DOCSLIB.ORG

Splicing and Immunomodulatory Function : a Gene with Extensive

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Splicing and Immunomodulatory Function : a Gene with Extensive LST1: A Gene with Extensive Alternative Splicing and Immunomodulatory Function Ingrid Rollinger-Holzinger, Brigitte Eibl, Marc Pauly, Ute Griesser, François Hentges, Bernhard Auer, Georg Pall, This information is current as Peter Schratzberger, Dietger Niederwieser, Elisabeth H. of September 28, 2021. Weiss and Heinz Zwierzina J Immunol 2000; 164:3169-3176; ; doi: 10.4049/jimmunol.164.6.3169 http://www.jimmunol.org/content/164/6/3169 Downloaded from References This article cites 21 articles, 6 of which you can access for free at: http://www.jimmunol.org/content/164/6/3169.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 • Fast Publication! 4 weeks from acceptance to publication by guest on September 28, 2021 *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 © 2000 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. LST1: A Gene with Extensive Alternative Splicing and Immunomodulatory Function1 2 † † ‡ Ingrid Rollinger-Holzinger, * Brigitte Eibl, Marc Pauly*, Ute Griesser, Franc¸ois Hentges, Bernhard Auer,§ Georg Pall,† Peter Schratzberger,† Dietger Niederwieser,¶ Elisabeth H. Weiss,ʈ and Heinz Zwierzina† The gene of the leukocyte-specific transcript (LST1) is encoded within the TNF region of the human MHC. The LST1 gene is constitutively expressed in leukocytes and dendritic cells, and it is characterized by extensive alternative splicing. We identified 7 different LST1 splice variants in PBMC; thus, 14 LST1 splice variants (LST1/A-LST1/N) have been detected in various cell types. These isoforms code for transmembrane as well as soluble LST1 proteins characterized by two alternative open reading frames at their 3؅ end. We demonstrate the presence of the transmembrane variant LST1/C on the cell surface of the monocytic cell lines U937 and THP1. Recombinant expression of LST1/C permitted its profound inhibitory effect on lymphocyte proliferation to be Downloaded from observed. In contrast, the alternative transmembrane variant LST1/A, the extracellular domain of which shows no amino acid sequence homology to LST1/C exerted a weaker but similar inhibitory effect on PBMC. These data demonstrate the protein expression of LST1 on the cell surface of mononuclear cells, and they show an inhibitory effect on lymphocyte proliferation of two LST1 proteins although they have only a very short amino acid homology. The Journal of Immunology, 2000, 164: 3169–3176. he leukocyte-specific transcript (LST1)3 gene is encoded whereas TNFd4 was negatively associated with rejection of renal http://www.jimmunol.org/ on the short arm of chromosome 6 within the designated transplants, implicating a role of LST1 in the immune response (9, T MHC class IV in the TNF complex (1–4). The MHC class 10). IV region spans the telomeric part of the former MHC III complex, Northern blot analysis has shown constitutive expression of the and it contains a high concentration of genes that may play a role LST1 cDNA in T cells, macrophages, and U937 cells and strong in various aspects of stress, inflammation, or infection (4). The induction of transcription by stimulation of monocytic cell lines LST1 gene is encoded ϳ9 kb centromeric of the TNF-␣ gene with IFN-␥ (2). Transcription was also detected in human tonsil, (TNFA), and it is flanked telomerically at a distance of 4 kb by lung, and placenta, the liver cell lines Hep G2 and Hep 3B, and by ␤ LTB, which codes for lymphotoxin and forms a heterotrimer means of expression-tagged sequences in fetal liver/spleen and by guest on September 28, 2021 with TNF-␤ (2, 5). Centromerically, the LST1 gene is flanked by adult brain. Because the hybridization signal of ϳ800 