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Wang T, Navenot JM, Rafail S, Kurtis C, Carroll M, Van Kerckhoven M, Van Rossom S, Schats K, Avraam K, Broad R, Howe K, Liddle A, Clayton A, Wang R, Quinn L, Sanderson JP, McAlpine C, Carozza C, Pimpinella E, Hsu S, Brophy F, Elefant E, Bayer P, Williams D, Butler MO, Clarke JM, Gainor JF, Govindan R, Moreno V, Johnson M, Tu J, Hong DS, Blumenschein GR. Identifying MAGE-A4-positive tumors for TCR T cell therapies in HLA-A∗02-eligible patients. Mol Ther Methods Clin Dev 2024; 32:101265. [PMID: 38872830 PMCID: PMC11170170 DOI: 10.1016/j.omtm.2024.101265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
T cell receptor (TCR) T cell therapies target tumor antigens in a human leukocyte antigen (HLA)-restricted manner. Biomarker-defined therapies require validation of assays suitable for determination of patient eligibility. For clinical trials evaluating TCR T cell therapies targeting melanoma-associated antigen A4 (MAGE-A4), screening in studies NCT02636855 and NCT04044768 assesses patient eligibility based on: (1) high-resolution HLA typing and (2) tumor MAGE-A4 testing via an immunohistochemical assay in HLA-eligible patients. The HLA/MAGE-A4 assays validation, biomarker data, and their relationship to covariates (demographics, cancer type, histopathology, tissue location) are reported here. HLA-A∗02 eligibility was 44.8% (2,959/6,606) in patients from 43 sites across North America and Europe. While HLA-A∗02:01 was the most frequent HLA-A∗02 allele, others (A∗02:02, A∗02:03, A∗02:06) considerably increased HLA eligibility in Hispanic, Black, and Asian populations. Overall, MAGE-A4 prevalence based on clinical trial enrollment was 26% (447/1,750) across 10 solid tumor types, and was highest in synovial sarcoma (70%) and lowest in gastric cancer (9%). The covariates were generally not associated with MAGE-A4 expression, except for patient age in ovarian cancer and histology in non-small cell lung cancer. This report shows the eligibility rate from biomarker screening for TCR T cell therapies and provides epidemiological data for future clinical development of MAGE-A4-targeted therapies.
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Affiliation(s)
- Tianjiao Wang
- Clinical Biomarkers & Companion Diagnostics, Adaptimmune, Philadelphia, PA, USA
| | - Jean-Marc Navenot
- Clinical Biomarkers & Companion Diagnostics, Adaptimmune, Philadelphia, PA, USA
| | - Stavros Rafail
- Biomarker Discovery and Platform, Adaptimmune, Philadelphia, PA, USA
| | - Cynthia Kurtis
- Clinical Biomarkers & Companion Diagnostics, Adaptimmune, Philadelphia, PA, USA
| | - Mark Carroll
- Information Management Clinical Systems, Adaptimmune, Philadelphia, PA, USA
| | | | | | - Kelly Schats
- Assay Development Histopathology, CellCarta, Antwerpen, Belgium
| | | | - Robyn Broad
- Translational Sciences, Adaptimmune, Abingdon, Oxfordshire, UK
| | - Karen Howe
- Target Validation, Adaptimmune, Abingdon, Oxfordshire, UK
| | - Ashley Liddle
- Translational Sciences, Adaptimmune, Abingdon, Oxfordshire, UK
| | - Amber Clayton
- Target Validation, Adaptimmune, Abingdon, Oxfordshire, UK
| | - Ruoxi Wang
- Information Management Clinical Systems, Adaptimmune, Philadelphia, PA, USA
| | - Laura Quinn
- Preclinical Research, Adaptimmune, Abingdon, Oxfordshire, UK
| | | | - Cheryl McAlpine
- Translational Sciences, Adaptimmune, Abingdon, Oxfordshire, UK
| | - Carly Carozza
- Histocompatibility Laboratory Services, American Red Cross, Philadelphia, PA, USA
| | - Eric Pimpinella
- Histocompatibility Laboratory Services, American Red Cross, Philadelphia, PA, USA
| | - Susan Hsu
- Histocompatibility Laboratory Services, American Red Cross, Philadelphia, PA, USA
| | | | - Erica Elefant
- Clinical Science, Adaptimmune, Philadelphia, PA, USA
| | - Paige Bayer
- Clinical Science, Adaptimmune, Philadelphia, PA, USA
| | | | - Marcus O. Butler
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Departments of Immunology and Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Justin F. Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Victor Moreno
- Oncology, START Madrid FJD, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Melissa Johnson
- Lung Cancer Research and Drug Development, Sarah Cannon Research Institute, Nashville, TN, USA
| | - Janet Tu
- Department of General Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David S. Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George R. Blumenschein
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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2
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Sanchez-Mazas A, Nunes JM. The most frequent HLA alleles around the world: A fundamental synopsis. Best Pract Res Clin Haematol 2024; 37:101559. [PMID: 39098805 DOI: 10.1016/j.beha.2024.101559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024]
Abstract
A comprehensive knowledge of human leukocyte antigen (HLA) molecular variation worldwide is essential in human population genetics research and disease association studies and is also indispensable for clinical applications such as allogeneic hematopoietic cell transplantation, where ensuring HLA compatibility between donors and recipients is paramount. Enormous progress has been made in this field thanks to several decades of HLA population studies allowing the development of helpful databases and bioinformatics tools. However, it is still difficult to appraise the global HLA population diversity in a synthetic way. We thus introduce here a novel approach, based on approximately 2000 data sets, to assess this complexity by providing a fundamental synopsis of the most frequent HLA alleles observed in different regions of the world. This new knowledge will be useful not only as a fundamental reference for basic research, but also as an efficient guide for clinicians working in the field of transplantation.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution & Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland.
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution & Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland.
