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Strnad A, Sikorova K, Rapti A, Adam K, Charikiopoulou M, Kocourkova L, Strakova G, Kallianos A, Bouros D, Petrek M. Association of HLA variants and related SNPs with sarcoidosis and its phenotypes in the Greek patients. Gene 2024; 927:148706. [PMID: 38885820 DOI: 10.1016/j.gene.2024.148706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Affiliation(s)
- Adam Strnad
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Katerina Sikorova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Angeliki Rapti
- General Hospital Chest Diseases of Athens "Sotiria", Athens, Greece
| | - Kalliopi Adam
- Department of Immunology and Histocompatibility, Laiko General Hospital, Athens, Greece
| | | | - Lenka Kocourkova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Gabriela Strakova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | | | - Demosthenes Bouros
- Medical School, National and Kapodistrian University of Athens First Academic Department of Pneumonology, Interstitial Lung Diseases Unit, Hospital for Diseases of the Chest "Sotiria", Athens, Greece
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
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2
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Yu SC, Lin ME. Kikuchi disease in acute leukaemia: a distinct clinical syndrome with HLA association. Histopathology 2024; 84:1003-1012. [PMID: 38275182 DOI: 10.1111/his.15145] [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: 11/07/2023] [Revised: 12/23/2023] [Accepted: 01/06/2024] [Indexed: 01/27/2024]
Abstract
AIMS To report the clinicopathological features of Kikuchi disease in patients with acute leukaemia, emphasising similarities among cases. METHODS AND RESULTS In a cohort of 454 Kikuchi disease patients, we identified three cases of concurrent acute leukaemia. These patients shared similar clinical traits, with Kikuchi disease emerging approximately a month after induction chemotherapy onset, featuring neck-region lymphadenopathy. Notably, two patients were middle-aged, deviating from the typical age distribution of Kikuchi disease. Histologically, these cases aligned with typical Kikuchi disease. Negative immunohistochemical stains (CD34, CD117, ERG, TdT) indicated the absence of extramedullary leukaemic infiltration. Herpes simplex virus immunohistochemical staining was also negative. Significantly, a human leucocyte antigen (HLA) association was observed in these three cases. HLA-B*15:01, C*04:01, and DRB1*04:06 were more prevalent in these patients compared to the general population (compared with three independent control cohorts: Taiwanese Han Chinese (n = 504), Tzu Chi Taiwanese bone marrow donors (n = 364) and Hong Kong Chinese (n = 5266)). CONCLUSIONS Our study underscores the unique link between Kikuchi disease and acute leukaemia, characterised by specific features and HLA associations. This underlines Kikuchi disease as a possible differential diagnosis in pertinent clinical scenarios. Furthermore, this syndrome offers insights into postchemotherapy immunology in acute leukaemia, enhancing comprehension.
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Affiliation(s)
- Shan-Chi Yu
- Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-En Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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3
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Nilsson JB, Kaabinejadian S, Yari H, Kester MG, van Balen P, Hildebrand WH, Nielsen M. Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning. SCIENCE ADVANCES 2023; 9:eadj6367. [PMID: 38000035 PMCID: PMC10672173 DOI: 10.1126/sciadv.adj6367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules is crucial for rational development of immunotherapies and vaccines targeting CD4+ T cell activation. So far, most prediction methods for HLA class II antigen presentation have focused on HLA-DR because of limited availability of immunopeptidomics data for HLA-DQ and HLA-DP while not taking into account alternative peptide binding modes. We present an update to the NetMHCIIpan prediction method, which closes the performance gap between all three HLA class II loci. We accomplish this by first integrating large immunopeptidomics datasets describing the HLA class II specificity space across all loci using a refined machine learning framework that accommodates inverted peptide binders. Next, we apply targeted immunopeptidomics assays to generate data that covers additional HLA-DP specificities. The final method, NetMHCIIpan-4.3, achieves high accuracy and molecular coverage across all HLA class II allotypes.