nucleotides the 1C7 gene which is located immediately adjacent to LST1, en- is very broad in the Northern blot analysis, a variation in length of coded by the opposite DNA strand such that the 3Ј ends of the two the LST1 mRNA has been suspected. In fact, previous studies have mRNA templates come within a few bases of overlapping (6). identified four protein-encoding exons and five alternative noncod- Several polymorphisms have been identified thus far within the ing exons 1 leading to eight different transcripts expressed in var- LST1 gene: intron 4 encompasses the polymorphic microsatellites ious cell lines which encode five different proteins (2, 11). TNFd and TNFe; and a polymorphic PvuII site is located down- To characterize the complex LST1 expression pattern, we ana- stream of the LST1 polyadenylation signal that is linked to 1C7 (2, lyzed LST1 transcription and protein expression in freshly isolated 7, 8). The d3 allele of TNFd has been associated with severe grade PBMC, T cells, and B cells and after incubation of these cells with acute graft-vs-host disease in HLA-identical sibling transplants, various cytokines. We describe essential parts of the biological function of two LST1 protein isoforms representing the two groups of LST1 polypeptides. *Laboratoire de Recherche sur le Cancer et les Maladies du Sang, Luxembourg, Luxembourg; †Department of Internal Medicine, Innsbruck University Hospital, Inns- bruck, Austria; ‡Department of Immunology and Allergology, Centre Hospitalier, Materials and Methods Luxembourg, Luxembourg; §Institute for Biochemistry, University of Innsbruck, Innsbruck, Austria; ¶Department of Hematology/Oncology, University of Leipzig, Cell separation Leipzig, Germany; and ʈInstitute for Anthropology and Human Genetics, Munich, Germany PBMC were isolated from buffy coats of healthy volunteer donors by den- sity gradient centrifugation on Lymphoprep (Nycomed, Oslo, Norway). T Received for publication January 6, 1999. Accepted for publication January 6, 2000. cells, monocytes, and B cells were separated from PBMC by positive se- The costs of publication of this article were defrayed in part by the payment of page lection with the immunomagnetic bead system using the respective Dyna- charges. This article must therefore be hereby marked advertisement in accordance beads M-450 (CD4), M-450 (CD8), M-450 (CD14), and M-450 (CD19) with 18 U.S.C. Section 1734 solely to indicate this fact. (Dynal, Oslo, Norway) as described previously (12–14). After selection, 1 This work was partly supported by the Fondation de Recherche Cancer et Sang and the cells were treated with Detachabeads (Dynal) to remove the CD4, CD8, by the O¨ sterreichischer Fonds zur Fo¨rderung der Wissenschaftlichen Forschung FWF and CD19 Abs from the membrane receptors (15). The purities of the P-9671. recovered cells were 98% for CD4ϩ cells, 99% for CD8ϩ cells, 99.6% for ϩ ϩ 2 Address correspondence and reprint requests to Dr. I. Rollinger-Holzinger, Recher- CD19 cells, and 80–90% for CD14 cells. che sur le Cancer et les Maladies du Sang, Centre Universitaire, Avenue de la Faı¨encerie 162A, L-1511 Luxembourg, Luxembourg. E-mail address: Culture of dendritic cells [email protected]. 3 Abbreviations used in this paper: LST1, leukocyte-specific transcript 1; TPO, throm- Dendritic cells were generated from PBMC as described (16–18). Briefly, bopoietin; DHFR, dihydrofolate reductase; ORF, open reading frame. mononuclear cells were isolated from leukocyte-enriched buffy coats by Copyright © 2000 by The American Association of Immunologists 0022-1767/00/$02.00 3170 LST1: COMPLEXLY SPLICED GENE WITH IMMUNOMODULATORY FUNCTION Downloaded from http://www.jimmunol.org/ FIGURE 1. LST1 expression and the control vectors. The vector pQE-16 was used for expression of the control protein DHFR. The clone ⌬LST1/C- DHFR