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3
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Sugio T, Uchida N, Miyawaki K, Ohno Y, Eto T, Mori Y, Yoshimoto G, Kikushige Y, Kunisaki Y, Mizuno S, Nagafuji K, Iwasaki H, Kamimura T, Ogawa R, Miyamoto T, Taniguchi S, Akashi K, Kato K. Prognostic impact of HLA supertype mismatch in single-unit cord blood transplantation. Bone Marrow Transplant 2024; 59:466-472. [PMID: 38238452 DOI: 10.1038/s41409-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 04/06/2024]
Abstract
The "human leukocyte antigen (HLA) supertype" is a functional classification of HLA alleles, which was defined by structural features and peptide specificities, and has been reportedly associated with the clinical outcomes of viral infections and autoimmune diseases. Although the disparity in each HLA locus was reported to have no clinical significance in single-unit cord blood transplantation (sCBT), the clinical significance of the HLA supertype in sCBT remains unknown. Therefore, we retrospectively analyzed clinical data of 1603 patients who received sCBT in eight institutes in Japan between 2000 and 2017. Each HLA allele was categorized into 19 supertypes, and the prognostic effect of disparities was then assessed. An HLA-B supertype mismatch was identified as a poor prognostic factor (PFS: hazard ratio [HR] = 1.23, p = 0.00044) and was associated with a higher cumulative incidence (CI) of relapse (HR = 1.24, p = 0.013). However, an HLA-B supertype mismatch was not associated with the CI of acute and chronic graft-versus-host-disease. The multivariate analysis for relapse and PFS showed the significance of an HLA-B supertype mismatch independent of allelic mismatches, and other previously reported prognostic factors. HLA-B supertype-matched grafts should be selected in sCBT.
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Affiliation(s)
- Takeshi Sugio
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuju Ohno
- Department of Hematology, Kitakyushu Municipal Medical Center, Fukuoka, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Yasuo Mori
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Goichi Yoshimoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuya Kunisaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinichi Mizuno
- Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Nagafuji
- Department of Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Hiromi Iwasaki
- Department of Hematology, National Hospital Organization Kyushu Medical Center, Fukuoka, Japan
| | | | - Ryosuke Ogawa
- Department of Hematology, JCHO Kyushu Hospital, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Hematology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
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4
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Zimmermann C, Watson GM, Bauersfeld L, Berry R, Ciblis B, Lan H, Gerke C, Oberhardt V, Fuchs J, Hofmann M, Freund C, Rossjohn J, Momburg F, Hengel H, Halenius A. Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids. Proc Natl Acad Sci U S A 2024; 121:e2315985121. [PMID: 38377192 PMCID: PMC10907249 DOI: 10.1073/pnas.2315985121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Recurrent, ancient arms races between viruses and hosts have shaped both host immunological defense strategies as well as viral countermeasures. One such battle is waged by the glycoprotein US11 encoded by the persisting human cytomegalovirus. US11 mediates degradation of major histocompatibility class I (MHC-I) molecules to prevent CD8+ T-cell activation. Here, we studied the consequences of the arms race between US11 and primate MHC-A proteins, leading us to uncover a tit-for-tat coevolution and its impact on MHC-A diversification. We found that US11 spurred MHC-A adaptation to evade viral antagonism: In an ancestor of great apes, the MHC-A A2 lineage acquired a Pro184Ala mutation, which confers resistance against the ancestral US11 targeting strategy. In response, US11 deployed a unique low-complexity region (LCR), which exploits the MHC-I peptide loading complex to target the MHC-A2 peptide-binding groove. In addition, the global spread of the human HLA-A*02 allelic family prompted US11 to employ a superior LCR strategy with an optimally fitting peptide mimetic that specifically antagonizes HLA-A*02. Thus, despite cytomegaloviruses low pathogenic potential, the increasing commitment of US11 to MHC-A has significantly promoted diversification of MHC-A in hominids.
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Affiliation(s)
- Cosima Zimmermann
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Gabrielle M. Watson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Liane Bauersfeld
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Barbara Ciblis
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Huan Lan
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Carolin Gerke
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Valerie Oberhardt
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, 69120Heidelberg, Germany
| | - Hartmut Hengel
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Anne Halenius
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
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5
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Buckley PR, Lee CH, Antanaviciute A, Simmons A, Koohy H. A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses. IMMUNOTHERAPY ADVANCES 2023; 3:ltad005. [PMID: 37082106 PMCID: PMC10112682 DOI: 10.1093/immadv/ltad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
T cell recognition of SARS-CoV-2 antigens after vaccination and/or natural infection has played a central role in resolving SARS-CoV-2 infections and generating adaptive immune memory. However, the clinical impact of SARS-CoV-2-specific T cell responses is variable and the mechanisms underlying T cell interaction with target antigens are not fully understood. This is especially true given the virus' rapid evolution, which leads to new variants with immune escape capacity. In this study, we used the Omicron variant as a model organism and took a systems approach to evaluate the impact of mutations on CD8+ T cell immunogenicity. We computed an immunogenicity potential score for each SARS-CoV-2 peptide antigen from the ancestral strain and Omicron, capturing both antigen presentation and T cell recognition probabilities. By comparing ancestral vs. Omicron immunogenicity scores, we reveal a divergent and heterogeneous landscape of impact for CD8+ T cell recognition of mutated targets in Omicron variants. While T cell recognition of Omicron peptides is broadly preserved, we observed mutated peptides with deteriorated immunogenicity that may assist breakthrough infection in some individuals. We then combined our scoring scheme with an in silico mutagenesis, to characterise the position- and residue-specific theoretical mutational impact on immunogenicity. While we predict many escape trajectories from the theoretical landscape of substitutions, our study suggests that Omicron mutations in T cell epitopes did not develop under cell-mediated pressure. Our study provides a generalisable platform for fostering a deeper understanding of existing and novel variant impact on antigen-specific vaccine- and/or infection-induced T cell immunity.