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Affiliation(s)
- Jonas B. Nilsson
- Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Saghar Kaabinejadian
- Pure MHC LLC, Oklahoma City, OK, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hooman Yari
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michel G. D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
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4
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Gupta S, Craig JW. Classic Hodgkin lymphoma in young people. Semin Diagn Pathol 2023; 40:379-391. [PMID: 37451943 DOI: 10.1053/j.semdp.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
Classic Hodgkin lymphoma (CHL) is a unique form of lymphoid cancer featuring a heterogeneous tumor microenvironment and a relative paucity of malignant Hodgkin and Reed-Sternberg (HRS) cells with characteristic phenotype. Younger individuals (children, adolescents and young adults) are affected as often as the elderly, producing a peculiar bimodal age-incidence profile that has generated immense interest in this disease and its origins. Decades of epidemiological investigations have documented the populations most susceptible and identified multiple risk factors that can be broadly categorized as either biological or environmental in nature. Most risk factors result in overt immunodeficiency or confer more subtle alterations to baseline health, physiology or immune function. Epstein Barr virus, however, is both a risk factor and well-established driver of lymphomagenesis in a significant subset of cases. Epigenetic changes, along with the accumulation of somatic driver mutations and cytogenetic abnormalities are required for the malignant transformation of germinal center-experienced HRS cell precursors. Chromosomal instability and the influence of endogenous mutational processes are critical in this regard, by impacting genes involved in key signaling pathways that promote the survival and proliferation of HRS cells and their escape from immune destruction. Here we review the principal features, known risk factors and lymphomagenic mechanisms relevant to newly diagnosed CHL, with an emphasis on those most applicable to young people.
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Affiliation(s)
- Srishti Gupta
- Department of Pathology, University of Virginia Health System, 1215 Lee Street, 3rd Floor Hospital Expansion Room 3032, PO Box 800904, Charlottesville, VA 22908, USA
| | - Jeffrey W Craig
- Department of Pathology, University of Virginia Health System, 1215 Lee Street, 3rd Floor Hospital Expansion Room 3032, PO Box 800904, Charlottesville, VA 22908, USA.
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5
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Ruaro-Moreno M, Monterrubio-López GP, Reyes-Gastellou A, Castelán-Vega JA, Jiménez-Alberto A, Aparicio-Ozores G, Delgadillo-Gutiérrez K, González-Y-Merchand JA, Ribas-Aparicio RM. Design of a Multi-Epitope Vaccine against Tuberculosis from Mycobacterium tuberculosis PE_PGRS49 and PE_PGRS56 Proteins by Reverse Vaccinology. Microorganisms 2023; 11:1647. [PMID: 37512820 PMCID: PMC10385543 DOI: 10.3390/microorganisms11071647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis, representing the second leading cause of death by an infectious agent worldwide. The available vaccine against this disease has insufficient coverage and variable efficacy, accounting for a high number of cases worldwide. In fact, an estimated third of the world's population has a latent infection. Therefore, developing new vaccines is crucial to preventing it. In this study, the highly antigenic PE_PGRS49 and PE_PGRS56 proteins were analyzed. These proteins were used for predicting T- and B-cell epitopes and for human leukocyte antigen (HLA) protein binding efficiency. Epitopes GGAGGNGSLSS, FAGAGGQGGLGG, GIGGGTQSATGLG (PE_PGRS49), and GTGWNGGKGDTG (PE_PGRS56) were selected based on their best physicochemical, antigenic, non-allergenic, and non-toxic properties and coupled to HLA I and HLA II structures for in silico assays. A construct with an adjuvant (RS09) plus each epitope joined by GPGPG linkers was designed, and the stability of the HLA-coupled construct was further evaluated by molecular dynamics simulations. Although experimental and in vivo studies are still necessary to ensure its protective effect against the disease, this study shows that the vaccine construct is dynamically stable and potentially effective against tuberculosis.