was created by cloning ⌬LST1/C cDNA into the BglII and HindIII restriction sites of the expression vector pQE-40, which contains the N-terminal part of the DHFR protein. The expression vector pQE-30 was used to generate the ⌬LST1/A clone by cloning the BglII-restricted cDNA into the BamHI site of pQE-30. All three expression vectors encode an N-terminal histidine tail (6ϫ His). The DNA and amino acid sequences of ⌬LST1/A and ⌬LST1/C are indicated. standard density gradient centrifugation on Ficoll-Paque (Pharmacia, Upp- RNA isolation and RT-PCR by guest on September 28, 2021 sala, Sweden) and resuspended in complete medium (Biological Industries, Beth Haemek, Israel; RPMI 1640 supplemented with 10% heat-inactivated With the use of Trizol, total RNA samples were prepared from cells at each FCS (30 min, 56°C), 50 U/ml penicillin, 50 ␮g/ml streptomycin, 2.5 ␮g/ml time indicated, according to the manufacturer’s instructions. To remove ␮ Fungizone, 2 mM L-glutamine, 10 mM HEPES, 0.1 mM nonessential traces of contaminating DNA, 2 g of total RNA were digested with 1 IU amino acids, 1 mM pyruvate, and 5 ϫ 10Ϫ5 M 2-ME), and 5.0 ϫ 107 DNase (Promega, Madison, WI) for 1 h, phenolized, and precipitated as PBMCs were allowed to adhere in 75-cm2 cell culture flasks (2 h, 37°C). described previously (19). One reverse transcription reaction for every cell ␮ Nonadherent cells were removed, and the adherent fraction of the mono- stimulation was performed with 2 g RNA using avian myeloblastosis nuclear cells was allowed to detach during overnight incubation in com- virus reverse transcriptase, oligo(dT)15, and RNasin (all purchased from plete medium in the absence of exogenous cytokines. These cells were Promega) for1hat37°C (19). The revealed cDNA was used for all PCR replated at high cell density (5 ϫ 106 cells/ml) resulting in rapid readher- amplifications of the respective cell stimulations and control amplifications ence.
Load more

Recommended publications
  • LST1 Sirna (M): Sc-149136
    SANTA CRUZ BIOTECHNOLOGY, INC. LST1 siRNA (m): sc-149136 BACKGROUND APPLICATIONS LST1 (leukocyte-specific transcript 1), also known as B144, is a 97 amino acid LST1 siRNA (m) is recommended for the inhibition of LST1 expression in protein single-pass membrane protein. LST1 may play a role in modulating mouse cells. immune responses, as well as dendritic cell maturation. LST1 has also been found to induce morphological changes, including microspikes and filopodia, SUPPORT REAGENTS when overexpressed in a variety of cell types. Localized to the endomembrane For optimal siRNA transfection efficiency, Santa Cruz Biotechnology’s system, LST1 is expressed as nine isoforms produced by alternative splicing. siRNA Transfection Reagent: sc-29528 (0.3 ml), siRNA Transfection Medium: Isoform 1, also designated LST1A, and isoform 2, also designated LST1C, sc-36868 (20 ml) and siRNA Dilution Buffer: sc-29527 (1.5 ml) are recom- γ have inhibitory effects on lymphocyte proliferation. Induced by IFN- , LST1 mended. Control siRNAs or Fluorescein Conjugated Control siRNAs are is expressed in adult lung, thymus, placenta, kidney and tonsil and fetal liver, available as 10 µM in 66 µl. Each contain a scrambled sequence that will spleen and brain. not lead to the specific degradation of any known cellular mRNA. Fluorescein Conjugated Control siRNAs include: sc-36869, sc-44239, sc-44240 and REFERENCES sc-44241. Control siRNAs include: sc-37007, sc-44230, sc-44231, sc-44232, 1. Neville, M.J. and Campbell, R.D. 1997. Alternative splicing of the LST1 gene sc-44233, sc-44234, sc-44235, sc-44236, sc-44237 and sc-44238. located in the major histocompatibility complex on human chromosome 6.
    [Show full text]
  • Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
    Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus.