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Affiliation(s)
- Paul R Buckley
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Chloe H Lee
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Alan Turing Fellow in Health and Medicine
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6
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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7
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The Use of Molecular Dynamics Simulation Method to Quantitatively Evaluate the Affinity between HBV Antigen T Cell Epitope Peptides and HLA-A Molecules. Int J Mol Sci 2022; 23:ijms23094629. [PMID: 35563019 PMCID: PMC9105472 DOI: 10.3390/ijms23094629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 12/10/2022] Open
Abstract
Chronic hepatitis B virus (HBV), a potentially life-threatening liver disease, makes people vulnerable to serious diseases such as cancer. T lymphocytes play a crucial role in clearing HBV virus, while the pathway depends on the strong binding of T cell epitope peptide and HLA. However, the experimental identification of HLA-restricted HBV antigenic peptides is extremely time-consuming. In this study, we provide a novel prediction strategy based on structure to assess the affinity between the HBV antigenic peptide and HLA molecule. We used residue scanning, peptide docking and molecular dynamics methods to obtain the molecular docking model of HBV peptide and HLA, and then adopted the MM-GBSA method to calculate the binding affinity of the HBV peptide–HLA complex. Overall, we collected 59 structures of HLA-A from Protein Data Bank, and finally obtained 352 numerical affinity results to figure out the optimal bind choice between the HLA-A molecules and 45 HBV T cell epitope peptides. The results were highly consistent with the qualitative affinity level determined by the competitive peptide binding assay, which confirmed that our affinity prediction process based on an HLA structure is accurate and also proved that the homologous modeling strategy for HLA-A molecules in this study was reliable. Hence, our work highlights an effective way by which to predict and screen for HLA-peptide binding that would improve the treatment of HBV infection.
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8
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Tang J, Li M, Zhao C, Shen D, Liu L, Zhang X, Wei L. Therapeutic DNA Vaccines against HPV-Related Malignancies: Promising Leads from Clinical Trials. Viruses 2022; 14:v14020239. [PMID: 35215833 PMCID: PMC8874761 DOI: 10.3390/v14020239] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/27/2023] Open
Abstract
In 2014 and 2021, two nucleic-acid vaccine candidates named MAV E2 and VGX-3100 completed phase III clinical trials in Mexico and U.S., respectively, for patients with human papillomavirus (HPV)-related, high-grade squamous intraepithelial lesions (HSIL). These well-tolerated but still unlicensed vaccines encode distinct HPV antigens (E2 versus E6+E7) to elicit cell-mediated immune responses; their clinical efficacy, as measured by HSIL regression or cure, was modest when compared with placebo or surgery (conization), but both proved highly effective in clearing HPV infection, which should help further optimize strategies for enhancing vaccine immunogenicity, toward an ultimate goal of preventing malignancies in millions of patients who are living with persistent, oncogenic HPV infection but are not expected to benefit from current, prophylactic vaccines. The major roadblocks to a highly efficacious and practical product remain challenging and can be classified into five categories: (i) getting the vaccines into the right cells for efficient expression and presentation of HPV antigens (fusion proteins or epitopes); (ii) having adequate coverage of oncogenic HPV types, beyond the current focus on HPV-16 and -18; (iii) directing immune protection to various epithelial niches, especially anogenital mucosa and upper aerodigestive tract where HPV-transformed cells wreak havoc; (iv) establishing the time window and vaccination regimen, including dosage, interval and even combination therapy, for achieving maximum efficacy; and (v) validating therapeutic efficacy in patients with poor prognosis because of advanced, recurrent or non-resectable malignancies. Overall, the room for improvements is still large enough that continuing efforts for research and development will very likely extend into the next decade.
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Affiliation(s)
- Jianming Tang
- Aeonvital Biomedical Research Institute, Beijing 102208, China; (L.L.); (X.Z.)
- Correspondence: or
| | - Mingzhu Li
- Department of Gynecology and Obstetrics, Peking University People’s Hospital, Beijing 100033, China; (M.L.); (C.Z.); (D.S.); (L.W.)
| | - Chao Zhao
- Department of Gynecology and Obstetrics, Peking University People’s Hospital, Beijing 100033, China; (M.L.); (C.Z.); (D.S.); (L.W.)
| | - Danhua Shen
- Department of Gynecology and Obstetrics, Peking University People’s Hospital, Beijing 100033, China; (M.L.); (C.Z.); (D.S.); (L.W.)
| | - Lei Liu
- Aeonvital Biomedical Research Institute, Beijing 102208, China; (L.L.); (X.Z.)
| | - Xiujun Zhang
- Aeonvital Biomedical Research Institute, Beijing 102208, China; (L.L.); (X.Z.)
| | - Lihui Wei
- Department of Gynecology and Obstetrics, Peking University People’s Hospital, Beijing 100033, China; (M.L.); (C.Z.); (D.S.); (L.W.)
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9
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Adaptive Immune Responses, Immune Escape and Immune-Mediated Pathogenesis during HDV Infection. Viruses 2022; 14:v14020198. [PMID: 35215790 PMCID: PMC8880046 DOI: 10.3390/v14020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/13/2022] Open
Abstract
The hepatitis delta virus (HDV) is the smallest known human virus, yet it causes great harm to patients co-infected with hepatitis B virus (HBV). As a satellite virus of HBV, HDV requires the surface antigen of HBV (HBsAg) for sufficient viral packaging and spread. The special circumstance of co-infection, albeit only one partner depends on the other, raises many virological, immunological, and pathophysiological questions. In the last years, breakthroughs were made in understanding the adaptive immune response, in particular, virus-specific CD4+ and CD8+ T cells, in self-limited versus persistent HBV/HDV co-infection. Indeed, the mechanisms of CD8+ T cell failure in persistent HBV/HDV co-infection include viral escape and T cell exhaustion, and mimic those in other persistent human viral infections, such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), and HBV mono-infection. However, compared to these larger viruses, the small HDV has perfectly adapted to evade recognition by CD8+ T cells restricted by common human leukocyte antigen (HLA) class I alleles. Furthermore, accelerated progression towards liver cirrhosis in persistent HBV/HDV co-infection was attributed to an increased immune-mediated pathology, either caused by innate pathways initiated by the interferon (IFN) system or triggered by misguided and dysfunctional T cells. These new insights into HDV-specific adaptive immunity will be discussed in this review and put into context with known well-described aspects in HBV, HCV, and HIV infections.
