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Orehova M, Plavec J, Kocman V. High-Resolution Structure of RNA G-Quadruplex Containing Unique Structural Motifs Originating from the 5'-UTR of Human Tyrosine Kinase 2 (TYK2). ACS OMEGA 2024; 9:7215-7229. [PMID: 38371751 PMCID: PMC10870306 DOI: 10.1021/acsomega.3c09592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Tyrosine kinase 2 (TYK2) is a member of the JAK family of nonreceptor-associated tyrosine kinases together with highly homologous JAK1, JAK2, and JAK3 paralogues. Overexpression of TYK2 is associated with several inflammatory diseases, including severe complications during the COVID-19 infection. Since the downregulation of JAK paralogues could lead to serious health consequences or even death, it is critical to avoid it when designing drugs to suppress TYK2. To achieve the required specificity only for TYK2, researchers have recently selectively targeted TYK2 mRNA by developing antisense oligonucleotides. In this work, we expand the target space of TYK2 mRNA by showing that the mRNA adopts tetra-helical noncanonical structures called G-quadruplexes. We identified a TYKwt RNA oligonucleotide from the 5'-UTR of TYK2 mRNA, which adopts multiple different parallel G-quadruplexes that exist at equilibrium. Using NMR spectroscopy, we showed that some of the G-quadruplexes adopt unique structural motifs, mainly due to the formation of a stable GA bulge. Using guanine to uridine substitutions, we prepared the oligonucleotide TYK3_U6, which serves as an excellent model for the bulged G-quadruplexes formed by the TYKwt oligonucleotide. NMR structural analysis, including data on the residual coupling constants (RDC) of the loop regions, unveiled that the studied three-quartet parallel G-quadruplex contains many unusual structural features such as a G(U)A bulge, a guanine residue in the syn conformation, A and U residues stacked on the top G-quartet, and a well-defined adenine from a three-residue long propeller loop oriented in the groove, all of which could be valuable targets for future drug design.
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Affiliation(s)
- Maria Orehova
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, 1000 Ljubljana, Slovenia
| | - Vojč Kocman
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
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2
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Huang M, Xu H. Genetic susceptibility to autoimmunity-Current status and challenges. Adv Immunol 2022; 156:25-54. [PMID: 36410874 DOI: 10.1016/bs.ai.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.
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Affiliation(s)
| | - Huji Xu
- School of Medicine, Tsinghua University, Beijing, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Navel Medical University, Shanghai, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
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3
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Zhou Y, Li X, Shen R, Wang X, Zhang F, Liu S, Li D, Liu J, Li P, Yan Y, Dong P, Zhang Z, Wu H, Zhuang L, Chowdhury R, Miller M, Issa M, Mao Y, Chen H, Feng J, Li J, Bai C, He F, Tao W. Novel Small Molecule Tyrosine Kinase 2 Pseudokinase Ligands Block Cytokine-Induced TYK2-Mediated Signaling Pathways. Front Immunol 2022; 13:884399. [PMID: 35693820 PMCID: PMC9186491 DOI: 10.3389/fimmu.2022.884399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/22/2022] [Indexed: 11/15/2022] Open
Abstract
A member of the Janus kinase (JAK) family, Tyrosine Kinase 2 (TYK2), is crucial in mediating various cytokine-signaling pathways such as interleukin-23 (IL23), interleukin-12 (IL12) and type I Interferons (IFN) which contribute to autoimmune disorders (e.g., psoriasis, lupus, and inflammatory bowel disease). Thus, TYK2 represents an attractive target to develop small-molecule therapeutics for the treatment of cytokine-driven inflammatory diseases. Selective inhibition of TYK2 over other JAK isoforms is critical to achieve a favorable therapeutic index in the development of TYK2 inhibitors. However, designing small molecule inhibitors to target the adenosine triphosphate (ATP) binding site of TYK2 kinase has been challenging due to the substantial structural homology of the JAK family catalytic domains. Here, we employed an approach to target the JAK homology 2 (JH2) pseudokinase regulatory domain of the TYK2 protein. We developed a series of small-molecule TYK2 pseudokinase ligands, which suppress the TYK2 catalytic activity through allosteric regulation. The TYK2 pseudokinase-binding small molecules in this study simultaneously achieve high affinity-binding for the TYK2 JH2 domain while also affording significantly reduced affinity for the TYK2 JAK homology 1 (JH1) kinase domain. These TYK2 JH2 selective molecules, although possessing little effect on suppressing the catalytic activity of the isolated TYK2 JH1 catalytic domain in the kinase assays, can still significantly block the TYK2-mediated receptor-stimulated pathways by binding to the TYK2 JH2 domain and allosterically regulating the TYK2 JH1 kinase. These compounds are potent towards human T-cell lines and primary immune cells as well as in human whole-blood specimens. Moreover, TYK2 JH2-binding ligands exhibit remarkable selectivity of TYK2 over JAK isoforms not only biochemically but also in a panel of receptor-stimulated JAK1/JAK2/JAK3-driven cellular functional assays. In addition, the TYK2 JH2-targeting ligands also demonstrate high selectivity in a multi-kinase screening panel. The data in the current study underscores that the TYK2 JH2 pseudokinase is a promising therapeutic target for achieving a high degree of biological selectivity. Meanwhile, targeting the JH2 domain represents an appealing strategy for the development of clinically well-tolerated TYK2 inhibitors that would have superior efficacy and a favorable safety profile compared to the existing Janus kinase inhibitors against autoimmune diseases.
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Affiliation(s)
- Yu Zhou
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
- *Correspondence: Yu Zhou, ; Xin Li,
| | - Xin Li
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
- *Correspondence: Yu Zhou, ; Xin Li,
| | - Ru Shen
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Xiangzhu Wang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Fan Zhang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Suxing Liu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Di Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Jian Liu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Puhui Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Yinfa Yan
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Ping Dong
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Zhigao Zhang
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Heping Wu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Linghang Zhuang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | | | - Matthew Miller
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Mena Issa
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Yuchang Mao
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Hongli Chen
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Jun Feng
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Jing Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Chang Bai
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Feng He
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Weikang Tao
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
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4
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Verma A, Tsao NL, Thomann LO, Ho YL, Iyengar SK, Luoh SW, Carr R, Crawford DC, Efird JT, Huffman JE, Hung A, Ivey KL, Levin MG, Lynch J, Natarajan P, Pyarajan S, Bick AG, Costa L, Genovese G, Hauger R, Madduri R, Pathak GA, Polimanti R, Voight B, Vujkovic M, Zekavat SM, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O’Donnell C, Damrauer SM, Liao KP. A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program. PLoS Genet 2022; 18:e1010113. [PMID: 35482673 PMCID: PMC9049369 DOI: 10.1371/journal.pgen.1010113] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/20/2022] [Indexed: 12/14/2022] Open
Abstract
The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n = 35) or hospitalization (n = 42) due to severe COVID-19 using genome-wide association summary data from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828 = 53 and nrs505922 = 59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p = 1.32 x 10-199), and thrombosis ORrs505922 1.33, p = 2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p = 4.12 × 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p = 2.26× 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p = 6.48 x10-23, lupus OR 0.84, p = 3.97 x 10-06. PheWAS stratified by ancestry demonstrated differences in genotype-phenotype associations. LMNA (rs581342) associated with neutropenia OR 1.29 p = 4.1 x 10-13 among Veterans of African and Hispanic ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.
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Affiliation(s)
- Anurag Verma
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Noah L. Tsao
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lauren O. Thomann
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Sudha K. Iyengar
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, Oregon, United States of America
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Rotonya Carr
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- University of Washington, Division of Gastroenterology, Seattle, Washington, United States of America
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jimmy T. Efird
- Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, United States of America
| | - Jennifer E. Huffman
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Adriana Hung
- Tennessee Valley Healthcare System (Nashville VA) & Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kerry L. Ivey
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- South Australian Health and Medical Research Institute, Infection and Immunity Theme, Adelaide, South Australia, Australia
- Harvard T.H. Chan School of Public Health, Department of Nutrition, Cambridge, Massachusetts, United States of America
| | - Michael G. Levin
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, United States of America
| | - Pradeep Natarajan
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexander G. Bick
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lauren Costa
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Giulio Genovese
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Hauger
- Department of Psychiatry, University of California, San Diego, La Jolla, California; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, California, United States of America
| | - Ravi Madduri
- University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, United States of America
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Gita A. Pathak
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Benjamin Voight
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marijana Vujkovic
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Seyedeh Maryam Zekavat
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- Yale School of Medicine New Haven, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Yale School of Medicine New Haven, New Haven, Connecticut, United States of America
- Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Juan P. Casas
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Philip S. Tsao
- VA Palo Alto Health Care System, Palo Alto, California, United States of America
- Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, California, United States of America
| | - J. Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Christopher O’Donnell
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Scott M. Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katherine P. Liao
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
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5
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Borrelia burgdorferi is a poor inducer of interferon-gamma: amplification induced by interleukin-12. Infect Immun 2022; 90:e0055821. [PMID: 35130450 DOI: 10.1128/iai.00558-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Laboratory diagnosis of Lyme borreliosis (LB) is mainly based on serology, which has limitations, particularly in the early stages of the disease. In recent years there have been conflicting reports concerning a new diagnostic tool using the cytokine interferon-gamma (IFN-γ). Previous studies have generally found low concentrations of IFN-γ in early LB infection. The goal of this study is to investigate IFN-γ regulation during early LB and provide insights into the host response to B. burgdorferi. Methods We performed in vitro experiments with whole blood assays and peripheral blood mononuclear cells (PBMCs) of LB patients and healthy volunteers exposed to B. burgdorferi and evaluated the IFN-γ response using ELISA and related interindividual variation in IFN-γ production to the presence of single nucleotide polymorphisms. Results IFN-γ production of B. burgdorferi-exposed PBMCs and whole blood was amplified by the addition of IL-12 to the stimulation system. This effect was observed after 24 hours of B. burgdorferi stimulation in both healthy individuals and LB patients. The effect was highly variable between individuals, but was significantly higher in LB patients six weeks since the start of antibiotic treatment compared to healthy individuals. IL-12 p40 and IL-18 mRNA was upregulated upon exposure to B. burgdorferi, whereas IL-12 p35 and IFN-γ mRNA expression remained relatively unchanged. SNP Rs280520 in the downstream IL-12 pathway, Tyrosine Kinase 2, was associated with increased IFN-γ production. Conclusions This study shows that IL-12 evokes an IFN-γ response in B. burgdorferi exposed cells, and LB patients and healthy controls respond differently to this stimulation.
