1
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Schetelig J, Heidenreich F, Baldauf H, Trost S, Falk B, Hoßbach C, Real R, Roers A, Lindemann D, Dalpke A, Kolditz M, de With K, Bornhäuser M, Bonifacio EE, Rücker-Braun E, Lange V, Markert J, Barth R, Hofmann JA, Sauter J, Bernas SN, Schmidt AH. Individual HLA-A, -B, -C, and -DRB1 Genotypes Are No Major Factors Which Determine COVID-19 Severity. Front Immunol 2021; 12:698193. [PMID: 34381451 PMCID: PMC8350391 DOI: 10.3389/fimmu.2021.698193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/02/2021] [Indexed: 01/02/2023] Open
Abstract
HLA molecules are key restrictive elements to present intracellular antigens at the crossroads of an effective T-cell response against SARS-CoV-2. To determine the impact of the HLA genotype on the severity of SARS-CoV-2 courses, we investigated data from 6,919 infected individuals. HLA-A, -B, and -DRB1 allotypes grouped into HLA supertypes by functional or predicted structural similarities of the peptide-binding grooves did not predict COVID-19 severity. Further, we did not observe a heterozygote advantage or a benefit from HLA diplotypes with more divergent physicochemical peptide-binding properties. Finally, numbers of in silico predicted viral T-cell epitopes did not correlate with the severity of SARS-CoV-2 infections. These findings suggest that the HLA genotype is no major factor determining COVID-19 severity. Moreover, our data suggest that the spike glycoprotein alone may allow for abundant T-cell epitopes to mount robust T-cell responses not limited by the HLA genotype.
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Affiliation(s)
- Johannes Schetelig
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | - Falk Heidenreich
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | | | - Sarah Trost
- Clinical Trials Unit, DKMS, Dresden, Germany
| | - Bose Falk
- Clinical Trials Unit, DKMS, Dresden, Germany
| | | | - Ruben Real
- Clinical Trials Unit, DKMS, Dresden, Germany
| | - Axel Roers
- Institute for Immunology, TU Dresden, Dresden, Germany
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Kolditz
- Division of Pulmonology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katja de With
- Division of Infectious Diseases, TU Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | - Ezio E Bonifacio
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
| | - Elke Rücker-Braun
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | | | - Jan Markert
- DKMS, Stem Cell Donor Registry, Tübingen, Germany
| | - Ralf Barth
- DKMS, Stem Cell Donor Registry, Tübingen, Germany
| | | | | | | | - Alexander H Schmidt
- Clinical Trials Unit, DKMS, Dresden, Germany.,DKMS Life Science Lab, Dresden, Germany.,DKMS, Stem Cell Donor Registry, Tübingen, Germany
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2
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Immel A, Pierini F, Rinne C, Meadows J, Barquera R, Szolek A, Susat J, Böhme L, Dose J, Bonczarowska J, Drummer C, Fuchs K, Ellinghaus D, Kässens JC, Furholt M, Kohlbacher O, Schade-Lindig S, Franke A, Schreiber S, Krause J, Müller J, Lenz TL, Nebel A, Krause-Kyora B. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Commun Biol 2021; 4:113. [PMID: 33495542 PMCID: PMC7835224 DOI: 10.1038/s42003-020-01627-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/20/2020] [Indexed: 02/08/2023] Open
Abstract
The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections. Alexander Immel et al. performed genome-wide analyses of 42 individuals from a collective burial in Niedertiefenbach, Germany from the Wartberg Culture. The authors find that this population had a large hunter-gatherer ancestry component and a distinct HLA pool, which indicates immune defenses against viral pathogens.
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Affiliation(s)
- Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - John Meadows
- Leibniz Laboratory for AMS Dating and Isotope Research, Kiel University, Max-Eyth-Strasse 11-13, 24118, Kiel, Germany.,Centre for Baltic and Scandinavian Archaeology (ZBSA), Schloss Gottorf, 24837, Schleswig, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Lisa Böhme
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Joanna Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Clara Drummer
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Katharina Fuchs
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Jan Christian Kässens
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Martin Furholt
- Department of Archaeology, Conservation and History, University of Oslo, Blindernveien 11, 0371, Oslo, Norway
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Strasse 9, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Sabine Schade-Lindig
- Landesamt für Denkmalpflege Hessen, hessenARCHÄOLOGIE, Schloss Biebrich, 65203, Wiesbaden, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.,Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - Johannes Müller
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.