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10
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Reguzova A, Fischer N, Müller M, Salomon F, Jaenisch T, Amann R. A Novel Orf Virus D1701-VrV-Based Dengue Virus (DENV) Vaccine Candidate Expressing HLA-Specific T Cell Epitopes: A Proof-of-Concept Study. Biomedicines 2021; 9:biomedicines9121862. [PMID: 34944678 PMCID: PMC8698572 DOI: 10.3390/biomedicines9121862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/02/2022] Open
Abstract
Although dengue virus (DENV) affects almost half of the world’s population there are neither preventive treatments nor any long-lasting and protective vaccines available at this time. The complexity of the protective immune response to DENV is still not fully understood. The most advanced vaccine candidates focus specifically on humoral immune responses and the production of virus-neutralizing antibodies. However, results from several recent studies have revealed the protective role of T cells in the immune response to DENV. Hence, in this study, we generated a novel and potent DENV vaccine candidate based on an Orf virus (ORFV, genus Parapoxvirus) vector platform engineered to encode five highly conserved or cross-reactive DENV human leukocyte antigen (HLA)-A*02- or HLA-B*07-restricted epitopes as minigenes (ORFV-DENV). We showed that ORFV-DENV facilitates the in vitro priming of CD8+ T cells from healthy blood donors based on responses to each of the encoded immunogenic peptides. Moreover, we demonstrated that peripheral blood mononuclear cells isolated from clinically confirmed DENV-positive donors stimulated with ORFV-DENV generate cytotoxic T cell responses to at least three of the expressed DENV peptides. Finally, we showed that ORFV-DENV could activate CD8+ T cells isolated from donors who had recovered from Zika virus (ZIKV) infection. ZIKV belongs to the same virus family (Flaviviridae) and has epitope sequences that are homologous to those of DENV. We found that highly conserved HLA-B*07-restricted ZIKV and DENV epitopes induced functional CD8+ T cell responses in PBMCs isolated from confirmed ZIKV-positive donors. In summary, this proof-of-concept study characterizes a promising new ORFV D1701-VrV-based DENV vaccine candidate that induces broad and functional epitope-specific CD8+ T cell responses.
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Affiliation(s)
- Alena Reguzova
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Nico Fischer
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Melanie Müller
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Ferdinand Salomon
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Thomas Jaenisch
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Ralf Amann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
- Correspondence: ; Tel.: +49-707-1298-7614
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11
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [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: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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12
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Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
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Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
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13
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Di D, Nunes JM, Jiang W, Sanchez-Mazas A. Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules. Mol Biol Evol 2021; 38:1580-1594. [PMID: 33320202 PMCID: PMC8355449 DOI: 10.1093/molbev/msaa325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Jose Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
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14
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Özer O, Lenz TL. Unique pathogen peptidomes facilitate pathogen-specific selection and specialization of MHC alleles. Mol Biol Evol 2021; 38:4376-4387. [PMID: 34110412 PMCID: PMC8476153 DOI: 10.1093/molbev/msab176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.
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Affiliation(s)
- Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
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15
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Mulpuru V, Mishra N. Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2. Sci Rep 2021; 11:4516. [PMID: 33633155 PMCID: PMC7907102 DOI: 10.1038/s41598-021-83949-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/19/2021] [Indexed: 01/29/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has turned into a pandemic with about thirty million confirmed cases worldwide as of September 2020. Being an airborne infection, it can be catastrophic to populous countries like India. This study sets to identify potential cytotoxic T lymphocyte (CTL) epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate for the majority of the Indian population. The immunogenicity and the foreignness of the epitopes towards the human body have to be studied to further confirm their candidacy. The top-scoring epitopes were subjected to molecular docking studies to study their interactions with the corresponding human leukocyte antigen (HLA) system. The CTL epitopes were observed to bind at the peptide-binding groove of the corresponding HLA system, indicating their potency as an epitope candidate. The candidacy was further analyzed using sequence conservation studies and molecular dynamics simulation. The identified epitopes can be subjected to further studies for the development of the SARS-CoV-2 vaccine.
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Affiliation(s)
- Viswajit Mulpuru
- Department of Applied Science, Indian Institute of Information Technology Allahabad, Prayagraj, 211012, India
| | - Nidhi Mishra
- Department of Applied Science, Indian Institute of Information Technology Allahabad, Prayagraj, 211012, India.
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16
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Frequency analysis of HLA-B allele in leukemia patients from a North Indian population: A case-control study. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Esoh KK, Apinjoh TO, Nyanjom SG, Wonkam A, Chimusa ER, Amenga-Etego L, Amambua-Ngwa A, Achidi EA. Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection. Sci Rep 2021; 11:1039. [PMID: 33441574 PMCID: PMC7807043 DOI: 10.1038/s41598-020-79124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023] Open
Abstract
Inferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.
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Affiliation(s)
- Kevin K Esoh
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon.
| | - Steven G Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | | | - Eric A Achidi
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
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18
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He J, Huang F, Zhang J, Chen Q, Zheng Z, Zhou Q, Chen D, Li J, Chen J. Vaccine design based on 16 epitopes of SARS-CoV-2 spike protein. J Med Virol 2020; 93:2115-2131. [PMID: 33091154 PMCID: PMC7675516 DOI: 10.1002/jmv.26596] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/18/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) urgently requires an effective vaccine for prevention. In this study, 66 epitopes containing pentapeptides of SARS‐CoV‐2 spike protein in the IEDB database were compared with the amino acid sequence of SARS‐CoV‐2 spike protein, and 66 potentially immune‐related peptides of SARS‐CoV‐2 spike protein were obtained. Based on the single‐nucleotide polymorphisms analysis of spike protein of 1218 SARS‐CoV‐2 isolates, 52 easily mutated sites were identified and used for vaccine epitope screening. The best vaccine candidate epitopes in the 66 peptides of SARS‐CoV‐2 spike protein were screened out through mutation and immunoinformatics analysis. The best candidate epitopes were connected by different linkers in silico to obtain vaccine candidate sequences. The results showed that 16 epitopes were relatively conservative, immunological, nontoxic, and nonallergenic, could induce the secretion of cytokines, and were more likely to be exposed on the surface of the spike protein. They were both B‐ and T‐cell epitopes, and could recognize a certain number of HLA molecules and had high coverage rates in different populations. Moreover, epitopes 897‐913 were predicted to have possible cross‐immunoprotection for SARS‐CoV and SARS‐CoV‐2. The results of vaccine candidate sequences screening suggested that sequences (without linker, with linker GGGSGGG, EAAAK, GPGPG, and KK, respectively) were the best. The proteins translated by these sequences were relatively stable, with a high antigenic index and good biological activity. Our study provided vaccine candidate epitopes and sequences for the research of the SARS‐CoV‐2 vaccine.