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6
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Verma A, Tsao N, Thomann L, Ho YL, Iyengar S, Luoh SW, Carr R, Crawford D, Efird JT, Huffman J, Hung A, Ivey K, Levin M, Lynch J, Natarajan P, Pyarajan S, Bick A, Costa L, Genovese G, Hauger R, Madduri R, Pathak G, Polimanti R, Voight B, Vujkovic M, Zekavat M, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O'Donnell C, Damrauer S, Liao K. A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34642702 PMCID: PMC8509103 DOI: 10.1101/2021.05.18.21257396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828=53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 × 10-199), and thrombosis ORrs505922 1.33, p=2.2 × 10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 × 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26 × 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 × 10-23, lupus OR 0.84, p=3.97 × 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 × 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.
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Affiliation(s)
- Anurag Verma
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Noah Tsao
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Sudha Iyengar
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland OR, USA.,Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rotonya Carr
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,University of Washington, Division of Gastroenterology Seattle, WA USA
| | - Dana Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jimmy T Efird
- Cardiovascular Medicine Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Adriana Hung
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA.,Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA
| | - Kerry Ivey
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Tennessee Valley Healthcare System (Nashville VA) & Vanderbilt University, Nashville, Tennessee, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael Levin
- VA Portland Health Care System, Portland OR, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA
| | - Pradeep Natarajan
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander Bick
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Vanderbilt University, Nashville, Tennessee, USA
| | - Lauren Costa
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Richard Hauger
- Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, USA
| | - Ravi Madduri
- University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA.,Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois
| | - Gita Pathak
- VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, Connecticut, USA
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, Connecticut, USA
| | - Benjamin Voight
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marijana Vujkovic
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maryam Zekavat
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Broad Institute of MIT & Harvard, Cambridge, MA, USA.,Yale School of Medicine New Haven, CT, USA
| | - Hongyu Zhao
- VA Connecticut Healthcare System, West Haven, CT, USA.,Yale School of Medicine New Haven, CT, USA.,Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | | | | | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Juan P Casas
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, California, USA.,Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Christopher O'Donnell
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine Liao
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
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7
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Pellenz FM, Dieter C, Lemos NE, Bauer AC, Souza BMD, Crispim D. Association of TYK2 polymorphisms with autoimmune diseases: A comprehensive and updated systematic review with meta-analysis. Genet Mol Biol 2021; 44:e20200425. [PMID: 33949620 PMCID: PMC8097517 DOI: 10.1590/1678-4685-gmb-2020-0425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Autoimmune diseases are characterized by the loss of self-tolerance, leading to
immune-mediated tissue destruction and chronic inflammation. Tyrosine kinase 2
(TYK2) protein plays a key role in immunity and apoptosis pathways. Studies have
reported associations between single nucleotide polymorphisms (SNPs) in the
TYK2 gene and autoimmune diseases; however, results are
still inconclusive. Thus, we conducted a systematic review followed by
meta-analysis. A literature search was performed to find studies that
investigated associations between TYK2 SNPs and autoimmune
diseases (multiple sclerosis, systemic lupus erythematosus, Crohn’s disease,
ulcerative colitis, psoriasis, rheumatoid arthritis, type 1 diabetes, and
inflammatory bowel disease). Pooled odds ratios (OR) with 95 % CI were
calculated using random (REM) or fixed (FEM) effects models in the Stata 11.0
Software. Thirty-four articles were eligible for inclusion in the meta-analyses,
comprising 9 different SNPs: rs280496, rs280500, rs280523, rs280519, rs2304256,
rs12720270, rs12720356, rs34536443, and rs35018800. Meta-analysis results showed
the minor alleles of rs2304256, rs12720270, rs12720356, rs34536443, and
rs35018800 SNPs were associated with protection against autoimmune diseases.
Moreover, the A allele of the rs280519 SNP was associated with risk for systemic
lupus erythematosus. Our meta-analyses demonstrated that the rs2304256,
rs12720270, rs12720356, rs34536443, rs35018800, and rs280519 SNPs in the
TYK2 gene are associated with different autoimmune
diseases.
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Affiliation(s)
- Felipe Mateus Pellenz
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Cristine Dieter
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Natália Emerim Lemos
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Andrea Carla Bauer
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Serviço de Nefrologia, Porto Alegre, RS, Brazil
| | - Bianca Marmontel de Souza
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Daisy Crispim
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
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8
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Alves-Leon SV, Ferreira CDS, Herlinger AL, Fontes-Dantas FL, Rueda-Lopes FC, Francisco RDS, Gonçalves JPDC, de Araújo AD, Rêgo CCDS, Higa LM, Gerber AL, Guimarães APDC, de Menezes MT, de Paula Tôrres MC, Maia RA, Nogueira BMG, França LC, da Silva MM, Naurath C, Correia ASDS, Vasconcelos CCF, Tanuri A, Ferreira OC, Cardoso CC, Aguiar RS, de Vasconcelos ATR. Exome-Wide Search for Genes Associated With Central Nervous System Inflammatory Demyelinating Diseases Following CHIKV Infection: The Tip of the Iceberg. Front Genet 2021; 12:639364. [PMID: 33815474 PMCID: PMC8010313 DOI: 10.3389/fgene.2021.639364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/08/2021] [Indexed: 12/31/2022] Open
Abstract
Chikungunya virus (CHIKV) is a re-emergent arbovirus that causes a disease characterized primarily by fever, rash and severe persistent polyarthralgia, although <1% of cases develop severe neurological manifestations such as inflammatory demyelinating diseases (IDD) of the central nervous system (CNS) like acute disseminated encephalomyelitis (ADEM) and extensive transverse myelitis. Genetic factors associated with host response and disease severity are still poorly understood. In this study, we performed whole-exome sequencing (WES) to identify HLA alleles, genes and cellular pathways associated with CNS IDD clinical phenotype outcomes following CHIKV infection. The cohort includes 345 patients of which 160 were confirmed for CHIKV. Six cases presented neurological manifestation mimetizing CNS IDD. WES data analysis was performed for 12 patients, including the CNS IDD cases and 6 CHIKV patients without any neurological manifestation. We identified 29 candidate genes harboring rare, pathogenic, or probably pathogenic variants in all exomes analyzed. HLA alleles were also determined and patients who developed CNS IDD shared a common signature with diseases such as Multiple sclerosis (MS) and Neuromyelitis Optica Spectrum Disorders (NMOSD). When these genes were included in Gene Ontology analyses, pathways associated with CNS IDD syndromes were retrieved, suggesting that CHIKV-induced CNS outcomesmay share a genetic background with other neurological disorders. To our knowledge, this study was the first genome-wide investigation of genetic risk factors for CNS phenotypes in CHIKV infection. Our data suggest that HLA-DRB1 alleles associated with demyelinating diseases may also confer risk of CNS IDD outcomes in patients with CHIKV infection.
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Affiliation(s)
- Soniza Vieira Alves-Leon
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - João Paulo da Costa Gonçalves
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Dutra de Araújo
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cláudia Cecília da Silva Rêgo
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza Mendonça Higa
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Richard Araújo Maia
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Laise Carolina França
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil
| | - Marcos Martins da Silva
- Department of Clinical Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christian Naurath
- Federal Hospital Cardoso Fontes, Ministry of Health, Rio de Janeiro, Brazil
| | | | | | - Amilcar Tanuri
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando Costa Ferreira
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Renato Santana Aguiar
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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9
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Ullrich KAM, Schulze LL, Paap EM, Müller TM, Neurath MF, Zundler S. Immunology of IL-12: An update on functional activities and implications for disease. EXCLI JOURNAL 2020; 19:1563-1589. [PMID: 33408595 PMCID: PMC7783470 DOI: 10.17179/excli2020-3104] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022]
Abstract
As its first identified member, Interleukin-12 (IL-12) named a whole family of cytokines. In response to pathogens, the heterodimeric protein, consisting of the two subunits p35 and p40, is secreted by phagocytic cells. Binding of IL-12 to the IL-12 receptor (IL-12R) on T and natural killer (NK) cells leads to signaling via signal transducer and activator of transcription 4 (STAT4) and subsequent interferon gamma (IFN-γ) production and secretion. Signaling downstream of IFN-γ includes activation of T-box transcription factor TBX21 (Tbet) and induces pro-inflammatory functions of T helper 1 (TH1) cells, thereby linking innate and adaptive immune responses. Initial views on the role of IL-12 and clinical efforts to translate them into therapeutic approaches had to be re-interpreted following the discovery of other members of the IL-12 family, such as IL-23, sharing a subunit with IL-12. However, the importance of IL-12 with regard to immune processes in the context of infection and (auto-) inflammation is still beyond doubt. In this review, we will provide an update on functional activities of IL-12 and their implications for disease. We will begin with a summary on structure and function of the cytokine itself as well as its receptor and outline the signal transduction and the transcriptional regulation of IL-12 secretion. In the second part of the review, we will depict the involvement of IL-12 in immune-mediated diseases and relevant experimental disease models, while also providing an outlook on potential translational approaches.
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Affiliation(s)
- Karen A-M Ullrich
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Lisa Lou Schulze
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Eva-Maria Paap
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Tanja M Müller
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Markus F Neurath
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Sebastian Zundler
- Department of Medicine and Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
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10
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Nayar S, Campos J, Smith CG, Iannizzotto V, Gardner DH, Mourcin F, Roulois D, Turner J, Sylvestre M, Asam S, Glaysher B, Bowman SJ, Fearon DT, Filer A, Tarte K, Luther SA, Fisher BA, Buckley CD, Coles MC, Barone F. Immunofibroblasts are pivotal drivers of tertiary lymphoid structure formation and local pathology. Proc Natl Acad Sci U S A 2019; 116:13490-13497. [PMID: 31213547 PMCID: PMC6613169 DOI: 10.1073/pnas.1905301116] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Resident fibroblasts at sites of infection, chronic inflammation, or cancer undergo phenotypic and functional changes to support leukocyte migration and, in some cases, aggregation into tertiary lymphoid structures (TLS). The molecular programming that shapes these changes and the functional requirements of this population in TLS development are unclear. Here, we demonstrate that external triggers at mucosal sites are able to induce the progressive differentiation of a population of podoplanin (pdpn)-positive stromal cells into a network of immunofibroblasts that are able to support the earliest phases of TLS establishment. This program of events, that precedes lymphocyte infiltration in the tissue, is mediated by paracrine and autocrine signals mainly regulated by IL13. This initial fibroblast network is expanded and stabilized, once lymphocytes are recruited, by the local production of the cytokines IL22 and lymphotoxin. Interfering with this regulated program of events or depleting the immunofibroblasts in vivo results in abrogation of local pathology, demonstrating the functional role of immunofibroblasts in supporting TLS maintenance in the tissue and suggesting novel therapeutic targets in TLS-associated diseases.