    [Show full text]
  • B Inhibition in a Mouse Model of Chronic Colitis1
    The Journal of Immunology Differential Expression of Inflammatory and Fibrogenic Genes and Their Regulation by NF-␬B Inhibition in a Mouse Model of Chronic Colitis1 Feng Wu and Shukti Chakravarti2 Fibrosis is a major complication of chronic inflammation, as seen in Crohn’s disease and ulcerative colitis, two forms of inflam- matory bowel diseases. To elucidate inflammatory signals that regulate fibrosis, we investigated gene expression changes under- lying chronic inflammation and fibrosis in trinitrobenzene sulfonic acid-induced murine colitis. Six weekly 2,4,6-trinitrobenzene sulfonic acid enemas were given to establish colitis and temporal gene expression patterns were obtained at 6-, 8-, 10-, and 12-wk time points. The 6-wk point, TNBS-w6, was the active, chronic inflammatory stage of the model marked by macrophage, neu- trophil, and CD3؉ and CD4؉ T cell infiltrates in the colon, consistent with the idea that this model is T cell immune response driven. Proinflammatory genes Cxcl1, Ccl2, Il1b, Lcn2, Pla2g2a, Saa3, S100a9, Nos2, Reg2, and Reg3g, and profibrogenic extra- cellular matrix genes Col1a1, Col1a2, Col3a1, and Lum (lumican), encoding a collagen-associated proteoglycan, were up-regulated at the active/chronic inflammatory stages. Rectal administration of the NF-␬B p65 antisense oligonucleotide reduced but did not abrogate inflammation and fibrosis completely. The antisense oligonucleotide treatment reduced total NF-␬B by 60% and down- regulated most proinflammatory genes. However, Ccl2, a proinflammatory chemokine known to promote fibrosis, was not down- regulated. Among extracellular matrix gene expressions Lum was suppressed while Col1a1 and Col3a1 were not. Thus, effective treatment of fibrosis in inflammatory bowel disease may require early and complete blockade of NF-␬B with particular attention to specific proinflammatory and profibrogenic genes that remain active at low levels of NF-␬B.
    [Show full text]
  • Pan-Cancer Analysis of DNA Methylation Identifies Genes And
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.20.449136; this version posted June 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Pan-Cancer Analysis of DNA Methylation Identifies Genes and Biological Functions Associated with Overall Survival Romola Cavet1, Peng Yue2, Guy Cavet*3 1The Nueva School, San Mateo, California, United States of America 2ReviR Therapeutics, Palo Alto, California, United States of America 3Paramune, Inc., Palo Alto, California, United States of America * Corresponding author E-Mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.06.20.449136; this version posted June 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract DNA methylation influences gene expression and is altered in many cancers, but the relationship between DNA methylation and cancer outcomes is not yet fully understood. If methylation of specific genes is associated with better or worse outcomes, it could implicate genes in driving cancer and suggest therapeutic strategies. To advance our understanding of DNA methylation in cancer biology, we conducted a pan-cancer analysis of the relationship between methylation and overall survival. Using data on 28 tumor types from The Cancer Genome Atlas (TCGA), we identified genes and genomic regions whose methylation was recurrently associated with survival across multiple cancer types.
    [Show full text]
  • Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection
    fgene-11-00358 April 9, 2020 Time: 15:55 # 1 ORIGINAL RESEARCH published: 15 April 2020 doi: 10.3389/fgene.2020.00358 Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection Allen F. Ryan1*, Chanond A. Nasamran2, Kwang Pak1, Clara Draf1, Kathleen M. Fisch2, Nicholas Webster3 and Arwa Kurabi1 1 Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 2 Medicine/Center for Computational Biology & Bioinformatics, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 3 Medicine/Endocrinology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States Single-cell transcriptomics was used to profile cells of the normal murine middle ear. Clustering analysis of 6770 transcriptomes identified 17 cell clusters corresponding to distinct cell types: five epithelial, three stromal, three lymphocyte, two monocyte, Edited by: two endothelial, one pericyte and one melanocyte cluster. Within some clusters, Amélie Bonnefond, Institut National de la Santé et de la cell subtypes were identified. While many corresponded to those cell types known Recherche Médicale (INSERM), from prior studies, several novel types or subtypes were noted. The results indicate France unexpected cellular diversity within the resting middle ear mucosa. The resolution of Reviewed by: Fabien Delahaye, uncomplicated, acute, otitis media is too rapid for cognate immunity to play a major Institut Pasteur de Lille, France role. Thus innate immunity is likely responsible for normal recovery from middle ear Nelson L. S. Tang, infection. The need for rapid response to pathogens suggests that innate immune The Chinese University of Hong Kong, China genes may be constitutively expressed by middle ear cells.