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Affiliation(s)
- Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Fan Huang
- Department of First Surgical, Chengdu Shuangliu Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiwei Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
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19
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Camacho-Bydume C, Wang T, Sees JA, Fernandez-Viña M, Abid MB, Askar M, Beitinjaneh A, Brown V, Castillo P, Chhabra S, Gadalla SM, Hsu JM, Kamoun M, Lazaryan A, Nishihori T, Page K, Schetelig J, Fleischhauer K, Marsh SGE, Paczesny S, Spellman SR, Lee SJ, Hsu KC. Specific Class I HLA Supertypes but Not HLA Zygosity or Expression Are Associated with Outcomes following HLA-Matched Allogeneic Hematopoietic Cell Transplant: HLA Supertypes Impact Allogeneic HCT Outcomes. Transplant Cell Ther 2020; 27:142.e1-142.e11. [PMID: 33053450 DOI: 10.1016/j.bbmt.2020.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
Maximizing the probability of antigen presentation to T cells through diversity in HLAs can enhance immune responsiveness and translate into improved clinical outcomes, as evidenced by the association of heterozygosity and supertypes at HLA class I loci with improved survival in patients with advanced solid tumors treated with immune checkpoint inhibitors. We investigated the impact of HLA heterozygosity, supertypes, and surface expression on outcomes in adult and pediatric patients with acute myeloid leukemia (AML), myelodysplastic syndrome, acute lymphoblastic leukemia, and non-Hodgkin lymphoma who underwent 8/8 HLA-matched, T cell replete, unrelated, allogeneic hematopoietic cell transplant (HCT) from 2000 to 2015 using patient data reported to the Center for International Blood and Marrow Transplant Research. HLA class I heterozygosity and HLA expression were not associated with overall survival, relapse, transplant-related mortality (TRM), disease-free survival (DFS), and acute graft-versus-host disease following HCT. The HLA-B62 supertype was associated with decreased TRM in the entire patient cohort (hazard ratio [HR], 0.79; 95% CI, 0.69 to 0.90; P = .00053). The HLA-B27 supertype was associated with worse DFS in patients with AML (HR = 1.21; 95% CI, 1.10 to 1.32; P = .00005). These findings suggest that the survival benefit of HLA heterozygosity seen in solid tumor patients receiving immune checkpoint inhibitors does not extend to patients undergoing allogeneic HCT. Certain HLA supertypes, however, are associated with TRM and DFS, suggesting that similarities in peptide presentation between supertype members play a role in these outcomes. Beyond implications for prognosis following HCT, these findings support the further investigation of these HLA supertypes and the specific immune peptides important for transplant outcomes.
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Affiliation(s)
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Jennifer A Sees
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | | | - Muhammad Bilal Abid
- Divisions of Hematology/Oncology and Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, Texas
| | - Amer Beitinjaneh
- Department of Medicine, Division of Transplantation and Cellular Therapy, University of Miami, Miami, Florida
| | - Valerie Brown
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Penn State Hershey Children's Hospital and College of Medicine, Hershey, Pennsylvania
| | - Paul Castillo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Florida Health Shands Children's Hospital, Gainesville, FL
| | - Saurabh Chhabra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, Maryland
| | - Jing-Mei Hsu
- Division of Hematology/Oncology, Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine/New York Presbyterian Hospital, New York, NY
| | - Malek Kamoun
- Deparment of Pathology and Laboratory Medicine, Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Aleksandr Lazaryan
- Department of Blood and Marrow Transplant and Cellular Immunotherapy (BMT CI), Moffitt Cancer Center, Tampa, Florida
| | - Taiga Nishihori
- Department of Blood and Marrow Transplant and Cellular Immunotherapy (BMT CI), Moffitt Cancer Center, Tampa, Florida
| | - Kristin Page
- Division of Pediatric Blood and Marrow Transplantation, Duke University Medical Center, Durham, North Carolina
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, London, UK
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, WA
| | - Katharine C Hsu
- Department of Medicine, Adult Bone Marrow Transplantation Service, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York; Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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20
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Antunes DA, Abella JR, Hall-Swan S, Devaurs D, Conev A, Moll M, Lizée G, Kavraki LE. HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. JCO Clin Cancer Inform 2020; 4:623-636. [PMID: 32667823 PMCID: PMC7397777 DOI: 10.1200/cci.19.00123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE HLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because T-cell activation is partially driven by structural features of these peptide-HLA complexes, their structural modeling and analysis are becoming central components of cancer immunotherapy projects. Unfortunately, this kind of analysis is limited by the small number of experimentally determined structures of peptide-HLA complexes. Overcoming this limitation requires developing novel computational methods to model and analyze peptide-HLA structures. METHODS Here we describe a new platform for the structural modeling and analysis of peptide-HLA complexes, called HLA-Arena, which we have implemented using Jupyter Notebook and Docker. It is a customizable environment that facilitates the use of computational tools, such as APE-Gen and DINC, which we have previously applied to peptide-HLA complexes. By integrating other commonly used tools, such as MODELLER and MHCflurry, this environment includes support for diverse tasks in structural modeling, analysis, and visualization. RESULTS To illustrate the capabilities of HLA-Arena, we describe 3 example workflows applied to peptide-HLA complexes. Leveraging the strengths of our tools, DINC and APE-Gen, the first 2 workflows show how to perform geometry prediction for peptide-HLA complexes and structure-based binding prediction, respectively. The third workflow presents an example of large-scale virtual screening of peptides for multiple HLA alleles. CONCLUSION These workflows illustrate the potential benefits of HLA-Arena for the structural modeling and analysis of peptide-HLA complexes. Because HLA-Arena can easily be integrated within larger computational pipelines, we expect its potential impact to vastly increase. For instance, it could be used to conduct structural analyses for personalized cancer immunotherapy, neoantigen discovery, or vaccine development.