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Affiliation(s)
- Saba Nayar
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Joana Campos
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Charlotte G Smith
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Valentina Iannizzotto
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - David H Gardner
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Frédéric Mourcin
- UMR INSERM U1236, Université Rennes 1, Etablissement Français du Sang, 35043 Rennes, France
| | - David Roulois
- UMR INSERM U1236, Université Rennes 1, Etablissement Français du Sang, 35043 Rennes, France
| | - Jason Turner
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Marvin Sylvestre
- UMR INSERM U1236, Université Rennes 1, Etablissement Français du Sang, 35043 Rennes, France
| | - Saba Asam
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Bridget Glaysher
- Centre for Immunology and Infection, Department of Biology, Hull York Medical School, University of York, YO10 5DD York, United Kingdom
| | - Simon J Bowman
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Douglas T Fearon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, CB2 0RE Cambridge, United Kingdom
| | - Andrew Filer
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Karin Tarte
- UMR INSERM U1236, Université Rennes 1, Etablissement Français du Sang, 35043 Rennes, France
| | - Sanjiv A Luther
- Department of Biochemistry, Center of Immunity and Infection, University of Lausanne, 1066 Epalinges, Switzerland
| | - Benjamin A Fisher
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Christopher D Buckley
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
| | - Mark C Coles
- Centre for Immunology and Infection, Department of Biology, Hull York Medical School, University of York, YO10 5DD York, United Kingdom;
| | - Francesca Barone
- Rheumatoid Arthritis Pathogenesis Centre of Excellence, Institute of Inflammation and Ageing, College of Medical & Dental Sciences, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, B15 2WB Birmingham, United Kingdom;
- bNIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, B15 2TT, Birmingham, UK
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11
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Gorman JA, Hundhausen C, Kinsman M, Arkatkar T, Allenspach EJ, Clough C, West SE, Thomas K, Eken A, Khim S, Hale M, Oukka M, Jackson SW, Cerosaletti K, Buckner JH, Rawlings DJ. The TYK2-P1104A Autoimmune Protective Variant Limits Coordinate Signals Required to Generate Specialized T Cell Subsets. Front Immunol 2019; 10:44. [PMID: 30740104 PMCID: PMC6355696 DOI: 10.3389/fimmu.2019.00044] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023] Open
Abstract
TYK2 is a JAK family member that functions downstream of multiple cytokine receptors. Genome wide association studies have linked a SNP (rs34536443) within TYK2 encoding a Proline to Alanine substitution at amino acid 1104, to protection from multiple autoimmune diseases including systemic lupus erythematosus (SLE) and multiple sclerosis (MS). The protective role of this SNP in autoimmune pathogenesis, however, remains incompletely understood. Here we found that T follicular helper (Tfh) cells, switched memory B cells, and IFNAR signaling were decreased in healthy individuals that expressed the protective variant TYK2 A1104 (TYK2 P ). To study this variant in vivo, we developed a knock-in murine model of this allele. Murine Tyk2 P expressing T cells homozygous for the protective allele, but not cells heterozygous for this change, manifest decreased IL-12 receptor signaling, important for Tfh lineage commitment. Further, homozygous Tyk2 P T cells exhibited diminished in vitro Th1 skewing. Surprisingly, despite these signaling changes, in vivo formation of Tfh and GC B cells was unaffected in two models of T cell dependent immune responses and in two alternative SLE models. TYK2 is also activated downstream of IL-23 receptor engagement. Here, we found that Tyk2 P expressing T cells had reduced IL-23 dependent signaling as well as a diminished ability to skew toward Th17 in vitro. Consistent with these findings, homozygous, but not heterozygous, Tyk2 P mice were fully protected in a murine model of MS. Homozygous Tyk2 P mice had fewer infiltrating CD4+ T cells within the CNS. Most strikingly, homozygous mice had a decreased proportion of IL-17+/IFNγ+, double positive, pathogenic CD4+ T cells in both the draining lymph nodes (LN) and CNS. Thus, in an autoimmune model, such as EAE, impacted by both altered Th1 and Th17 signaling, the Tyk2 P allele can effectively shield animals from disease. Taken together, our findings suggest that TYK2P diminishes IL-12, IL-23, and IFN I signaling and that its protective effect is most likely manifest in the setting of autoimmune triggers that concurrently dysregulate at least two of these important signaling cascades.
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Affiliation(s)
- Jacquelyn A Gorman
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Christian Hundhausen
- Translational Research Program, Benaroya Research Institute, Seattle, WA, United States
| | - Mackenzie Kinsman
- Translational Research Program, Benaroya Research Institute, Seattle, WA, United States
| | - Tanvi Arkatkar
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Eric J Allenspach
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Courtnee Clough
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Samuel E West
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Kerri Thomas
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Immunology, University of Washington, Seattle, WA, United States
| | - Ahmet Eken
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Socheath Khim
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States
| | - Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Immunology, University of Washington, Seattle, WA, United States
| | - Mohamed Oukka
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Department of Immunology, University of Washington, Seattle, WA, United States
| | - Shaun W Jackson
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute, Seattle, WA, United States
| | - Jane H Buckner
- Translational Research Program, Benaroya Research Institute, Seattle, WA, United States
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Department of Immunology, University of Washington, Seattle, WA, United States
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12
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Mohamadhosseini A, Mansouri R, Javinani A, Ganjouei AA, Akhlaghi M, Aslani S, Hamzeh E, Jamshidi A, Ahmadzadeh N, Mahmoudi M. Single Nucleotide Polymorphism of TYK2 Gene and Susceptibility to Rheumatoid Arthritis in Iranian Population. Avicenna J Med Biotechnol 2019; 11:187-191. [PMID: 31057722 PMCID: PMC6490405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Rheumatoid Arthritis (RA) is a debilitating disorder in which the immune system mainly targets the synovial tissue. Janus kinase family including tyrosine kinase 2 (TYK2) is one of the crucial mediators of the downstream signaling pathway of inflammatory cytokines that further contributes to RA pathogenesis. In this study, the association of TYK2 gene rs34536443 polymorphism, which may affect the function of TYK protein and, hence, the inflammatory settings, with RA susceptibility was investigated. Moreover, its correlation with demographic and serological features of the patients was assessed. METHODS In the present study, 700 RA patients and 700 sex, age and ethnicity-matched healthy individuals as the control group were included. MGB TaqMan real-time allelic discrimination method was used to determine the rs34536443 polymorphism. Rheumatoid factor, anti-cyclic citrullinated peptide antibody, erythrocyte sedimentation rate and C-reactive protein were also measured. RESULTS The frequency of rs34536443 minor allele (C allele) was not different between patients and control group [1.7 vs. 2.61 percent, OR (95% CI)=1.35 (0.78-2.33);p=0.27]. There was not a statistically significant association between rs34536443 genotypes and RA susceptibility. Genotypes of rs34536443 polymorphism were associated nor with demographic neither with serological features of RA patients. CONCLUSION In the present study, there was not any association between TYK2 gene rs34536443 polymorphism with either disease susceptibility, demographic and serological features of Iranian RA patients. These findings are not compatible with previous works from other ethnicities, further supporting the role of genetics in disease susceptibility.
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Affiliation(s)
- Azadeh Mohamadhosseini
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Reza Mansouri
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran,Reza Mansouri, Ph.D., Immunology Department, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran, Tel/Fax: +98 2188220067, +98 3538203410, E-mail:,
| | - Ali Javinani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ashraf Ganjouei
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoumeh Akhlaghi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Hamzeh
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nooshin Ahmadzadeh
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran,Corresponding authors: Mahdi Mahmoudi, Ph.D., Rheumatology Research Center, Shariati Hospital, Tehran, Iran
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13
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Yuan X, Wu H, Bu H, Zhou J, Zhang H. Targeting the immunity protein kinases for immuno-oncology. Eur J Med Chem 2018; 163:413-427. [PMID: 30530193 DOI: 10.1016/j.ejmech.2018.11.072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 01/09/2023]
Abstract
With the rise of immuno-oncology, small-molecule modulators targeting immune system and inflammatory processes are becoming a research hotspot. This work mainly focuses on key kinases acting as central nodes in immune signaling pathways. Although over thirty small-molecule kinase inhibitors have been approved by FDA for the treatment of various cancers, only a few are associated with immuno-oncology. With the going deep of the research work, more and more immunity protein kinase inhibitors are approved for clinical trials to treat solid tumors and hematologic malignancies by FDA, which remain good prospects. Meanwhile, in-depth understanding of biological function of immunity protein kinases in immune system is pushing the field forward. This article focuses on the development of safe and effective small-molecule immunity protein kinase inhibitors and further work needs to keep the promises of these inhibitors for patients' welfare.
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Affiliation(s)
- Xinrui Yuan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Hanshu Wu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Hong Bu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
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14
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Liu Y, Gibson SA, Benveniste EN, Qin H. Opportunities for Translation from the Bench: Therapeutic Intervention of the JAK/STAT Pathway in Neuroinflammatory Diseases. Crit Rev Immunol 2018; 35:505-27. [PMID: 27279046 DOI: 10.1615/critrevimmunol.2016015517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogenic CD4+ T cells and myeloid cells play critical roles in the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. These immune cells secrete aberrantly high levels of pro-inflammatory cytokines that pathogenically bridge the innate and adaptive immune systems and damage neurons and oligodendrocytes. These cytokines include interleukin-2 (IL-2), IL-6, IL-12, IL-21, IL-23, granulocyte macrophage-colony stimulating factor (GM-CSF), and interferon-γ (IFN-γ). It is, therefore, not surprising that both the dysregulated expression of these cytokines and the subsequent activation of their downstream signaling cascades is a common feature in MS/EAE. The Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway is utilized by numerous cytokines for signal transduction and is essential for the development and regulation of immune responses. Unbridled activation of the JAK/STAT pathway by pro-inflammatory cytokines has been demonstrated to be critically involved in the pathogenesis of MS/EAE. In this review, we discuss recent advancements in our understanding of the involvement of the JAK/STAT signaling pathway in the pathogenesis of MS/EAE, with a particular focus on therapeutic approaches to target the JAK/STAT pathway.
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Affiliation(s)
- Yudong Liu
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, 35294; Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sara A Gibson
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Etty N Benveniste
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Hongwei Qin
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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15
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Dendrou CA, Cortes A, Shipman L, Evans HG, Attfield KE, Jostins L, Barber T, Kaur G, Kuttikkatte SB, Leach OA, Desel C, Faergeman SL, Cheeseman J, Neville MJ, Sawcer S, Compston A, Johnson AR, Everett C, Bell JI, Karpe F, Ultsch M, Eigenbrot C, McVean G, Fugger L. Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity. Sci Transl Med 2017; 8:363ra149. [PMID: 27807284 DOI: 10.1126/scitranslmed.aag1974] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023]
Abstract
Thousands of genetic variants have been identified, which contribute to the development of complex diseases, but determining how to elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders; subsequent molecular, cellular, in vivo, and structural functional follow-up; and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for certain common autoimmune disorders.