    [Show full text]
  • ID AKI Vs Control Fold Change P Value Symbol Entrez Gene Name *In
    ID AKI vs control P value Symbol Entrez Gene Name *In case of multiple probesets per gene, one with the highest fold change was selected. Fold Change 208083_s_at 7.88 0.000932 ITGB6 integrin, beta 6 202376_at 6.12 0.000518 SERPINA3 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 1553575_at 5.62 0.0033 MT-ND6 NADH dehydrogenase, subunit 6 (complex I) 212768_s_at 5.50 0.000896 OLFM4 olfactomedin 4 206157_at 5.26 0.00177 PTX3 pentraxin 3, long 212531_at 4.26 0.00405 LCN2 lipocalin 2 215646_s_at 4.13 0.00408 VCAN versican 202018_s_at 4.12 0.0318 LTF lactotransferrin 203021_at 4.05 0.0129 SLPI secretory leukocyte peptidase inhibitor 222486_s_at 4.03 0.000329 ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif, 1 1552439_s_at 3.82 0.000714 MEGF11 multiple EGF-like-domains 11 210602_s_at 3.74 0.000408 CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 229947_at 3.62 0.00843 PI15 peptidase inhibitor 15 204006_s_at 3.39 0.00241 FCGR3A Fc fragment of IgG, low affinity IIIa, receptor (CD16a) 202238_s_at 3.29 0.00492 NNMT nicotinamide N-methyltransferase 202917_s_at 3.20 0.00369 S100A8 S100 calcium binding protein A8 215223_s_at 3.17 0.000516 SOD2 superoxide dismutase 2, mitochondrial 204627_s_at 3.04 0.00619 ITGB3 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) 223217_s_at 2.99 0.00397 NFKBIZ nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta 231067_s_at 2.97 0.00681 AKAP12 A kinase (PRKA) anchor protein 12 224917_at 2.94 0.00256 VMP1/ mir-21likely ortholog
    [Show full text]
  • Functional Genomic Annotation of Genetic Risk Loci Highlights Inflammation and Epithelial Biology Networks in CKD
    BASIC RESEARCH www.jasn.org Functional Genomic Annotation of Genetic Risk Loci Highlights Inflammation and Epithelial Biology Networks in CKD Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Hyun-Mi Kang, Sang-Youb Han, Peter Choi, and Katalin Susztak Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania ABSTRACT Genome-wide association studies (GWASs) have identified multiple loci associated with the risk of CKD. Almost all risk variants are localized to the noncoding region of the genome; therefore, the role of these variants in CKD development is largely unknown. We hypothesized that polymorphisms alter transcription factor binding, thereby influencing the expression of nearby genes. Here, we examined the regulation of transcripts in the vicinity of CKD-associated polymorphisms in control and diseased human kidney samples and used systems biology approaches to identify potentially causal genes for prioritization. We interro- gated the expression and regulation of 226 transcripts in the vicinity of 44 single nucleotide polymorphisms using RNA sequencing and gene expression arrays from 95 microdissected control and diseased tubule samples and 51 glomerular samples. Gene expression analysis from 41 tubule samples served for external validation. 92 transcripts in the tubule compartment and 34 transcripts in glomeruli showed statistically significant correlation with eGFR. Many novel genes, including ACSM2A/2B, FAM47E, and PLXDC1, were identified. We observed that the expression of multiple genes in the vicinity of any single CKD risk allele correlated with renal function, potentially indicating that genetic variants influence multiple transcripts. Network analysis of GFR-correlating transcripts highlighted two major clusters; a positive correlation with epithelial and vascular functions and an inverse correlation with inflammatory gene cluster.