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3
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Debebe BJ, Boelen L, Lee JC, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B. Identifying the immune interactions underlying HLA class I disease associations. eLife 2020; 9:54558. [PMID: 32238263 PMCID: PMC7253178 DOI: 10.7554/elife.54558] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.
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Affiliation(s)
- Bisrat J Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - James C Lee
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
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- Johns Hopkins University, Baltimore, United States.,Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chloe L Thio
- Johns Hopkins University, Baltimore, United States
| | | | - Gregory Kirk
- Johns Hopkins University, Baltimore, United States
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, United States
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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4
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Dewi SK, Ali S, Prasasty VD. Broad Spectrum Peptide Vaccine Design Against Hepatitis C Virus. Curr Comput Aided Drug Des 2019; 15:120-135. [PMID: 30280672 DOI: 10.2174/1573409914666181003151222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 08/12/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a global burden. There is no peptide vaccine found as modality to cure the disease is available due to the weak cellular immune response and the limitation to induce humoral immune response. METHODS Five predominated HCV subtypes in Indonesia (1a, 1b, 1c, 3a, and 3k) were aligned and the conserved regions were selected. Twenty alleles of class I MHC including HLA-A, HLA-B, and HLAC types were used to predict the potential epitopes by using NetMHCPan and IEDB. Eight alleles of HLA-DRB1, together with a combination of 3 alleles of HLA-DQA1 and 5 alleles of HLA-DQB1 were utilized for Class II MHC epitopes prediction using NetMHCIIPan and IEDB. LBtope and Ig- Pred were used to predict B cells epitopes. Moreover, proteasome analysis was performed by NetCTL and the stability of the epitopes in HLA was calculated using NetMHCStabPan for Class I. All predicted epitopes were analyzed for its antigenicity, toxicity, and stability. Population coverage, molecular docking and molecular dynamics were performed for several best epitopes. RESULTS The results showed that two best epitopes from envelop protein, GHRMAWDMMMNWSP (E1) and PALSTGLIHLHQN (E2) were selected as promising B cell and CD8+ T cell inducers. Other two peptides, LGIGTVLDQAETAG and VLVLNPSVAATLGF, taken from NS3 protein were selected as CD4+ T cell inducer. CONCLUSION This study suggested the utilization of all four peptides to make a combinational peptide vaccine for in vivo study to prove its ability in inducing secondary response toward HCV.
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Affiliation(s)
- Sherly Kurnia Dewi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Soegianto Ali
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia.,Faculty of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
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5
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Huang H, Duggal P, Thio CL, Latanich R, Goedert JJ, Mangia A, Cox AL, Kirk GD, Mehta S, Aneja J, Alric L, Donfield SM, Cramp ME, Khakoo SI, Tobler LH, Busch M, Alexander GJ, Rosen HR, Edlin BR, Segal FP, Lauer GM, Thomas DL, Daly MJ, Chung RT, Kim AY. Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection. Sci Rep 2017; 7:15843. [PMID: 29158528 PMCID: PMC5696522 DOI: 10.1038/s41598-017-16011-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022] Open
Abstract
Approximately three quarters of acute hepatitis C (HCV) infections evolve to a chronic state, while one quarter are spontaneously cleared. Genetic predispositions strongly contribute to the development of chronicity. We have conducted a genome-wide association study to identify genomic variants underlying HCV spontaneous clearance using ImmunoChip in European and African ancestries. We confirmed two previously reported significant associations, in the IL28B/IFNL4 and the major histocompatibility complex (MHC) regions, with spontaneous clearance in the European population. We further fine-mapped the association in the MHC to a region of about 50 kilo base pairs, down from 1 mega base pairs in the previous study. Additional analyses suggested that the association in MHC is stronger in samples from North America than those from Europe.