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Affiliation(s)
- Calliope A Dendrou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Adrian Cortes
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Lydia Shipman
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hayley G Evans
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Kathrine E Attfield
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Barber
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gurman Kaur
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Subita Balaram Kuttikkatte
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Oliver A Leach
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Christiane Desel
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Soren L Faergeman
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Department of Clinical Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Jane Cheeseman
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alastair Compston
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Adam R Johnson
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Everett
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John I Bell
- University of Oxford, Richard Doll Building, Roosevelt Drive, Oxford OX3 7DG, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Mark Ultsch
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Charles Eigenbrot
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK. .,Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Department of Clinical Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
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16
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Moslin R, Gardner D, Santella J, Zhang Y, Duncia JV, Liu C, Lin J, Tokarski JS, Strnad J, Pedicord D, Chen J, Blat Y, Zupa-Fernandez A, Cheng L, Sun H, Chaudhry C, Huang C, D'Arienzo C, Sack JS, Muckelbauer JK, Chang C, Tredup J, Xie D, Aranibar N, Burke JR, Carter PH, Weinstein DS. Identification of imidazo[1,2- b]pyridazine TYK2 pseudokinase ligands as potent and selective allosteric inhibitors of TYK2 signalling. MEDCHEMCOMM 2017; 8:700-712. [PMID: 30108788 PMCID: PMC6071835 DOI: 10.1039/c6md00560h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/06/2016] [Indexed: 12/19/2022]
Abstract
As a member of the Janus (JAK) family of non-receptor tyrosine kinases, TYK2 mediates the signaling of pro-inflammatory cytokines including IL-12, IL-23 and type 1 interferon (IFN), and therefore represents an attractive potential target for treating the various immuno-inflammatory diseases in which these cytokines have been shown to play a role. Following up on our previous report that ligands to the pseudokinase domain (JH2) of TYK2 suppress cytokine-mediated receptor activation of the catalytic (JH1) domain, the imidazo[1,2-b]pyridazine (IZP) 7 was identified as a promising hit compound. Through iterative modification of each of the substituents of the IZP scaffold, the cellular potency was improved while maintaining selectivity over the JH1 domain. These studies led to the discovery of the JH2-selective TYK2 inhibitor 29, which provided encouraging systemic exposures after oral dosing in mice. Phosphodiesterase 4 (PDE4) was identified as an off-target and potential liability of the IZP ligands, and selectivity for TYK2 JH2 over this enzyme was obtained by elaborating along selectivity vectors determined from analyses of X-ray co-crystal structures of representative ligands of the IZP class bound to both proteins.
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Affiliation(s)
- R Moslin
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - D Gardner
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J Santella
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - Y Zhang
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J V Duncia
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - C Liu
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J Lin
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J S Tokarski
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J Strnad
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - D Pedicord
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J Chen
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - Y Blat
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | | | - L Cheng
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - H Sun
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - C Chaudhry
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - C Huang
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - C D'Arienzo
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J S Sack
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J K Muckelbauer
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - C Chang
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J Tredup
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - D Xie
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - N Aranibar
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - J R Burke
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - P H Carter
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
| | - D S Weinstein
- Bristol-Myers Squibb Research , Princeton , New Jersey , USA .
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17
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Majoros A, Platanitis E, Kernbauer-Hölzl E, Rosebrock F, Müller M, Decker T. Canonical and Non-Canonical Aspects of JAK-STAT Signaling: Lessons from Interferons for Cytokine Responses. Front Immunol 2017; 8:29. [PMID: 28184222 PMCID: PMC5266721 DOI: 10.3389/fimmu.2017.00029] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/09/2017] [Indexed: 01/07/2023] Open
Abstract
Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signal transduction mediates cytokine responses. Canonical signaling is based on STAT tyrosine phosphorylation by activated JAKs. Downstream of interferon (IFN) receptors, activated JAKs cause the formation of the transcription factors IFN-stimulated gene factor 3 (ISGF3), a heterotrimer of STAT1, STAT2 and interferon regulatory factor 9 (IRF9) subunits, and gamma interferon-activated factor (GAF), a STAT1 homodimer. In recent years, several deviations from this paradigm were reported. These include kinase-independent JAK functions as well as extra- and intranuclear activities of U-STATs without phosphotyrosines. Additionally, transcriptional control by STAT complexes resembling neither GAF nor ISGF3 contributes to transcriptome changes in IFN-treated cells. Our review summarizes the contribution of non-canonical JAK-STAT signaling to the innate antimicrobial immunity imparted by IFN. Moreover, we touch upon functions of IFN pathway proteins beyond the IFN response. These include metabolic functions of IRF9 as well as the regulation of natural killer cell activity by kinase-dead TYK2 and different phosphorylation isoforms of STAT1.
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Affiliation(s)
- Andrea Majoros
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Ekaterini Platanitis
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Elisabeth Kernbauer-Hölzl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Felix Rosebrock
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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18
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Dendrou CA, McVean G, Fugger L. Neuroinflammation - using big data to inform clinical practice. Nat Rev Neurol 2016; 12:685-698. [PMID: 27857124 DOI: 10.1038/nrneurol.2016.171] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuroinflammation is emerging as a central process in many neurological conditions, either as a causative factor or as a secondary response to nervous system insult. Understanding the causes and consequences of neuroinflammation could, therefore, provide insight that is needed to improve therapeutic interventions across many diseases. However, the complexity of the pathways involved necessitates the use of high-throughput approaches to extensively interrogate the process, and appropriate strategies to translate the data generated into clinical benefit. Use of 'big data' aims to generate, integrate and analyse large, heterogeneous datasets to provide in-depth insights into complex processes, and has the potential to unravel the complexities of neuroinflammation. Limitations in data analysis approaches currently prevent the full potential of big data being reached, but some aspects of big data are already yielding results. The implementation of 'omics' analyses in particular is becoming routine practice in biomedical research, and neuroimaging is producing large sets of complex data. In this Review, we evaluate the impact of the drive to collect and analyse big data on our understanding of neuroinflammation in disease. We describe the breadth of big data that are leading to an evolution in our understanding of this field, exemplify how these data are beginning to be of use in a clinical setting, and consider possible future directions.
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Affiliation(s)
- Calliope A Dendrou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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19
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20
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Yogo T, Nagamiya H, Seto M, Sasaki S, Shih-Chung H, Ohba Y, Tokunaga N, Lee GN, Rhim CY, Yoon CH, Cho SY, Skene R, Yamamoto S, Satou Y, Kuno M, Miyazaki T, Nakagawa H, Okabe A, Marui S, Aso K, Yoshida M. Structure-Based Design and Synthesis of 3-Amino-1,5-dihydro-4H-pyrazolopyridin-4-one Derivatives as Tyrosine Kinase 2 Inhibitors. J Med Chem 2016; 59:733-49. [PMID: 26701356 DOI: 10.1021/acs.jmedchem.5b01857] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report herein the discovery and optimization of 3-amino-1,5-dihydro-4H-pyrazolopyridin-4-one TYK2 inhibitors. High-throughput screening against TYK2 and JAK1-3 provided aminoindazole derivative 1 as a hit compound. Scaffold hopping of the aminoindazole core led to the discovery of 3-amino-1,5-dihydro-4H-pyrazolopyridin-4-one derivative 3 as a novel chemotype of TYK2 inhibitors. Interestingly, initial SAR study suggested that this scaffold could have a vertically flipped binding mode, which prompted us to introduce a substituent at the 7-position as a moiety directed toward the solvent-exposed region. Introduction of a 1-methyl-3-pyrazolyl moiety at the 7-position resulted in a dramatic increase in TYK2 inhibitory activity, and further optimization led to the discovery of 20. Compound 20 inhibited IL-23-induced IL-22 production in a rat PD assay, as well as inhibited IL-23 signaling in human PBMC. Furthermore, 20 showed selectivity for IL-23 signaling inhibition against GM-CSF, demonstrating the unique cytokine selectivity of the novel TYK2 inhibitor.
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Affiliation(s)
- Takatoshi Yogo
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroyuki Nagamiya
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaki Seto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Sasaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Huang Shih-Chung
- Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited , 40 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Yusuke Ohba
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Norihito Tokunaga
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Gil Nam Lee
- Chemizon , 3F Dongbang Rental Building, 333-1 Sangdaewon-Dong, Jungwon-Gu, Seongnam-Si, Kyunggi-Do 462-120, Korea
| | - Chul Yun Rhim
- Chemizon , 3F Dongbang Rental Building, 333-1 Sangdaewon-Dong, Jungwon-Gu, Seongnam-Si, Kyunggi-Do 462-120, Korea
| | - Cheol Hwan Yoon
- Chemizon , 3F Dongbang Rental Building, 333-1 Sangdaewon-Dong, Jungwon-Gu, Seongnam-Si, Kyunggi-Do 462-120, Korea
| | - Suk Young Cho
- Chemizon , 3F Dongbang Rental Building, 333-1 Sangdaewon-Dong, Jungwon-Gu, Seongnam-Si, Kyunggi-Do 462-120, Korea
| | - Robert Skene
- Takeda California , 10410 Science Center Drive, San Diego, California 92121, United States
| | - Syunsuke Yamamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yousuke Satou
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masako Kuno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takahiro Miyazaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Nakagawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Atsutoshi Okabe
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shogo Marui
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazuyoshi Aso
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masato Yoshida
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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21
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D'Cunha MA, Pandit L, Malli C. CD6 gene polymorphism rs17824933 is associated with multiple sclerosis in Indian population. Ann Indian Acad Neurol 2016; 19:491-494. [PMID: 27994359 PMCID: PMC5144471 DOI: 10.4103/0972-2327.192384] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Multiple sclerosis (MS) prevalence has increased worldwide. The known genetic association for MS in the west has not been studied in detail in nonwhite populations and particularly Indians. Objective: The objective of this study was to evaluate some known genetic variations outside the major histocompatibility complex (MHC) region associated with MS in patients of Indian origin. Materials and Methods: We investigated 10 gene-associated single nucleotide polymorphisms (SNP's) outside the MHC region in 300 patients and 720 unrelated controls. Genotyping was performed on an ABI7500 real-time polymerase chain reaction genotyping platform using predesigned TaqMan SNP genotyping assays. Results: CD6 gene associated SNP (rs17824933) showed significant association with MS (P = 4.2 × 10−5, odds ratio [OR] = 2.24, confidence interval (CI) = 1.51–3.33). A modest association was also noted for TMEM39A rs1132200 (P = 0.023, OR = 1.41, CI = 1.05–1.91) and IL2RA rs2104286 (P = 0.04, OR = 1.3, CI = 1.006–1.67). In the remaining SNPs, the allele frequencies were overexpressed in patients when compared to healthy controls. Conclusion: Our data illustrate the similarity in risk association between Indian and European populations for MS.
