
    European Journal of Human Genetics (2011) 19, 655–661 & 2011 Macmillan Publishers Limited All rights reserved 1018-4813/11 www.nature.com/ejhg ARTICLE Genome-wide association study confirms extant PD risk loci among the Dutch Javier Simo´n-Sa´nchez*,1, Jacobus J van Hilten2, Bart van de Warrenburg3, Bart Post3, Henk W Berendse4, Sampath Arepalli5, Dena G Hernandez5, Rob MA de Bie6, Daan Velseboer6, Hans Scheffer7, Bas Bloem3, Karin D van Dijk4, Fernando Rivadeneira8,9, Albert Hofman8, Andre´ G Uitterlinden8,9, Patrizia Rizzu1, Zoltan Bochdanovits1, Andrew B Singleton5 and Peter Heutink1 In view of the population-specific heterogeneity in reported genetic risk factors for Parkinson’s disease (PD), we conducted a genome-wide association study (GWAS) in a large sample of PD cases and controls from the Netherlands. After quality control (QC), a total of 514 799 SNPs genotyped in 772 PD cases and 2024 controls were included in our analyses. Direct replication of SNPs within SNCA and BST1 confirmed these two genes to be associated with PD in the Netherlands (SNCA, rs2736990: P¼1.63Â10À5,OR¼1.325 and BST1, rs12502586: P¼1.63Â10À3,OR¼1.337). Within SNCA, two independent signals in two different linkage disequilibrium (LD) blocks in the 3¢ and 5¢ ends of the gene were detected. Besides, post-hoc analysis confirmed GAK/DGKQ, HLA and MAPT as PD risk loci among the Dutch (GAK/DGKQ, rs2242235: P¼1.22Â10À4,OR¼1.51; HLA, rs4248166: P¼4.39Â10À5,OR¼1.36; and MAPT, rs3785880: P¼1.9Â10À3,OR¼1.19). European Journal of Human Genetics (2011) 19, 655–661; doi:10.1038/ejhg.2010.254; published online 19 January 2011 Keywords: SNCA; BST1; GAK/DGKQ; HLA; MAPT;PD INTRODUCTION self-reported Caucasian individuals from the Netherlands.
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • ADHD) Gene Networks in Children of Both African American and European American Ancestry
    G C A T T A C G G C A T genes Article Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry Yichuan Liu 1 , Xiao Chang 1, Hui-Qi Qu 1 , Lifeng Tian 1 , Joseph Glessner 1, Jingchun Qu 1, Dong Li 1, Haijun Qiu 1, Patrick Sleiman 1,2 and Hakon Hakonarson 1,2,3,* 1 Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; [email protected] (Y.L.); [email protected] (X.C.); [email protected] (H.-Q.Q.); [email protected] (L.T.); [email protected] (J.G.); [email protected] (J.Q.); [email protected] (D.L.); [email protected] (H.Q.); [email protected] (P.S.) 2 Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 3 Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA * Correspondence: [email protected]; Tel.: +1-267-426-0088 Abstract: Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with poorly understood molecular mechanisms that results in significant impairment in children. In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, Citation: Liu, Y.; Chang, X.; Qu, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans H.-Q.; Tian, L.; Glessner, J.; Qu, J.; Li, (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA.