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Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Priya Duggal
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Chloe L Thio
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rachel Latanich
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20852, USA
| | - Alessandra Mangia
- IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Andrea L Cox
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gregory D Kirk
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shruti Mehta
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jasneet Aneja
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Laurent Alric
- Department of Medicine, Purpan Hospital, University of Toulouse III, Toulouse, France
| | | | - Matthew E Cramp
- South West Liver Unit, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Salim I Khakoo
- Henry Welcome Laboratories, Southampton General Hospital, Southampton, UK
| | - Leslie H Tobler
- University of California and Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Michael Busch
- University of California and Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Graeme J Alexander
- Cambridge University Hospitals NHS Foundation Trust and Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Hugo R Rosen
- University of Colorado, Aurora, Colorado, 90045, United States
| | - Brian R Edlin
- State University of New York Downstate College of Medicine, Brooklyn, New York, USA
| | - Florencia P Segal
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Georg M Lauer
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - David L Thomas
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Raymond T Chung
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| | - Arthur Y Kim
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
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6
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Sankar S, Ramamurthy M, Nandagopal B, Sridharan G. Short peptide epitope design from hantaviruses causing HFRS. Bioinformation 2017; 13:231-236. [PMID: 28943728 PMCID: PMC5602290 DOI: 10.6026/97320630013231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/15/2022] Open
Abstract
Several genotypes of the hantavirus cause hemorrhagic fever with renal syndrome (HFRS) and is an important public health problem
worldwide. There is now growing interest to develop subunit vaccines especially focused to elicit cytotoxic T lymphocyte responses
which are important against viral infection. We identified candidate T-cell epitopes that bind to Class I HLA supertypes towards
identifying potential subunit vaccine entity. These epitopes are conserved in all 5 hantavirus genotypes of HFRS (Hantaan, Dobrava-
Belgrade, Seoul, Gou virus and Amur). The epitopes identified from S and M segment genomes were analyzed for human proteasome
cleavage, transporter associated antigen processing (TAP) efficiency and antigenicity using bioinformatic approaches. The epitope
MRNTIMASK which had the two characteristics of high proteasomal cleavage score and TAP score, also had high antigenicity score.
Our results indicate that this epitope from the nucleocapsid protein may be considered the most favorable moiety for the development
of subunit peptide vaccine.
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Affiliation(s)
- Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Mageshbabu Ramamurthy
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
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7
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Association of Genotype and Haplotype of IL-28B Gene with Hepatitis C Infection Outcome in Iran: Spontaneous Clearance Versus Chronic Infection. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.45745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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8
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Lazaryan A, Wang T, Spellman SR, Wang HL, Pidala J, Nishihori T, Askar M, Olsson R, Oudshoorn M, Abdel-Azim H, Yong A, Gandhi M, Dandoy C, Savani B, Hale G, Page K, Bitan M, Reshef R, Drobyski W, Marsh SG, Schultz K, Müller CR, Fernandez-Viña MA, Verneris MR, Horowitz MM, Arora M, Weisdorf DJ, Lee SJ. Human leukocyte antigen supertype matching after myeloablative hematopoietic cell transplantation with 7/8 matched unrelated donor allografts: a report from the Center for International Blood and Marrow Transplant Research. Haematologica 2016; 101:1267-1274. [PMID: 27247320 DOI: 10.3324/haematol.2016.143271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
The diversity of the human leukocyte antigen (HLA) class I and II alleles can be simplified by consolidating them into fewer supertypes based on functional or predicted structural similarities in epitope-binding grooves of HLA molecules. We studied the impact of matched and mismatched HLA-A (265 versus 429), -B (230 versus 92), -C (365 versus 349), and -DRB1 (153 versus 51) supertypes on clinical outcomes of 1934 patients with acute leukemias or myelodysplasia/myeloproliferative disorders. All patients were reported to the Center for International Blood and Marrow Transplant Research following single-allele mismatched unrelated donor myeloablative conditioning hematopoietic cell transplantation. Single mismatched alleles were categorized into six HLA-A (A01, A01A03, A01A24, A02, A03, A24), six HLA-B (B07, B08, B27, B44, B58, B62), two HLA-C (C1, C2), and five HLA-DRB1 (DR1, DR3, DR4, DR5, DR9) supertypes. Supertype B mismatch was associated with increased risk of grade II-IV acute graft-versus-host disease (hazard ratio =1.78, P=0.0025) compared to supertype B match. Supertype B07-B44 mismatch was associated with a higher incidence of both grade II-IV (hazard ratio=3.11, P=0.002) and III-IV (hazard ratio=3.15, P=0.01) acute graft-versus-host disease. No significant associations were detected between supertype-matched versus -mismatched groups at other HLA loci. These data suggest that avoiding HLA-B supertype mismatches can mitigate the risk of grade II-IV acute graft-versus-host disease in 7/8-mismatched unrelated donor hematopoietic cell transplantation when multiple HLA-B supertype-matched donors are available. Future studies are needed to define the mechanisms by which supertype mismatching affects outcomes after alternative donor hematopoietic cell transplantation.