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Affiliation(s)
- Mary Anitha D'Cunha
- Center for Advanced Neurological Research, KS Hegde Medical Academy, Nitte University, Mangalore, Karnataka, India
| | - Lekha Pandit
- Center for Advanced Neurological Research, KS Hegde Medical Academy, Nitte University, Mangalore, Karnataka, India
| | - Chaithra Malli
- Center for Advanced Neurological Research, KS Hegde Medical Academy, Nitte University, Mangalore, Karnataka, India
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22
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Leitner NR, Witalisz-Siepracka A, Strobl B, Müller M. Tyrosine kinase 2 - Surveillant of tumours and bona fide oncogene. Cytokine 2015; 89:209-218. [PMID: 26631911 DOI: 10.1016/j.cyto.2015.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 10/29/2015] [Indexed: 12/16/2022]
Abstract
Tyrosine kinase 2 (TYK2) is a member of the Janus kinase (JAK) family, which transduces cytokine and growth factor signalling. Analysis of TYK2 loss-of-function revealed its important role in immunity to infection, (auto-) immunity and (auto-) inflammation. TYK2-deficient patients unravelled high similarity between mice and men with respect to cellular signalling functions and basic immunology. Genome-wide association studies link TYK2 to several autoimmune and inflammatory diseases as well as carcinogenesis. Due to its cytokine signalling functions TYK2 was found to be essential in tumour surveillance. Lately TYK2 activating mutants and fusion proteins were detected in patients diagnosed with leukaemic diseases suggesting that TYK2 is a potent oncogene. Here we review the cell intrinsic and extrinsic functions of TYK2 in the characteristics preventing and enabling carcinogenesis. In addition we describe an unexpected function of kinase-inactive TYK2 in tumour rejection.
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Affiliation(s)
- Nicole R Leitner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Agnieszka Witalisz-Siepracka
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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23
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Multiple sclerosis: getting personal with induced pluripotent stem cells. Cell Death Dis 2015; 6:e1806. [PMID: 26158512 PMCID: PMC4650727 DOI: 10.1038/cddis.2015.179] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 12/13/2022]
Abstract
Human induced pluripotent stem (iPS) cells can be derived from lineage-restricted cells and represent an important tool to develop novel patient-specific cell therapies and research models for inherited and acquired diseases. Recently, patient-derived iPS cells, containing donor genetic background, have offered a breakthrough approach to study human genetics of neurodegenerative diseases. By offering an unlimited source of patient-specific disease-relevant cells, iPS cells hold great promise for understanding disease mechanisms, identifying molecular targets and developing phenotypic screens for drug discovery. This review will discuss the potential impact of using iPS cell-derived models in multiple sclerosis (MS) research and highlight some of the current challenges and prospective for generating novel therapeutic treatments for MS patients.
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Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet 2015; 47:692-5. [PMID: 26111507 PMCID: PMC5426533 DOI: 10.1038/ng.3312] [Citation(s) in RCA: 240] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The European Genome-phenome Archive (EGA) is a permanent archive that promotes distribution and sharing of genetic and phenotype data consented for specific approved uses, but not fully open public distribution. The EGA follows strict protocols for information management, data storage, security and dissemination. Authorized access to the data is managed in partnership with the data providing organizations. The EGA includes major reference data collections for human genetics research.
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Affiliation(s)
- Ilkka Lappalainen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jeff Almeida-King
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Vasudev Kumanduri
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Alexander Senf
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - John Dylan Spalding
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Saif Ur-Rehman
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Gary Saunders
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jag Kandasamy
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Mario Caccamo
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Brendan Vaughan
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Thomas Laurent
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Francis Rowland
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Pablo Marin-Garcia
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jonathan Barker
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Petteri Jokinen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Ignacio Medina
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Arcadi Navarro
- 1] Centre for Genomic Regulation, Barcelona, Spain. [2] Institute of Evolutionary Biology, Universitat Pompeu Fabra-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain. [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Justin Paschall
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
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25
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Tokarski JS, Zupa-Fernandez A, Tredup JA, Pike K, Chang C, Xie D, Cheng L, Pedicord D, Muckelbauer J, Johnson SR, Wu S, Edavettal SC, Hong Y, Witmer MR, Elkin LL, Blat Y, Pitts WJ, Weinstein DS, Burke JR. Tyrosine Kinase 2-mediated Signal Transduction in T Lymphocytes Is Blocked by Pharmacological Stabilization of Its Pseudokinase Domain. J Biol Chem 2015; 290:11061-74. [PMID: 25762719 DOI: 10.1074/jbc.m114.619502] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Indexed: 01/04/2023] Open
Abstract
Inhibition of signal transduction downstream of the IL-23 receptor represents an intriguing approach to the treatment of autoimmunity. Using a chemogenomics approach marrying kinome-wide inhibitory profiles of a compound library with the cellular activity against an IL-23-stimulated transcriptional response in T lymphocytes, a class of inhibitors was identified that bind to and stabilize the pseudokinase domain of the Janus kinase tyrosine kinase 2 (Tyk2), resulting in blockade of receptor-mediated activation of the adjacent catalytic domain. These Tyk2 pseudokinase domain stabilizers were also shown to inhibit Tyk2-dependent signaling through the Type I interferon receptor but not Tyk2-independent signaling and transcriptional cellular assays, including stimulation through the receptors for IL-2 (JAK1- and JAK3-dependent) and thrombopoietin (JAK2-dependent), demonstrating the high functional selectivity of this approach. A crystal structure of the pseudokinase domain liganded with a representative example showed the compound bound to a site analogous to the ATP-binding site in catalytic kinases with features consistent with high ligand selectivity. The results support a model where the pseudokinase domain regulates activation of the catalytic domain by forming receptor-regulated inhibitory interactions. Tyk2 pseudokinase stabilizers, therefore, represent a novel approach to the design of potent and selective agents for the treatment of autoimmunity.
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Affiliation(s)
| | | | | | - Kristen Pike
- the Department of Leads Discovery and Optimization, Bristol-Myers Squibb Research and Development, Wallingford, Connecticut 06492
| | | | | | | | | | | | | | | | | | - Yang Hong
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, Princeton, New Jersey 08543 and
| | | | - Lisa L Elkin
- the Department of Leads Discovery and Optimization, Bristol-Myers Squibb Research and Development, Wallingford, Connecticut 06492
| | | | - William J Pitts
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, Princeton, New Jersey 08543 and
| | - David S Weinstein
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, Princeton, New Jersey 08543 and
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Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases. PLoS Genet 2014; 10:e1004369. [PMID: 24852434 PMCID: PMC4031051 DOI: 10.1371/journal.pgen.1004369] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/24/2014] [Indexed: 02/01/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is highly polymorphic at the population level, and specific mtDNA variants affect mitochondrial function. With emerging evidence that mitochondrial mechanisms are central to common human diseases, it is plausible that mtDNA variants contribute to the “missing heritability” of several complex traits. Given the central role of mtDNA genes in oxidative phosphorylation, the same genetic variants would be expected to alter the risk of developing several different disorders, but this has not been shown to date. Here we studied 38,638 individuals with 11 major diseases, and 17,483 healthy controls. Imputing missing variants from 7,729 complete mitochondrial genomes, we captured 40.41% of European mtDNA variation. We show that mtDNA variants modifying the risk of developing one disease also modify the risk of developing other diseases, thus providing independent replication of a disease association in different case and control cohorts. High-risk alleles were more common than protective alleles, indicating that mtDNA is not at equilibrium in the human population, and that recent mutations interact with nuclear loci to modify the risk of developing multiple common diseases. There is a growing body of evidence indicating that mitochondrial dysfunction, a result of genetic variation in the mitochondrial genome, is a critical component in the aetiology of a number of complex traits. Here, we take advantage of recent technical and methodological advances to examine the role of common mitochondrial DNA variants in several complex diseases. By examining over 50,000 individuals, from 11 different diseases we show that mitochondrial DNA variants can both increase or decrease an individual's risk of disease, replicating and expanding upon several previously reported studies. Moreover, by analysing several large disease groups in tandem, we are able to show a commonality of association, with the same mitochondrial DNA variants associated with several distinct disease phenotypes. These shared genetic associations implicate a shared underlying functional effect, likely changing cellular energy, which manifests as distinct phenotypes. Our study confirms the important role that mitochondrial DNA variation plays on complex traits and additionally supports the utility of a GWAS-based approach for analysing mitochondrial genetics.
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Liang Y, Zhu Y, Xia Y, Peng H, Yang XK, Liu YY, Xu WD, Pan HF, Ye DQ. Therapeutic potential of tyrosine kinase 2 in autoimmunity. Expert Opin Ther Targets 2014; 18:571-80. [PMID: 24654603 DOI: 10.1517/14728222.2014.892925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Tyrosine kinase 2 (Tyk2) is a Janus kinase family member that is crucial for signaling transduction in response to a wide variety of cytokines, including type I IFNs, IL-6, IL-10, IL-12 and IL-23. An appropriate expression of Tyk2-mediated signaling might be essential for maintaining normal immune responses. AREAS COVERED This review summarizes that Tyk2 is essential for the differentiation and function of a wide variety of immune cells, including natural killer cells, B cells, as well as T helper cells. In addition, Tyk2-mediated signaling promoted the production of autoimmune-associated components, which is implicated in the pathogenesis of autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis. Aberrant expression of Tyk2 was observed in many autoimmune conditions. EXPERT OPINION Until recently, no patent filings had claimed selective inhibitors of Tyk2. Both CP-690,500 and CMP6 failed to be used in clinical treatment due to the difficulties of finding suitable selective leads or due to detrimental toxicities. Although the result of Cmpd1 is promising, it remains to be seen how specific the Tyk2 inhibitor is and how they are working. Currently, structure-based drug design (SBDD) technology has provided us with a quite useful window for SBDD of Tyk2 inhibitors.