    [Show full text]
  • Supplementary Information – Postema Et Al., the Genetics of Situs Inversus Totalis Without Primary Ciliary Dyskinesia
    1 Supplementary information – Postema et al., The genetics of situs inversus totalis without primary ciliary dyskinesia Table of Contents: Supplementary Methods 2 Supplementary Results 5 Supplementary References 6 Supplementary Tables and Figures Table S1. Subject characteristics 9 Table S2. Inbreeding coefficients per subject 10 Figure S1. Multidimensional scaling to capture overall genomic diversity 11 among the 30 study samples Table S3. Significantly enriched gene-sets under a recessive mutation model 12 Table S4. Broader list of candidate genes, and the sources that led to their 13 inclusion Table S5. Potential recessive and X-linked mutations in the unsolved cases 15 Table S6. Potential mutations in the unsolved cases, dominant model 22 2 1.0 Supplementary Methods 1.1 Participants Fifteen people with radiologically documented SIT, including nine without PCD and six with Kartagener syndrome, and 15 healthy controls matched for age, sex, education and handedness, were recruited from Ghent University Hospital and Middelheim Hospital Antwerp. Details about the recruitment and selection procedure have been described elsewhere (1). Briefly, among the 15 people with radiologically documented SIT, those who had symptoms reminiscent of PCD, or who were formally diagnosed with PCD according to their medical record, were categorized as having Kartagener syndrome. Those who had no reported symptoms or formal diagnosis of PCD were assigned to the non-PCD SIT group. Handedness was assessed using the Edinburgh Handedness Inventory (EHI) (2). Tables 1 and S1 give overviews of the participants and their characteristics. Note that one non-PCD SIT subject reported being forced to switch from left- to right-handedness in childhood, in which case five out of nine of the non-PCD SIT cases are naturally left-handed (Table 1, Table S1).
    [Show full text]
  • Supplementary Figure 1. Dystrophic Mice Show Unbalanced Stem Cell Niche
    Supplementary Figure 1. Dystrophic mice show unbalanced stem cell niche. (A) Single channel images for the merged panels shown in Figure 1A, for of PAX7, MYOD and Laminin immunohistochemical staining in Lmna Δ8-11 mice of PAX7 and MYOD markers at the indicated days of post-natal growth. Basement membrane of muscle fibers was stained with Laminin. Scale bars, 50 µm. (B) Quantification of the % of PAX7+ MuSCs per 100 fibers at the indicated days of post-natal growth in (A). n =3-6 animals per genotype. (C) Immunohistochemical staining in Lmna Δ8-11 mice of activated, ASCs (PAX7+/KI67+) and quiescent QSCs (PAX7+/Ki67-) MuSCs at d19 and relative quantification (below). n= 4-6 animals per genotype. Scale bars, 50 µm. (D) Quantification of the number of cells per cluster in single myofibers extracted from d19 Lmna Δ8-11 mice and cultured 96h. n= 4-5 animals per group. Data are box with median and whiskers min to max. B, C, Data are mean ± s.e.m. Statistics by one-way (B) or two-way (C, D) analysis of variance (ANOVA) with multiple comparisons. * * P < 0.01, * * * P < 0.001. wt= Lmna Δ8-11 +/+; het= Lmna Δ8-11 +/; hom= Lmna Δ8-11 -/-. Supplementary Figure 2. Heterozygous mice show intermediate Lamin A levels. (A) RNA-seq signal tracks as the effective genome size normalized coverage of each biological replicate of Lmna Δ8-11 mice on Lmna locus. Neomycine cassette is indicated as a dark blue rectangle. (B) Western blot of total protein extracted from the whole Lmna Δ8-11 muscles at d19 hybridized with indicated antibodies.