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Affiliation(s)
| | | | - Sarah Hall-Swan
- Department of Computer Science, Rice University, Houston, TX
| | | | - Anja Conev
- Department of Computer Science, Rice University, Houston, TX
| | - Mark Moll
- Department of Computer Science, Rice University, Houston, TX
| | - Gregory Lizée
- Department of Melanoma Medical Oncology–Research, The University of Texas MD Anderson Cancer Center, Houston, TX
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21
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Barquera R, Collen E, Di D, Buhler S, Teixeira J, Llamas B, Nunes JM, Sanchez-Mazas A. Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide. HLA 2020; 96:277-298. [PMID: 32475052 PMCID: PMC7300650 DOI: 10.1111/tan.13956] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
We report detailed peptide‐binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV‐1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide‐binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV‐1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA‐A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV‐1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Evelyn Collen
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia
| | - Da Di
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - João Teixeira
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia.,School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia.,The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - José M Nunes
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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22
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Baruah V, Bose S. Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV. J Med Virol 2020; 92:495-500. [PMID: 32022276 PMCID: PMC7166505 DOI: 10.1002/jmv.25698] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 11/10/2022]
Abstract
The 2019 novel coronavirus (2019-nCoV) outbreak has caused a large number of deaths with thousands of confirmed cases worldwide, especially in East Asia. This study took an immunoinformatics approach to identify significant cytotoxic T lymphocyte (CTL) and B cell epitopes in the 2019-nCoV surface glycoprotein. Also, interactions between identified CTL epitopes and their corresponding major histocompatibility complex (MHC) class I supertype representatives prevalent in China were studied by molecular dynamics simulations. We identified five CTL epitopes, three sequential B cell epitopes and five discontinuous B cell epitopes in the viral surface glycoprotein. Also, during simulations, the CTL epitopes were observed to be binding MHC class I peptide-binding grooves via multiple contacts, with continuous hydrogen bonds and salt bridge anchors, indicating their potential in generating immune responses. Some of these identified epitopes can be potential candidates for the development of 2019-nCoV vaccines.
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Affiliation(s)
- Vargab Baruah
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
| | - Sujoy Bose
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
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23
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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24
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Spirito G, Mangoni D, Sanges R, Gustincich S. Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data. BMC Bioinformatics 2019; 20:495. [PMID: 31757210 PMCID: PMC6873650 DOI: 10.1186/s12859-019-3113-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. RESULTS In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. CONCLUSION We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.
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Affiliation(s)
- Giovanni Spirito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
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25
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- 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, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- 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 (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- 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, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- 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 (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M 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, University of Geneva, Geneva, Switzerland
| | - A 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, University of Geneva, Geneva, Switzerland
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26
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Sanchez-Mazas A, Nunes JM. Does NGS typing highlight our understanding of HLA population diversity? Hum Immunol 2019; 80:62-66. [DOI: 10.1016/j.humimm.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/08/2023]
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27
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Capittini C, Messina F, Puglisi F, Azzaro M, Toscano S, De Silvestri A, Tinelli C, Sortino G. An historical approach to the genetic distribution of KIR and HLA ligands in Eastern Sicilians compared to modern descendants of their invaders. Hum Immunol 2018; 79:5-12. [DOI: 10.1016/j.humimm.2017.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
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28
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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29
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Lighten J, Papadopulos AST, Mohammed RS, Ward BJ, G Paterson I, Baillie L, Bradbury IR, Hendry AP, Bentzen P, van Oosterhout C. Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen. Nat Commun 2017; 8:1294. [PMID: 29101318 PMCID: PMC5670221 DOI: 10.1038/s41467-017-01183-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/23/2017] [Indexed: 11/09/2022] Open
Abstract
Red Queen host-parasite co-evolution can drive adaptations of immune genes by positive selection that erodes genetic variation (Red Queen arms race) or results in a balanced polymorphism (Red Queen dynamics) and long-term preservation of genetic variation (trans-species polymorphism). These two Red Queen processes are opposite extremes of the co-evolutionary spectrum. Here we show that both Red Queen processes can operate simultaneously by analysing the major histocompatibility complex (MHC) in guppies (Poecilia reticulata and P. obscura) and swamp guppies (Micropoecilia picta). Sub-functionalisation of MHC alleles into 'supertypes' explains how polymorphisms persist during rapid host-parasite co-evolution. Simulations show the maintenance of supertypes as balanced polymorphisms, consistent with Red Queen dynamics, whereas alleles within supertypes are subject to positive selection in a Red Queen arms race. Building on the divergent allele advantage hypothesis, we show that functional aspects of allelic diversity help to elucidate the evolution of polymorphic genes involved in Red Queen co-evolution.
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Affiliation(s)
- Jackie Lighten
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Ryan S Mohammed
- Department of Life Sciences, The University of the West Indies, St Augustine, Trinidad and Tobago
| | - Ben J Ward
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
| | - Ian G Paterson
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Lyndsey Baillie
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Ian R Bradbury
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2.,Science Branch, Department of Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, NL, Canada, A1C 5X1
| | - Andrew P Hendry
- McGill University, 859 Sherbrooke Street West, Montreal, QC, Canada, H3A 0C4.,Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, QC, Canada, H3A 0C4
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
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30
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Tu B, Masaberg C, Hou L, Behm D, Brescia P, Cha N, Kariyawasam K, Lee JH, Nong T, Sells J, Tausch P, Yang R, Ng J, Hurley CK. Combining one-step Sanger sequencing with phasing probe hybridization for HLA class I typing yields rapid, G-group resolution predicting 99% of unique full length protein sequences. HLA 2017; 89:90-97. [PMID: 28102036 DOI: 10.1111/tan.12951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 11/25/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry. Next generation DNA sequencing (NGS) was applied to over 1000 of these samples to identify the alleles present within the G group designations. RESULTS Single genotypes at G level resolution were obtained for over 95% of the loci without additional assays. The vast majority of alleles identified (>99%) were the primary allele giving the G groups their name. Only 0.7% of the alleles identified encoded protein variants that were not detected by a focus on the antigen recognition domain (ARD)-encoding exons. CONCLUSION Our combined method routinely provides biologically relevant typing resolution at the level of the ARD. It can be applied to both single samples or to large volume typing supporting either bone marrow or solid organ transplantation using technologies currently available in many HLA laboratories.