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Affiliation(s)
- Yan Liang
- Anhui Medical University, School of Public Health, Department of Epidemiology and Biostatistics , 81 Meishan Road, Hefei, Anhui, 230032 , PR China +86 551 65167726 ; +86 551 65161171 ;
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Pulit SL, Leusink M, Menelaou A, de Bakker PIW. Association claims in the sequencing era. Genes (Basel) 2014; 5:196-213. [PMID: 24705293 PMCID: PMC3978519 DOI: 10.3390/genes5010196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 12/13/2022] Open
Abstract
Since the completion of the Human Genome Project, the field of human genetics has been in great flux, largely due to technological advances in studying DNA sequence variation. Although community-wide adoption of statistical standards was key to the success of genome-wide association studies, similar standards have not yet been globally applied to the processing and interpretation of sequencing data. It has proven particularly challenging to pinpoint unequivocally disease variants in sequencing studies of polygenic traits. Here, we comment on a number of factors that may contribute to irreproducible claims of association in scientific literature and discuss possible steps that we can take towards cultural change.
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Affiliation(s)
- Sara L Pulit
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Maarten Leusink
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Androniki Menelaou
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Paul I W de Bakker
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
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Marinoni B, Ceribelli A, Massarotti MS, Selmi C. The Th17 axis in psoriatic disease: pathogenetic and therapeutic implications. AUTOIMMUNITY HIGHLIGHTS 2014; 5:9-19. [PMID: 26000152 PMCID: PMC4389010 DOI: 10.1007/s13317-013-0057-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/05/2013] [Indexed: 02/06/2023]
Abstract
Psoriasis and psoriatic arthritis represent two paradigmatic conditions characterized by chronic inflammation and possibly autoimmunity, despite the absence of known serum autoantibodies. The two diseases, albeit strongly correlated from clinical, genetic, and epidemiogical standpoints, manifest significant differences in terms of etiology and pathogenetic mechanisms. Nonetheless, Th17 cells appear crucial to both diseases, and IL23 is the cytokine involved in determining the fate of naive CD4+ cells to differentiate into a pathogenic phenotype. This basic experimental observation led to a clear understanding of the immune dysfunction causing psoriasis and psoriatic arthritis but, more importantly, also led to new therapeutic approaches. In recent years, monoclonal antibodies directed to IL12/IL23 (ustekinumab) or IL17 (secukinumab, ixekizumab, brodalumab) are being investigated or have proven to be beneficial for patients with psoriatic disease, thus further supporting the view that Th17 cells play a pivotal role in disease onset and perpetuation. These most recent reports indeed represent significant developments that may allow overcoming the TNFα pathway as the major therapeutic target in chronic inflammation.
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Affiliation(s)
- Beatrice Marinoni
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Rozzano, Milan Italy
- Biometra Department, University of Milan, Milan, Italy
| | - Angela Ceribelli
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Rozzano, Milan Italy
- Biometra Department, University of Milan, Milan, Italy
| | - Marco S. Massarotti
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Rozzano, Milan Italy
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Rozzano, Milan Italy
- Biometra Department, University of Milan, Milan, Italy
- Division of Rheumatology, Allergy and Clinical Immunology, Genome and Biomedical Sciences Facility, University of California at Davis School of Medicine, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616 USA
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Abstract
Familial aggregation and the studies of twins indicate that heredity contributes to multiple sclerosis (MS) risk. Immunologic studies of leukocyte antigens subsequently followed by gene-mapping techniques identified the primary MS susceptibility locus to be within the major histocompatibility complex (MHC). The primary risk allele is HLA-DRB1*15, although other alleles of this gene also influence MS susceptibility. Other genes within the MHC also contribute to MS susceptibility. Genome-wide association studies have identified over 50 additional common variants of genes across the genome. Estimates suggest that there may be as many as 200 genes involved in MS susceptibility. In addition to these common polymorphisms, studies have identified several rare risk alleles in some families. Interestingly, the majority of the genes identified have known immunologic functions and many contribute to the risk of inheriting other autoimmune diseases. Genetic variants in the vitamin D metabolic pathway have also been identified. That vitamin D contributes to MS susceptibility as both an environmental as well as genetic risk factor underscores the importance of this metabolic pathway in disease pathogenesis. Current efforts are focused on understanding how the myriad of genetic risk alleles interact within networks to influence MS risk at family level as well as within populations.
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Affiliation(s)
- Bruce A C Cree
- Department of Neurology, University of California, San Francisco, USA.
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31
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Owens T, Khorooshi R, Wlodarczyk A, Asgari N. Interferons in the central nervous system: A few instruments play many tunes. Glia 2013; 62:339-55. [DOI: 10.1002/glia.22608] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trevor Owens
- Department of Neurobiology Research, Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | - Reza Khorooshi
- Department of Neurobiology Research, Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | - Agnieszka Wlodarczyk
- Department of Neurobiology Research, Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | - Nasrin Asgari
- Department of Neurobiology Research, Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
- Department of Neurology; Vejle Hospital; Denmark
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Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TMC, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BAC, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 2013; 45:1353-60. [PMID: 24076602 PMCID: PMC3832895 DOI: 10.1038/ng.2770] [Citation(s) in RCA: 997] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022]
Abstract
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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Mowry EM, Carey RF, Blasco MR, Pelletier J, Duquette P, Villoslada P, Malikova I, Roger E, Kinkel RP, McDonald J, Bacchetti P, Waubant E. Association of multiple sclerosis susceptibility variants and early attack location in the CNS. PLoS One 2013; 8:e75565. [PMID: 24130718 PMCID: PMC3794979 DOI: 10.1371/journal.pone.0075565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/13/2013] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE The anatomic location of subsequent relapses in early multiple sclerosis (MS) appears to be predicted by the first attack location. We sought to determine if genetic polymorphisms associated with MS susceptibility are associated with attack location. METHODS 17 genome-wide association study-identified MS susceptibility polymorphisms were genotyped in 503 white, non-Hispanic patients seen within a year of MS onset. Their association with the CNS location of the first two MS attacks was assessed in multivariate repeated measures analyses (generalized estimating equations with robust standard errors). RESULTS The IL12A polymorphism was independently associated with increased odds of attacks involving the spinal cord (OR = 1.52, 95% CI 1.11, 2.07, p = 0.009), as was the IRF8 polymorphism (OR = 2.40, 95% CI [1.04, 5.50], p = 0.040). The IL7R polymorphism was associated with reduced odds of attacks involving the brainstem/cerebellum (OR = 0.46, 95% CI 0.22, 0.97, p = 0.041), as were the TNFRSF1A and IL12A polymorphisms. The CD6 polymorphism conferred reduced odds of optic neuritis as an attack location (OR = 0.69, 95% CI [0.49, 0.97], p = 0.034). Several other genes showed trends for association with attack location. CONCLUSIONS Some of the MS susceptibility genes may be associated with MS attack location. The IL12A polymorphism is of particular interest given that interferon beta therapy appears to influence IL12 levels. These findings may lead to improved understanding of MS pathogenesis and treatment.
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Affiliation(s)
- Ellen M. Mowry
- Multiple Sclerosis Center, Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| | - Robert F. Carey
- Multiple Sclerosis Center, Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Maria R. Blasco
- Department of Neurology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Jean Pelletier
- Pole de Neurosciences Cliniques, Service de Neurologie, Centre de Résonance Magnétique Biologique et Médicale, Centre Hospitalier Universitaire Timone, Aix Marseille Université, Marseille, France
| | - Pierre Duquette
- Multiple Sclerosis Clinic, Centre Hospitalier de L'Universite de Montreal, Montreal, Canada
| | - Pablo Villoslada
- Center of Neuroimmunology, Institute of Biomedical Research August Pi Sunyer-Hospital Clinic, Barcelona, Spain
| | - Irina Malikova
- Pole de Neurosciences Cliniques, Service de Neurologie, Centre de Résonance Magnétique Biologique et Médicale, Centre Hospitalier Universitaire Timone, Aix Marseille Université, Marseille, France
| | - Elaine Roger
- Multiple Sclerosis Clinic, Centre Hospitalier de L'Universite de Montreal, Montreal, Canada
| | - R. Phillip Kinkel
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jamie McDonald
- Multiple Sclerosis Center, Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Emmanuelle Waubant
- Multiple Sclerosis Center, Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
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Mowry EM, Carey RF, Blasco MR, Pelletier J, Duquette P, Villoslada P, Malikova I, Roger E, Kinkel RP, McDonald J, Bacchetti P, Waubant E. Multiple sclerosis susceptibility genes: associations with relapse severity and recovery. PLoS One 2013; 8:e75416. [PMID: 24130709 PMCID: PMC3793991 DOI: 10.1371/journal.pone.0075416] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/12/2013] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Patients with early multiple sclerosis (MS) have stereotyped attack severity and recovery. We sought to determine if polymorphisms in MS susceptibility genes are associated with these attack features or with the risk of a second attack. METHODS 503 white subjects evaluated within a year of MS onset were included in the study. The severity of and recovery from the first two attacks were determined based on published definitions. Seventeen MS susceptibility genes were genotyped at the UCSF MS Genetics laboratory. Each polymorphism was evaluated in multivariate ordinal models, adjusted for the other polymorphisms, for its association with attack severity and recovery. We also assessed if these polymorphisms were associated with increased risk of a second attack. RESULTS The MPHOSPH9 polymorphism was associated with greater attack severity (odds ratios [OR] = 1.47, 95% CI [1.11, 1.94], p = 0.008), while the RGS1 and TNFRSF1A polymorphisms tended to be associated with reduced attack severity. The CD6 polymorphism tended to be associated with increased odds of worse attack recovery (OR = 1.25, 95% CI [0.93, 1.68], p = 0.13). In those who were HLA-DRB1-negative, the EVI5 polymorphism was associated with attacks of less severity; in HLA-DRB1 positive patients, EVI5 was associated with attacks of greater severity and worse recovery. The IL7R, TNFRSF1A, and GPC5 polymorphisms tended to be associated with having a second event within a year. CONCLUSIONS Some MS susceptibility polymorphisms may be associated with attack severity, recovery, or frequency. Further characterization of these genes may lead to a better understanding of MS pathogenesis and to a more individualized treatment approach.
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Affiliation(s)
- Ellen M Mowry
- Multiple Sclerosis Center, Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
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Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013; 14:661-73. [PMID: 23917628 DOI: 10.1038/nrg3502] [Citation(s) in RCA: 389] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Shared aetiopathogenic factors among immune-mediated diseases have long been suggested by their co-familiality and co-occurrence, and molecular support has been provided by analysis of human leukocyte antigen (HLA) haplotypes and genome-wide association studies. The interrelationships can now be better appreciated following the genotyping of large immune disease sample sets on a shared SNP array: the 'Immunochip'. Here, we systematically analyse loci shared among major immune-mediated diseases. This reveals that several diseases share multiple susceptibility loci, but there are many nuances. The most associated variant at a given locus frequently differs and, even when shared, the same allele often has opposite associations. Interestingly, risk alleles conferring the largest effect sizes are usually disease-specific. These factors help to explain why early evidence of extensive 'sharing' is not always reflected in epidemiological overlap.