    [Show full text]
  • SVA) Retrotransposons in Shaping the Human Genome
    Edinburgh Research Explorer The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome Citation for published version: Gianfrancesco, O, Geary, B, Savage, A, Billingsley, K, Bubb, V & Quinn, J 2019, 'The Role of SINE-VNTR- Alu (SVA) Retrotransposons in Shaping the Human Genome', International Journal of Molecular Sciences, vol. 20, no. 23. https://doi.org/10.3390/ijms20235977 Digital Object Identifier (DOI): 10.3390/ijms20235977 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: International Journal of Molecular Sciences General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 International Journal of Molecular Sciences Article The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome Olympia Gianfrancesco 1,2, Bethany Geary 3 , Abigail L. Savage 1 , Kimberley J. Billingsley 1, Vivien
    [Show full text]
  • Supplemental Figures 04 12 2017
    Jung et al. 1 SUPPLEMENTAL FIGURES 2 3 Supplemental Figure 1. Clinical relevance of natural product methyltransferases (NPMTs) in brain disorders. (A) 4 Table summarizing characteristics of 11 NPMTs using data derived from the TCGA GBM and Rembrandt datasets for 5 relative expression levels and survival. In addition, published studies of the 11 NPMTs are summarized. (B) The 1 Jung et al. 6 expression levels of 10 NPMTs in glioblastoma versus non‐tumor brain are displayed in a heatmap, ranked by 7 significance and expression levels. *, p<0.05; **, p<0.01; ***, p<0.001. 8 2 Jung et al. 9 10 Supplemental Figure 2. Anatomical distribution of methyltransferase and metabolic signatures within 11 glioblastomas. The Ivy GAP dataset was downloaded and interrogated by histological structure for NNMT, NAMPT, 12 DNMT mRNA expression and selected gene expression signatures. The results are displayed on a heatmap. The 13 sample size of each histological region as indicated on the figure. 14 3 Jung et al. 15 16 Supplemental Figure 3. Altered expression of nicotinamide and nicotinate metabolism‐related enzymes in 17 glioblastoma. (A) Heatmap (fold change of expression) of whole 25 enzymes in the KEGG nicotinate and 18 nicotinamide metabolism gene set were analyzed in indicated glioblastoma expression datasets with Oncomine. 4 Jung et al. 19 Color bar intensity indicates percentile of fold change in glioblastoma relative to normal brain. (B) Nicotinamide and 20 nicotinate and methionine salvage pathways are displayed with the relative expression levels in glioblastoma 21 specimens in the TCGA GBM dataset indicated. 22 5 Jung et al. 23 24 Supplementary Figure 4.
    [Show full text]
  • Genetic Basis of Parkinson Disease
    Neurosurg Focus 28 (1):E7, 2010 Genetic basis of Parkinson disease GEOR G IA XIROMERISIOU , M.D.,1 EFTHIMIOS DAR D IOTIS , M.D.,1,2 VAÏ A TSIMOURTOU , M.D.,2 PERSA MARIA KOUNTRA , M.D.,2 KONSTANTINOS N. PATERA K IS , M.D.,3 EFTYCHIA Z. KA P SALA K I , M.D.,4 KOSTAS N. FOUNTAS , M.D.,3 AN D GEOR G IOS M. HA D JI G EOR G IOU , M.D.1,2 1Institute for Biomedical Technology (BIOMED), Centre for Research and Technology—Thessaly (CERETETH); 2Department of Neurology, Laboratory of Neurogenetics; 3Department of Neurosurgery; and 4Department of Diagnostic Radiology, University of Thessaly, University Hospital of Larissa, Greece Over the past few years, considerable progress has been made in understanding the molecular mechanisms of Parkinson disease (PD). Mutations in certain genes are found to cause monogenic forms of the disorder, with au- tosomal dominant or autosomal recessive inheritance. These genes include alpha-synuclein, parkin, PINK1, DJ-1, LRRK2, and ATP13A2. The monogenic variants are important tools in identifying cellular pathways that shed light on the pathogenesis of this disease. Certain common genetic variants are also likely to modulate the risk of PD. In- ternational collaborative studies and meta-analyses have identified common variants as genetic susceptibility risk/ protective factors for sporadic PD. (DOI: 10.3171/2009.10.FOCUS09220) KEY WOR D S • Parkinson disease • genetic association study • polymorphism • gene mutation ARKINSON disease is the second most common neu- ance of certain clinical features, and also the disease pro- rodegenerative disorder after Alzheimer disease. gression. The average age at onset is between 60 and 80 In this paper, a concise summary of the main genes Pyears, and ~ 1% of the general population older than 65 responsible for monogenic forms of PD (Table 1), and is affected.12,89 some of the common genetic variants that may play a role Although PD appears to be sporadic in most cases, in the disease, is provided.
    [Show full text]