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Affiliation(s)
- Bin Tu
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Carly Masaberg
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Lihua Hou
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | | | - Peter Brescia
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Nuri Cha
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Kanthi Kariyawasam
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Jar How Lee
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Thoa Nong
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | | | - Paul Tausch
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Ruyan Yang
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Jennifer Ng
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Carolyn Katovich Hurley
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
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31
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Yasukochi Y, Ohashi J. Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression? Immunogenetics 2016; 69:63-67. [PMID: 27695917 PMCID: PMC5203853 DOI: 10.1007/s00251-016-0952-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/16/2016] [Indexed: 12/01/2022]
Abstract
A previous study reported that some of the human leukocyte antigen (HLA) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged HLA-B*73 allele was proposed to be transmitted from Denisovans, although the DNA sequence of HLA-B*73 has not been detected in the Denisovan genome. Here, we argue against the hypothesis that HLA-B*73 introgressed from Denisovans into early modern humans. A phylogenetic analysis revealed that HLA-B*73:01 formed a monophyletic group with a chimpanzee MHC-B allele, strongly suggesting that the HLA-B*73 allelic lineage has been maintained in humans as well as in chimpanzees since the divergence of humans and chimpanzees. The global distribution of HLA-B*73 allele showed that the population frequency of HLA-B*73 in west Asia (0.24 %)—a possible site of admixture with Denisovans—is lower than that in Europe (0.72 %) and in south Asia (0.69 %). Furthermore, HLA-B*73 is not observed in Melanesia even though the Melanesian genome contains the highest proportion of Denisovan ancestry in present-day human populations. Single nucleotide polymorphisms in HLA-A*11-HLA-C*12:02 or HLA-A*11-C*15 haplotypes, one of which was assumed to be transmitted together with HLA-B*73 from Denisovans by the study of Abi-Rached and colleagues, were not differentiated from those in other HLA-A-C haplotypes in modern humans. These results do not support the introgression hypothesis. Thus, we conclude that it is highly likely that HLA-B*73 allelic lineage has been maintained in the direct ancestors of modern humans.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Miettinen ME, Kinnunen L, Harjutsalo V, Aimonen K, Surcel HM, Lamberg-Allardt C, Tuomilehto J. Association of serum 25-hydroxyvitamin D concentration with HLA-B, -DRB1 and -DQB1 genetic polymorphisms. Eur J Clin Nutr 2016; 71:128-131. [PMID: 27623983 DOI: 10.1038/ejcn.2016.160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/27/2016] [Accepted: 07/18/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND/OBJECTIVES The human leukocyte antigen (HLA) gene region associates with the risk for several autoimmune diseases, including type 1 diabetes. An association between vitamin D deficiency and several autoimmune diseases has been suggested. We tested the association between serum 25-hydroxyvitamin D (25OHD) concentrations and HLA alleles in pregnant Finnish women. SUBJECTS/METHODS HLA-B (n=395), HLA-DRB1 (n=501) and HLA-DQB1 (n=475) alleles were genotyped in pregnant women (mothers of children who later developed type 1 diabetes and mothers of non-diabetic children). HLA-B alleles were divided into supertypes that share similar peptide-binding specificity. Serum 25OHD concentration had been previously measured in these women from sera collected during the first trimester of pregnancy. Multiple testing was controlled for using the false discovery rate method. RESULTS An association was found between 25OHD concentration and HLA-B44 supertype (P=0.009); women with HLA-B44 supertype (B*18, B*37, B*40 and B*44 alleles) had lower 25OHD concentrations. No association was found between HLA-DRB1 or -DQB1 alleles and 25OHD concentration. CONCLUSIONS In this study we found for the first time an association between HLA genetic polymorphisms and 25OHD concentration. In future studies, the mechanistic background of this association and the role of vitamin D in the regulation of HLA gene expression should be investigated.
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Affiliation(s)
- M E Miettinen
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - L Kinnunen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - V Harjutsalo
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, University of Helsinki, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - K Aimonen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - H-M Surcel
- Impact Assessment Unit, National Institute for Health and Welfare, Oulu, Finland
| | - C Lamberg-Allardt
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - J Tuomilehto
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.,Center for Vascular Prevention, Danube-University Krems, Krems, Austria.,South Ostrobothnia Central Hospital, Seinäjoki, Finland.,Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia.,Dasman Diabetes Institute, Dasman, Kuwait
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E Silva RDF, Ferreira LFGR, Hernandes MZ, de Brito MEF, de Oliveira BC, da Silva AA, de-Melo-Neto OP, Rezende AM, Pereira VRA. Combination of In Silico Methods in the Search for Potential CD4(+) and CD8(+) T Cell Epitopes in the Proteome of Leishmania braziliensis. Front Immunol 2016; 7:327. [PMID: 27621732 PMCID: PMC5002431 DOI: 10.3389/fimmu.2016.00327] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/16/2016] [Indexed: 11/28/2022] Open
Abstract
The leishmaniases are neglected tropical diseases widespread throughout the globe, which are caused by protozoans from the genus Leishmania and are transmitted by infected phlebotomine flies. The development of a safe and effective vaccine against these diseases has been seen as the best alternative to control and reduce the number of cases. To support vaccine development, this work has applied an in silico approach to search for high potential peptide epitopes able to bind to different major histocompatibility complex Class I and Class II (MHC I and MHC II) molecules from different human populations. First, the predicted proteome of Leishmania braziliensis was compared and analyzed by modern linear programs to find epitopes with the capacity to trigger an immune response. This approach resulted in thousands of epitopes derived from 8,000 proteins conserved among different Leishmania species. Epitopes from proteins similar to those found in host species were excluded, and epitopes from proteins conserved between different Leishmania species and belonging to surface proteins were preferentially selected. The resulting epitopes were then clustered, to avoid redundancies, resulting in a total of 230 individual epitopes for MHC I and 2,319 for MHC II. These were used for molecular modeling and docking with MHC structures retrieved from the Protein Data Bank. Molecular docking then ranked epitopes based on their predicted binding affinity to both MHC I and II. Peptides corresponding to the top 10 ranked epitopes were synthesized and evaluated in vitro for their capacity to stimulate peripheral blood mononuclear cells (PBMC) from post-treated cutaneous leishmaniasis patients, with PBMC from healthy donors used as control. From the 10 peptides tested, 50% showed to be immunogenic and capable to stimulate the proliferation of lymphocytes from recovered individuals.