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Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat Genet 2013; 45:730-8. [PMID: 23749187 DOI: 10.1038/ng.2667] [Citation(s) in RCA: 610] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 05/15/2013] [Indexed: 02/07/2023]
Abstract
Ankylosing spondylitis is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. In addition to HLA-B*27 alleles, 12 loci have previously been identified that are associated with ankylosing spondylitis in populations of European ancestry, and 2 associated loci have been identified in Asians. In this study, we used the Illumina Immunochip microarray to perform a case-control association study involving 10,619 individuals with ankylosing spondylitis (cases) and 15,145 controls. We identified 13 new risk loci and 12 additional ankylosing spondylitis-associated haplotypes at 11 loci. Two ankylosing spondylitis-associated regions have now been identified encoding four aminopeptidases that are involved in peptide processing before major histocompatibility complex (MHC) class I presentation. Protective variants at two of these loci are associated both with reduced aminopeptidase function and with MHC class I cell surface expression.
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Goris A, Pauwels I, Dubois B. Progress in multiple sclerosis genetics. Curr Genomics 2013; 13:646-63. [PMID: 23730204 PMCID: PMC3492804 DOI: 10.2174/138920212803759695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 01/06/2023] Open
Abstract
A genetic component in the susceptibility to multiple sclerosis (MS) has long been known, and the first and major genetic risk factor, the HLA region, was identified in the 1970’s. However, only with the advent of genome-wide association studies in the past five years did the list of risk factors for MS grow from 1 to over 50. In this review, we summarize the search for MS risk genes and the latest results. Comparison with data from other autoimmune and neurological diseases and from animal models indicates parallels and differences between diseases. We discuss how these translate into an improved understanding of disease mechanisms, and address current challenges such as genotype-phenotype correlations, functional mechanisms of risk variants and the missing heritability.
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Affiliation(s)
- An Goris
- Laboratory for Neuroimmunology, Section of Experimental Neurology, KU Leuven, Leuven, Belgium
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Qiu W, Pham K, James I, Nolan D, Castley A, Christiansen FT, Czarniak P, Luo Y, Wu J, Garlepp M, Wilton S, Carroll WM, Mastaglia FL, Kermode AG. The influence of non-HLA gene polymorphisms and interactions on disease risk in a Western Australian multiple sclerosis cohort. J Neuroimmunol 2013; 261:92-7. [PMID: 23726763 DOI: 10.1016/j.jneuroim.2013.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 03/17/2013] [Accepted: 04/30/2013] [Indexed: 01/01/2023]
Abstract
Non-Human Leukocyte Antigen (HLA) genes have concomitant, although modest, effects on multiple sclerosis (MS) susceptibility; however findings have varied in different populations. Here we present the results of an association study of 16 single nucleotide polymorphisms (SNPs) in 10 non-HLA genes (IL7R, IL2RA, CLEC-16A, TYK2, CD58, IRF5, STAT3, CTLA-4, APOE, ICAM-1) in a Western Australian cohort of 350 MS patients and 498 population control subjects. Our results indicate that in this population, SNPs in IL7R, TYK2, IRF5 and APOE have modifying effects on MS susceptibility. We also found evidence of interactive protective effects between polymorphisms in the IL7R/CD58, CLEC-16A/CTLA-4, and TYK2/IRF5 genes, which in some instances are restricted within HLA- or gender-defined groups.
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Affiliation(s)
- Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Swaminathan B, Cuapio A, Alloza I, Matesanz F, Alcina A, García-Barcina M, Fedetz M, Fernández Ó, Lucas M, Órpez T, Pinto-Medel MJ, Otaegui D, Olascoaga J, Urcelay E, Ortiz MA, Arroyo R, Oksenberg JR, Antigüedad A, Tolosa E, Vandenbroeck K. Fine mapping and functional analysis of the multiple sclerosis risk gene CD6. PLoS One 2013; 8:e62376. [PMID: 23638056 PMCID: PMC3634811 DOI: 10.1371/journal.pone.0062376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 03/22/2013] [Indexed: 12/18/2022] Open
Abstract
CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2nd SRCR domain with susceptibility to MS (Pmax(T) permutation = 1×10−4). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. – CD4+ naïve cells, P = 0.0001; CD8+ naïve cells, P<0.0001; CD4+ and CD8+ central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4+ and CD8+ T cells.
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MESH Headings
- Adult
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation, T-Lymphocyte/chemistry
- Antigens, Differentiation, T-Lymphocyte/genetics
- Antigens, Differentiation, T-Lymphocyte/metabolism
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/metabolism
- Chromosome Mapping
- Cluster Analysis
- Cytokines/metabolism
- Female
- Gene Order
- Genetic Loci
- Genetic Predisposition to Disease
- Haplotypes
- Humans
- Linkage Disequilibrium
- Lymphocyte Activation/immunology
- Male
- Multiple Sclerosis/genetics
- Multiple Sclerosis/metabolism
- Polymorphism, Single Nucleotide
- Protein Interaction Domains and Motifs
- Spain
- White People/genetics
- Young Adult
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Affiliation(s)
- Bhairavi Swaminathan
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Angélica Cuapio
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Iraide Alloza
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fuencisla Matesanz
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Alcina
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Maria Fedetz
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Óscar Fernández
- Department of Neurology, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - Miguel Lucas
- Unidad de Esclerosis Múltiple, Hospital Virgen Macarena, Sevilla, Spain
| | - Teresa Órpez
- Research Laboratory, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - Mª Jesus Pinto-Medel
- Research Laboratory, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - David Otaegui
- Área de Neurociencias, Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
| | - Javier Olascoaga
- Servicio de Neurología, Unidad de Esclerosis Múltiple, Hospital Donostia, San Sebastián, Spain
| | - Elena Urcelay
- Immunology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Miguel A. Ortiz
- Immunology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Rafael Arroyo
- Multiple Sclerosis Unit, Neurology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Jorge R. Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | | | - Eva Tolosa
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Koen Vandenbroeck
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
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Identity-by-descent mapping to detect rare variants conferring susceptibility to multiple sclerosis. PLoS One 2013; 8:e56379. [PMID: 23472070 PMCID: PMC3589405 DOI: 10.1371/journal.pone.0056379] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/08/2013] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified around 60 common variants associated with multiple sclerosis (MS), but these loci only explain a fraction of the heritability of MS. Some missing heritability may be caused by rare variants that have been suggested to play an important role in the aetiology of complex diseases such as MS. However current genetic and statistical methods for detecting rare variants are expensive and time consuming. ‘Population-based linkage analysis’ (PBLA) or so called identity-by-descent (IBD) mapping is a novel way to detect rare variants in extant GWAS datasets. We employed BEAGLE fastIBD to search for rare MS variants utilising IBD mapping in a large GWAS dataset of 3,543 cases and 5,898 controls. We identified a genome-wide significant linkage signal on chromosome 19 (LOD = 4.65; p = 1.9×10−6). Network analysis of cases and controls sharing haplotypes on chromosome 19 further strengthened the association as there are more large networks of cases sharing haplotypes than controls. This linkage region includes a cluster of zinc finger genes of unknown function. Analysis of genome wide transcriptome data suggests that genes in this zinc finger cluster may be involved in very early developmental regulation of the CNS. Our study also indicates that BEAGLE fastIBD allowed identification of rare variants in large unrelated population with moderate computational intensity. Even with the development of whole-genome sequencing, IBD mapping still may be a promising way to narrow down the region of interest for sequencing priority.
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Impact of microbes on autoimmune diseases. Arch Immunol Ther Exp (Warsz) 2013; 61:175-86. [PMID: 23417246 DOI: 10.1007/s00005-013-0216-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 02/01/2013] [Indexed: 12/15/2022]
Abstract
Autoimmune and autoinflammatory diseases arise as a consequence of complex interactions of environmental factors with genetic traits. Although specific allelic variations cluster in predisposed individuals and promote the generation and/or expansion of autoreactive T and B lymphocytes, autoimmunity appears in various disease phenotypes and localizes to diverging tissues. Furthermore, the discovery that allelic variations within genes encoding components of the innate immune system drive self-reactive immune responses as well, led to the distinction of immune responses against host tissues into autoimmune and autoinflammatory diseases. In both categories of disorders, different pathogenic mechanisms and/or subsequent orders of tissue assaults may underlie the target cell specificity of the respective autoimmune attack. Furthermore, the transition from the initial tissue assault to the development of full-blown disease is likely driven by several factors. Thus, the development of specific forms of autoimmunity and autoinflammation reflects a multi-factorial process. The delineation of the specific factors involved in the pathogenic process is hampered by the fact that certain symptoms are assembled under the umbrella of a specific disease, although they might originate from diverging pathogenic pathways. These multi-factorial triggers and pathogenic pathways may also explain the inter-individual divergent courses and outcomes of diseases among humans. Here, we will discuss the impact of different environmental factors in general and microbial pathogens in particular on the regulation/expression of genes encoded within susceptibility alleles, and its consequences on subsequent autoimmune and/or autoinflammatory tissue damage utilizing primarily the chronic cholestatic liver disease primary biliary cirrhosis as model.
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Li Z, Gakovic M, Ragimbeau J, Eloranta ML, Rönnblom L, Michel F, Pellegrini S. Two rare disease-associated Tyk2 variants are catalytically impaired but signaling competent. THE JOURNAL OF IMMUNOLOGY 2013; 190:2335-44. [PMID: 23359498 DOI: 10.4049/jimmunol.1203118] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tyk2 belongs to the Janus protein tyrosine kinase family and is involved in signaling of immunoregulatory cytokines (type I and III IFNs, IL-6, IL-10, and IL-12 families) via its interaction with shared receptor subunits. Depending on the receptor complex, Tyk2 is coactivated with either Jak1 or Jak2, but a detailed molecular characterization of the interplay between the two enzymes is missing. In human populations, the Tyk2 gene presents high levels of genetic diversity with >100 nonsynonymous variants being detected. In this study, we characterized two rare Tyk2 variants, I684S and P1104A, which have been associated with susceptibility to autoimmune disease. Specifically, we measured their in vitro catalytic activity and their ability to mediate Stat activation in fibroblasts and genotyped B cell lines. Both variants were found to be catalytically impaired but rescued signaling in response to IFN-α/β, IL-6, and IL-10. These data, coupled with functional study of an engineered Jak1 P1084A, support a model of nonhierarchical activation of Janus kinases in which one catalytically competent Jak is sufficient for signaling provided that its partner behaves as proper scaffold, even if inactive. Through the analysis of IFN-α and IFN-γ signaling in cells with different Jak1 P1084A levels, we also illustrate a context in which a hypomorphic Jak can hamper signaling in a cytokine-specific manner. Given the multitude of Tyk2-activating cytokines, the cell context-dependent requirement for Tyk2 and the catalytic defect of the two disease-associated variants studied in this paper, we predict that these alleles are functionally significant in complex immune disorders.