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Affiliation(s)
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Hai-Lin Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Joseph Pidala
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Taiga Nishihori
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | - Richard Olsson
- Karolinska University Hospital, Centre for Allogeneic Stem Cell Transplantation, Stockholm, Sweden
| | | | | | - Agnes Yong
- Royal Adelaide Hospital/SA Pathology, Australia
| | | | | | - Bipin Savani
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gregory Hale
- All Children's Hospital, St. Petersburg, FL, USA
| | - Kristin Page
- Duke University Medical Center, Pediatric Blood and Marrow Transplant, Durham, NC, USA
| | | | - Ran Reshef
- Columbia University Medical Center, New York, NY, USA
| | | | - Steven Ge Marsh
- Anthony Nolan Research Institute & University College London Cancer Institute, Royal Free Campus, UK
| | - Kirk Schultz
- British Columbia's Children's Hospital, Vancouver, British Columbia, Canada
| | | | | | | | - Mary M Horowitz
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Mukta Arora
- University of Minnesota Medical Center, Fairview, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- University of Minnesota Medical Center, Fairview, Minneapolis, MN, USA
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9
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Dos Santos Francisco R, Buhler S, Nunes JM, Bitarello BD, França GS, Meyer D, Sanchez-Mazas A. HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms. Immunogenetics 2015; 67:651-63. [PMID: 26459025 PMCID: PMC4636516 DOI: 10.1007/s00251-015-0875-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/29/2015] [Indexed: 01/03/2023]
Abstract
Supertypes are groups of human leukocyte antigen (HLA) alleles which bind overlapping sets of peptides due to sharing specific residues at the anchor positions-the B and F pockets-of the peptide-binding region (PBR). HLA alleles within the same supertype are expected to be functionally similar, while those from different supertypes are expected to be functionally distinct, presenting different sets of peptides. In this study, we applied the supertype classification to the HLA-A and HLA-B data of 55 worldwide populations in order to investigate the effect of natural selection on supertype rather than allelic variation at these loci. We compared the nucleotide diversity of the B and F pockets with that of the other PBR regions through a resampling procedure and compared the patterns of within-population heterozygosity (He) and between-population differentiation (G ST) observed when using the supertype definition to those estimated when using randomized groups of alleles. At HLA-A, low levels of variation are observed at B and F pockets and randomized He and G ST do not differ from the observed data. By contrast, HLA-B concentrates most of the differences between supertypes, the B pocket showing a particularly high level of variation. Moreover, at HLA-B, the reassignment of alleles into random groups does not reproduce the patterns of population differentiation observed with supertypes. We thus conclude that differently from HLA-A, for which supertype and allelic variation show similar patterns of nucleotide diversity within and between populations, HLA-B has likely evolved through specific adaptations of its B pocket to local pathogens.
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Affiliation(s)
- Rodrigo Dos Santos Francisco
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. .,Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Hospital Israelita Albert Einstein, São Paulo, Brazil.
| | - Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | | | - Gustavo Starvaggi França
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, Brazil.,Molecular Oncology Center, Sírio-Libanês Hospital, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil.
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.
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10
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Sarvari J, Moattari A, Pirbonyeh N, Moini M, Hosseini SY. The Impact of IFN-γ Gene Polymorphisms on Spontaneous Clearance of HCV Infection in Fars Province, Southern of Iran. J Clin Lab Anal 2015; 30:301-7. [PMID: 25990657 DOI: 10.1002/jcla.21855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 04/08/2015] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Certain polymorphisms in cytokine genes such as IFN-γ may influence the outcome of hepatitis C virus (HCV) infection. Here the frequency of the genotype, allele, and haplotype of IFN-γ gene at some loci is investigated in HCV-infected patients. METHODS Totally 255 patients with chronic HCV infection and 44 spontaneously cleared individuals were included. The chronic or clearance states were confirmed using enzyme-linked immunosorbent assay (ELISA) and two different qualitative reverse transcriptase polymerase chain reaction (RT-PCR) techniques. IFN-γ gene polymorphisms were performed by PCR using sequence-specific primers and PCR-RLFP on extracted genomic DNA. RESULTS The frequency of GG genotype (P = 0.0001, OR: 5.69 and CI: 2.21-14.62) and allele (P = 0.0003, OR: 2.73 and CI: 1.54-4.83) of IFN-γ gene at +2109 locus was significantly higher in cases that spontaneously cleared the infection. Haplotype analysis showed the association of AG haplotype (P = 0.0046, OR = 6.14 and CI = 1.56-25) with spontaneous clearance of the infection. CONCLUSION Our finding indicated that individuals with GG genotype at +2109 loci of IFN-γ gene and also AG haplotype (A allele at +874 loci and G allele at +2109 loci) may clear HCV infection more frequently than those with AA and AG genotype at +2109 loci and AA, TA, and TG haplotype.
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Affiliation(s)
- Jamal Sarvari
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Moini
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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