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Affiliation(s)
- Rafael de Freitas E Silva
- Department of Natural Sciences, Universidade de Pernambuco, Garanhuns, Pernambuco, Brazil; Department of Immunology, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | | | - Marcelo Zaldini Hernandes
- Department of Pharmaceutical Sciences, Universidade Federal de Pernambuco , Recife, Pernambuco , Brazil
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Buhler S, Nunes JM, Sanchez-Mazas A. HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics 2016; 68:401-416. [PMID: 27233953 PMCID: PMC4911380 DOI: 10.1007/s00251-016-0918-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023]
Abstract
The main function of HLA class I molecules is to present pathogen-derived peptides to cytotoxic T lymphocytes. This function is assumed to drive the maintenance of an extraordinary amount of polymorphism at each HLA locus, providing an immune advantage to heterozygote individuals capable to present larger repertories of peptides than homozygotes. This seems contradictory, however, with a reduced diversity at individual HLA loci exhibited by some isolated populations. This study shows that the level of functional diversity predicted for the two HLA-A and HLA-B genes considered simultaneously is similar (almost invariant) between 46 human populations, even when a reduced diversity exists at each locus. We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential. The distinct pattern observed for HLA-C is explained by its functional evolution towards killer cell immunoglobulin-like receptor (KIR) activity regulation rather than peptide presentation.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Transplantation Immunology Unit & 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), University of Geneva, Geneva, Switzerland
| | - 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), University of Geneva, Geneva, Switzerland
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Podgorná E, Diallo I, Vangenot C, Sanchez-Mazas A, Sabbagh A, Černý V, Poloni ES. Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa. BMC Evol Biol 2015; 15:263. [PMID: 26620671 PMCID: PMC4665893 DOI: 10.1186/s12862-015-0543-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background Dietary changes associated to shifts in subsistence strategies during human evolution may have induced new selective pressures on phenotypes, as currently held for lactase persistence. Similar hypotheses exist for arylamine N-acetyltransferase 2 (NAT2) mediated acetylation capacity, a well-known pharmacogenetic trait with wide inter-individual variation explained by polymorphisms in the NAT2 gene. The environmental causative factor (if any) driving its evolution is as yet unknown, but significant differences in prevalence of acetylation phenotypes are found between hunter-gatherer and food-producing populations, both in sub-Saharan Africa and worldwide, and between agriculturalists and pastoralists in Central Asia. These two subsistence strategies also prevail among sympatric populations of the African Sahel, but knowledge on NAT2 variation among African pastoral nomads was up to now very scarce. Here we addressed the hypothesis of different selective pressures associated to the agriculturalist or pastoralist lifestyles having acted on the evolution of NAT2 by sequencing the gene in 287 individuals from five pastoralist and one agriculturalist Sahelian populations. Results We show that the significant NAT2 genetic structure of African populations is mainly due to frequency differences of three major haplotypes, two of which are categorized as decreased function alleles (NAT2*5B and NAT2*6A), particularly common in populations living in arid environments, and one fast allele (NAT2*12A), more frequently detected in populations living in tropical humid environments. This genetic structure does associate more strongly with a classification of populations according to ecoregions than to subsistence strategies, mainly because most Sahelian and East African populations display little to no genetic differentiation between them, although both regions hold nomadic or semi-nomadic pastoralist and sedentary agriculturalist communities. Furthermore, we found significantly higher predicted proportions of slow acetylators in pastoralists than in agriculturalists, but also among food-producing populations living in the Sahelian and dry savanna zones than in those living in humid environments, irrespective of their mode of subsistence. Conclusion Our results suggest a possible independent influence of both the dietary habits associated with subsistence modes and the chemical environment associated with climatic zones and biomes on the evolution of NAT2 diversity in sub-Saharan African populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0543-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic. .,Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Issa Diallo
- Département de Linguistique et Langues Nationales, Institut des Sciences des Sociétés, CNRST, Ouagadougou, Burkina Faso.
| | - Christelle Vangenot
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Audrey Sabbagh
- IRD, UMR216, Mère et enfant face aux infections tropicales, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.
| | - Viktor Černý
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Estella S Poloni
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
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Heterogeneity of dN/dS Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny. J Mol Evol 2015; 82:38-50. [PMID: 26573803 DOI: 10.1007/s00239-015-9713-9] [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: 09/24/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
Abstract
The classical class I HLA loci of humans show an excess of nonsynonymous with respect to synonymous substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. Additionally, high polymporphism, linkage disequilibrium, and disease associations suggest that one or more balancing selection regimes have acted upon these genes. However, several questions about these selective regimes remain open. First, it is unclear if stronger evidence for selection on deep timescales is due to changes in the intensity of selection over time or to a lack of power of most methods to detect selection on recent timescales. Another question concerns the functional entities which define the selected phenotype. While most analyses focus on selection acting on individual alleles, it is also plausible that phylogenetically defined groups of alleles ("lineages") are targets of selection. To address these questions, we analyzed how dN/dS (ω) varies with respect to divergence times between alleles and phylogenetic placement (position of branches). We find that ω for ARS codons of class I HLA genes increases with divergence time and is higher for inter-lineage branches. Throughout our analyses, we used non-selected codons to control for possible effects of inflation of ω associated to intra-specific analysis, and showed that our results are not artifactual. Our findings indicate the importance of considering the timescale effect when analysing ω over a wide spectrum of divergences. Finally, our results support the divergent allele advantage model, whereby heterozygotes with more divergent alleles have higher fitness than those carrying similar alleles.
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