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Affiliation(s)
- Zhi Li
- Unit of Cytokine Signaling, Institut Pasteur, Paris 75724, France
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43
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Harbo HF, Mero IL. From genes to characteristics of multiple sclerosis. Acta Neurol Scand 2012:76-83. [PMID: 23278661 DOI: 10.1111/ane.12027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2012] [Indexed: 02/03/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory, demyelinating heterogeneous disease of the central nervous system, probably caused by an interaction of common genetic and environmental factors. Much progress has been made through the last few years in genetic studies of MS, and a growing list of genetic risk factors is now available. Biobanking and large collaborations have been prerequisites for this research, and detailed genetic and molecular characterizations are underway, with hopes for to translating new knowledge about MS pathogenesis and characteristics of the disease to personalized, better treatment options for each patient with MS.
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Affiliation(s)
- H F Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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44
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Abstract
Multiple sclerosis (MS) is a disease in which genetic, environmental, and stochastic factors interact to trigger an inflammatory disease of the CNS that also has a neurodegenerative component. Over the past 3 years, progress in high-throughput technologies and analysis methods has synergized with the collaborative efforts of investigators studying MS genetics to enable the discovery of more than a dozen genes involved in making individuals susceptible to MS. These genes are beginning to suggest molecular pathways that may be particularly vulnerable to genetic variation in MS. Soon, a comprehensive map of common genetic variants affecting MS susceptibility will be assembled, and communal efforts will need to focus on the more challenging issue of understanding the genetic architecture of disease course and treatment response in MS. Early efforts integrating different dimensions of information, including genomics, imaging, transcriptomics, and proteomics, with precise phenotypic data from clinicians illustrate the way forward for prognostic algorithms in MS and suggest that these approaches will yield a new series of insights in the next decade.
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45
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Liu JZ, Almarri MA, Gaffney DJ, Mells GF, Jostins L, Cordell HJ, Ducker SJ, Day DB, Heneghan MA, Neuberger JM, Donaldson PT, Bathgate AJ, Burroughs A, Davies MH, Jones DE, Alexander GJ, Barrett JC, Sandford RN, Anderson CA. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat Genet 2012; 44:1137-41. [PMID: 22961000 PMCID: PMC3459817 DOI: 10.1038/ng.2395] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/09/2012] [Indexed: 12/12/2022]
Abstract
We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P<5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2>0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.
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Affiliation(s)
- Jimmy Z Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Peluso C, Christofolini DM, Goldman CS, Mafra FA, Cavalcanti V, Barbosa CP, Bianco B. TYK2 rs34536443 polymorphism is associated with a decreased susceptibility to endometriosis-related infertility. Hum Immunol 2012; 74:93-7. [PMID: 23000200 DOI: 10.1016/j.humimm.2012.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/23/2012] [Accepted: 09/10/2012] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Tyrosine kinase 2 gene (TYK2) is part of the janus kinase (JAK) that binds to the type I interferon-α receptor (IFNAR) on the cell surface of IFN-producing cells, and have crucial importance in the etiology of autoimmune and inflammatory diseases. Many polymorphisms of the TYK2 gene have been identified, and recently, a number of case-control studies were conducted to investigate the association of these polymorphisms with autoimmune and inflammatory diseases, with conflicting results. Based on these observations, we hypothesized that the TYK2 polymorphisms (rs34536443, rs2304256, rs280523, rs12720270 and rs12720356) might be involved in the pathogenesis of endometriosis and/or infertility. METHODS Genetic association study comprising 275 infertile women with endometriosis, 92 women with idiopathic infertility and 307 fertile women as controls. TYK2 polymorphisms were identified by TaqMan PCR. Genotype distribution, allele frequency and haplotype analysis of the TYK2 polymorphisms were performed. A p-value <0.05 was considered significant. RESULTS Single-marker analysis revealed that TYK2 rs34536443 was significantly associated with protection against endometriosis-related infertility, especially in moderate/severe disease (p = 0.002; OR = 0.24, 95% IC = 0.09-0.62). No difference was found considering the infertile group without endometriosis. No associations were found considering rs2304256, rs280523, rs12720270 and rs12720356 either for endometriosis-related infertility group or idiopathic infertility group. Haplotype analysis of five TYK2 polymorphisms identified a haplotype "CTATG" associated with protection against endometriosis-related infertility, especially in moderate/severe disease (p = 0.027). CONCLUSION This is the first study to report an association between TYK2 polymorphisms and endometriosis and/or infertility. These findings require replication in other populations but suggest the TYK2 rs34536443 polymorphisms and "CTATG" haplotype can be associated with a decreased susceptibility to endometriosis-related infertility in Brazilian women.
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Affiliation(s)
- Carla Peluso
- Human Reproduction and Genetics Center, Department of Gynecology and Obstetrics, Faculdade de Medicina do Santo Andre, Sao Bernardo do Campo and Sao Caetano do Sul County, Santo Andre, Brazil
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Dyment DA, Cader MZ, Chao MJ, Lincoln MR, Morrison KM, Disanto G, Morahan JM, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC, Ramagopalan SV. Exome sequencing identifies a novel multiple sclerosis susceptibility variant in the TYK2 gene. Neurology 2012; 79:406-11. [PMID: 22744673 DOI: 10.1212/wnl.0b013e3182616fc4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify rare variants contributing to multiple sclerosis (MS) susceptibility in a family we have previously reported with up to 15 individuals affected across 4 generations. METHODS We performed exome sequencing in a subset of affected individuals to identify novel variants contributing to MS risk within this unique family. The candidate variant was genotyped in a validation cohort of 2,104 MS trio families. RESULTS Four family members with MS were sequenced and 21,583 variants were found to be shared among these individuals. Refining the variants to those with 1) a predicted loss of function and 2) present within regions of modest haplotype sharing identified 1 novel mutation (rs55762744) in the tyrosine kinase 2 (TYK2) gene. A different polymorphism within this gene has been shown to be protective in genome-wide association studies. In contrast, the TYK2 variant identified here is a novel, missense mutation and was found to be present in 10/14 (72%) cases and 28/60 (47%) of the unaffected family members. Genotyping additional 2,104 trio families showed the variant to be transmitted preferentially from heterozygous parents (transmitted 16: not transmitted 5; χ(2) = 5.76, p = 0.016). CONCLUSIONS Rs55762744 is a rare variant of modest effect on MS risk affecting a subset of patients (0.8%). Within this pedigree, rs55762744 is common and appears to be a modifier of modest risk effect. Exome sequencing is a quick and cost-effective method and we show here the utility of sequencing a few cases from a single, unique family to identify a novel variant. The sequencing of additional family members or other families may help identify other variants important in MS.
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Affiliation(s)
- David A Dyment
- The Department of Medical Genetics, University of Ottawa, Ottawa, Canada
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The emerging role of IL-17 in the pathogenesis of psoriasis: preclinical and clinical findings. J Invest Dermatol 2012; 133:17-26. [PMID: 22673731 DOI: 10.1038/jid.2012.194] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although the histological changes seen in psoriasis have long been well characterized, the underlying cellular and molecular mechanisms have only begun to be elucidated over the past 20 years. Proinflammatory factors such as tumor necrosis factor (TNF)-α have a central role in psoriasis pathogenesis, and many T-helper 1 (Th1) cytokines and messenger RNAs are elevated in psoriatic lesions. IL-17A, IL-17F, and other Th17 cell-derived cytokines have been shown in murine models to induce features that mimic human psoriasis. This review focuses on the emerging biology of the IL-17 cytokine family in psoriasis, and on the molecular and genetic information gained from animal models and human clinical studies that confirm IL-17 as a crucial proinflammatory cytokine in psoriasis. Expression of IL-17A, IL-17C, and IL-17F is strikingly increased in psoriatic lesions, and successful therapy is associated with restoration of the expression of a wide range of genes (including effector molecules downstream of IL-17 such as cytokines, chemokines, and antimicrobial peptides) to near-normal levels. Therapeutic agents in development that target IL-17 are discussed, and an emerging model of the key role of IL-17 in the pathogenesis of psoriasis is presented.
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Zaritsky LA, Gama L, Clements JE. Canonical type I IFN signaling in simian immunodeficiency virus-infected macrophages is disrupted by astrocyte-secreted CCL2. THE JOURNAL OF IMMUNOLOGY 2012; 188:3876-85. [PMID: 22407919 DOI: 10.4049/jimmunol.1103024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
HIV-associated neurologic disorders are a mounting problem despite the advent of highly active antiretroviral therapy. To address mechanisms of HIV-associated neurologic disorders, we used an SIV pigtailed macaque model to study innate immune responses in brain that suppress viral replication during acute infection. We previously reported that during acute infection in brain, noncanonical type I IFN signaling occurs, where IFN-β mRNA is induced while IFN-α is simultaneously suppressed. Two downstream IFN-stimulated genes, MxA and TRAIL, also show differential expression patterns. In this study, we show that differential signaling is due to interactions between macrophages and astrocytes. Astrocytes produce high levels of CCL2 upon SIV infection, which binds to CCR2 receptors on macrophages, leading to a selective suppression of IFN-α and the IFN-stimulated gene TRAIL while simultaneously inducing IFN-β and MxA. The interactions between chemokine and cytokine pathways are a novel finding that may specifically occur in the CNS.
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Affiliation(s)
- Luna Alammar Zaritsky
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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50
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Lopez de Lapuente A, Alloza I, Goertsches R, Zettl UK, Urcelay E, Arroyo R, Comabella M, Montalban X, Antigüedad A, Vandenbroeck K. Analysis of the IL28RA locus as genetic risk factor for multiple sclerosis. J Neuroimmunol 2012; 245:98-101. [PMID: 22386267 DOI: 10.1016/j.jneuroim.2012.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/24/2012] [Accepted: 02/06/2012] [Indexed: 01/07/2023]
Abstract
Recently, we reported an association between a SNP in IL28RA and MS. Here, we performed a fine-mapping of the IL28RA locus by genotyping 10 haplotype-tagging SNPs in a Basque-Spanish population. In addition, based on shared genetic risk loci between autoimmune diseases, a psoriasis-associated SNP located at this locus, rs4649203, was genotyped in four independent populations, comprising a total of 2582 cases and 2614 controls. We did not find any consistent association between IL28RA and MS in these populations, suggesting that, although it may play a role in other autoimmune diseases, this gene is unlikely of general relevance to MS pathogenesis.
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