    [Show full text]
  • Six Microsatellite Markers on the Short Arm of Chromosome 6 in Relation to HLA-DR3 and TNF−308A in Systemic Lupus Erythematosus
    Genes and Immunity (2001) 2, 373–380 2001 Nature Publishing Group All rights reserved 1466-4879/01 $15.00 www.nature.com/gene Six microsatellite markers on the short arm of chromosome 6 in relation to HLA-DR3 and TNF−308A in systemic lupus erythematosus MW van der Linden1,2, AR van der Slik3, E Zanelli3, MJ Giphart3, E Pieterman2, GMTh Schreuder3, RGJ Westendorp4 and TWJ Huizinga2 Departments of 1Clinical Epidemiology, 2Rheumatology, 3Immunohaematology and Blood Transfusion, 4General Internal Medicine, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands Differences in allelic distribution at loci surrounding the human HLA-DRB1 and tumor necrosis factor (TNF) genes have been observed in association with systemic lupus erythematosus (SLE). We investigated whether the association of HLA- DRB1*0301 (HLA-DR3) and TNF−308A with SLE could be attributed to polymorphic markers in the chromosomal region encompassed by HLA-DRB1 and HLA-C. Ninety-one consecutive Caucasian patients with SLE and 253 controls (organ donors) were typed for HLA-DRB1, microsatellites D6S1014, D6S273, TNFa, MIB, C1F2F5, and C1F3F2 and the single nucleotide polymorphism at position −308 in the promoter of TNF. The independent contribution of alleles to disease susceptibility was estimated by cross-tabulation and multivariate logistic regression. Possession of TNF−308A was associated with susceptibility to SLE (odds ratio [95% confidence interval], 3.70 [2.24–6.11]). This remained present after stratification on possession of HLA-DR3 (pooled odds ratio, 2.53 [1.37–4.70]). Stratification revealed a possible association of possession of C1F2F5*192 with protection from SLE beyond the effects of HLA-DR3 and TNF−308A.
    [Show full text]
  • Extended LTA, TNF, LST1 and HLA Gene Haplotypes and Their Association with Rubella Vaccine-Induced Immunity
    Extended LTA, TNF, LST1 and HLA Gene Haplotypes and Their Association with Rubella Vaccine-Induced Immunity Inna G. Ovsyannikova1,4*, Robert A. Vierkant3, V. Shane Pankratz3, Robert M. Jacobson1,2, Gregory A. Poland1,2,4* 1 Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America, 2 Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America, 3 Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America, 4 Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America Abstract Background: Recent studies have suggested the importance of HLA genes in determining immune responses following rubella vaccine. The telomeric class III region of the HLA complex harbors several genes, including lymphotoxin alpha (LTA), tumor necrosis factor (TNF) and leukocyte specific transcript -1 (LST1) genes, located between the class I B and class II DRB1 loci. Apart from HLA, little is known about the effect of this extended genetic region on HLA haplotypic backgrounds as applied to immune responses. Methodology/Principal Findings: We examined the association between immune responses and extended class I-class II- class III haplotypes among 714 healthy children after two doses of rubella vaccination. These extended haplotypes were then compared to the HLA-only haplotypes. The most significant association was observed between haplotypes extending across the HLA class I region, ten-SNP haplotypes, and the HLA class II region (i.e. A-C-B-LTA-TNF-LST1-DRB1-DQA1-DQB1- DPA1-DPB1) and rubella-specific antibodies (global p-value of 0.03). Associations were found between both extended A*02- C*03-B*15-AAAACGGGGC-DRB1*04-DQA1*03-DQB1*03-DPA1*01-DPB1*04 (p = 0.002) and HLA-only A*02-C*03-B*15- DRB1*04-DQA1*03-DQB1*03-DPA1*01-DPB1*04 haplotypes (p = 0.009) and higher levels of rubella antibodies.
    [Show full text]
  • Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
    Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,092,998 B2 Stuhlmiller Et Al
    USO08092998B2 (12) United States Patent (10) Patent No.: US 8,092,998 B2 Stuhlmiller et al. (45) Date of Patent: Jan. 10, 2012 (54) BOMARKERS PREDCTIVE OF THE 2007/0172475 A1 7/2007 Matheus et al. RESPONSIVENESS TO TNFO INHIBITORS IN 2007/0172897 A1 7/2007 Maksymowych et al. 2007. O184045 A1 8, 2007 Doctor et al. AUTOIMMUNE DISORDERS 2007/0202051 A1 8/2007 Schusching 2007/0202104 A1 8/2007 Banerjee et al. (75) Inventors: Bruno Stuhlmiller, Berlin (DE): 2007/0237831 A1 10/2007 Sung et al. 2007,0269.463 A1 11/2007 Donavan Gerd-Reudiger Burmester, Berlin (DE) 2007,0292442 A1 12/2007 Wan et al. 2008.0118496 A1 5/2008 Medich et al. (73) Assignee: Abbott Laboratories, Abbott Park, IL 2008. O1313.74 A1 6/2008 Medich et al. (US) 2008. O166348 A1 7/2008 Kupper et al. 2008.0193466 A1 8/2008 Banerjee et al. 2008/0227136 A1 9, 2008 Pla et al. (*) Notice: Subject to any disclaimer, the term of this 2008/0311043 A1 12/2008 Hoffman et al. patent is extended or adjusted under 35 2009/0028794 A1 1/2009 Medich et al. U.S.C. 154(b) by 5 days. 2009/0110679 A1 4/2009 Li et al. 2009/O123378 A1 5/2009 Wong et al. (21) Appl. No.: 12/130,373 2009, O1485.13 A1 6/2009 Fraunhofer et al. (Continued) (22) Filed: May 30, 2008 FOREIGN PATENT DOCUMENTS (65) Prior Publication Data EP 1795610 A1 * 6, 2007 US 2009/OO17472 A1 Jan. 15, 2009 (Continued) Related U.S. Application Data OTHER PUBLICATIONS (60) Provisional application No.
    [Show full text]
  • An Upstream Open Reading Frame Regulates LST1 Expression During Monocyte Differentiation
    An Upstream Open Reading Frame Regulates LST1 Expression during Monocyte Differentiation Christian Schiller1, Carina Nowak1, Kalliope N. Diakopoulos1, Ulrich H. Weidle2, Elisabeth H. Weiss1 1 Department of Biology II, Ludwig-Maximilians-Universita¨tMu¨nchen, Germany, 2 Division Pharma, Roche Diagnostics, Penzberg, Germany Abstract The regulation of gene expression depends on the interplay of multiple factors at the transcriptional and translational level. Upstream open reading frames (uORFs) play an important role as translational repressors of main ORFs and their presence or usage in transcripts can be regulated by different mechanisms. The main objective of the present study was to assess whether uORFs regulate the expression of the MHC class III gene LST1. We report that expression of LST1 is tightly regulated by alternative transcription initiation and the presence of an uORF in the 59-UTR of transcripts. Specifically, using EGFP reporter constructs in human HeLa and HEK-293T cells and flow cytometry as well as western blot analysis we found the uORF to reduce the expression of the main ORF by roughly two-thirds. Furthermore, we were able to correlate a previously detected increase in LST1 protein expression during monocyte differentiation with an increase of transcription initiation at an alternative exon that does not contain an uORF. Citation: Schiller C, Nowak C, Diakopoulos KN, Weidle UH, Weiss EH (2014) An Upstream Open Reading Frame Regulates LST1 Expression during Monocyte Differentiation. PLoS ONE 9(5): e96245. doi:10.1371/journal.pone.0096245 Editor: Eric Jan, University of British Columbia, Canada Received August 22, 2013; Accepted April 4, 2014; Published May 9, 2014 Copyright: ß 2014 Schiller et al.
    [Show full text]