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Affiliation(s)
- Maritriny Ruaro-Moreno
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gloria Paulina Monterrubio-López
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Abraham Reyes-Gastellou
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Juan Arturo Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Jorge Alberto González-Y-Merchand
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
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Wung CH, Wang CW, Lai KC, Chen CB, Chen WT, Hung SI, Chung WH. Current understanding of genetic associations with delayed hypersensitivity reactions induced by antibiotics and anti-osteoporotic drugs. Front Pharmacol 2023; 14:1183491. [PMID: 37180708 PMCID: PMC10169607 DOI: 10.3389/fphar.2023.1183491] [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: 03/10/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Drug-induced delayed hypersensitivity reactions (DHRs) is still a clinical and healthcare burden in every country. Increasing reports of DHRs have caught our attention to explore the genetic relationship, especially life-threatening severe cutaneous adverse drug reactions (SCARs), including acute generalized exanthematous pustulosis (AGEP), drug reactions with eosinophilia and systemic symptoms (DRESS), Stevens-Johnson syndrome (SJS), and toxic epidermal necrolysis (TEN). In recent years, many studies have investigated the immune mechanism and genetic markers of DHRs. Besides, several studies have stated the associations between antibiotics-as well as anti-osteoporotic drugs (AOD)-induced SCARs and specific human leukocyte antigens (HLA) alleles. Strong associations between drugs and HLA alleles such as co-trimoxazole-induced DRESS and HLA-B*13:01 (Odds ratio (OR) = 45), dapsone-DRESS and HLA-B*13:01 (OR = 122.1), vancomycin-DRESS and HLA-A*32:01 (OR = 403), clindamycin-DHRs and HLA-B*15:27 (OR = 55.6), and strontium ranelate (SR)-SJS/TEN and HLA-A*33:03 (OR = 25.97) are listed. We summarized the immune mechanism of SCARs, update the latest knowledge of pharmacogenomics of antibiotics- and AOD-induced SCARs, and indicate the potential clinical use of these genetic markers for SCARs prevention in this mini review article.
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Affiliation(s)
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei and Keelung, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
| | - Kuo-Chu Lai
- Department of Physiology and Pharmacology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, New Taipei Municipal TuCheng Hospital (Built and Operated by Chang Gung Medical Foundation), New Taipei City, Taiwan
| | - Chun-Bing Chen
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei and Keelung, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Ti Chen
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei and Keelung, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shuen-Iu Hung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei and Keelung, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei and Keelung, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Beijing Tsinghua Chang Gung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
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7
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Masmoudi HC, Afify N, Alnaqbi H, Alhalwachi Z, Tay GK, Alsafar H. HLA pharmacogenetic markers of drug hypersensitivity from the perspective of the populations of the Greater Middle East. Pharmacogenomics 2022; 23:695-708. [PMID: 35971864 DOI: 10.2217/pgs-2022-0078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Specific HLA associations with drug hypersensitivity may vary between geographic regions and ethnic groups. There are little to no data related to HLA-drug hypersensitivity on populations who reside in the Greater Middle East (GME), a vast region spanning from Morocco in the west to Pakistan in the east. In this review, the authors intended to summarize the significant HLA alleles associated with hypersensitive drug reactions induced by different drugs, as have been found in different populations, and to summarize the prevalence of these alleles in the specific and diverse populations of the GME. For example, HLA-B*57:01 allele prevalence, associated with abacavir-induced hypersensitivity, ranges from 1% to 3%, and HLA-DPB1*03:01 prevalence, associated with aspirin-induced asthma, ranges from 10% to 14% in the GME population. Studying pharmacogenomic associations in the ethnic groups of the GME may allow the discovery of new associations, confirm ones found with a low evidence rate and enable cost-effectiveness analysis of allele screening before drug use.
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Affiliation(s)
- Hend Chaker Masmoudi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Pharmaceutical Sciences Department, Faculty of Pharmacy of Monastir, Monastir, 5000, Tunisia.,Department of Histology & Cytogenetics, Institute Pasteur de Tunis, Tunis, 1002, Tunisia
| | - Nariman Afify
- College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Zainab Alhalwachi
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,Faculty of Health & Medical Sciences, UWA Medical School, University of Western Australia, Perth, 6009, Western Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, 6027, Western Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates.,College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science & Technology, Abu Dhabi, P.O. Box 127788, United Arab Emirates
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8
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Sikorová K, Moon SJ, Yoon HY, Strnad A, Song JW, Petrek M. HLA class II variants defined by next generation sequencing are associated with sarcoidosis in Korean patients. Sci Rep 2022; 12:9302. [PMID: 35661780 PMCID: PMC9166778 DOI: 10.1038/s41598-022-13199-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Polymorphic genes with immune functions, namely those of the human leukocyte antigen (HLA) system, have been implicated in sarcoidosis pathogenesis. As HLA polymorphisms in sarcoidosis have not been yet investigated in the Korean population, we used next-generation sequencing (NGS), allowing detailed characterization of HLA alleles to investigate the role of HLA variation in Korean sarcoidosis patients. We enrolled 103 patients diagnosed by the ATS/ERS/WASOG guidelines at Asan Medical Centre, Seoul, Korea. Among those, genotyping of 7 HLA loci (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPB1) was performed using Omixon Holotype™ kit and HLATwin software™. HLA allele frequencies were compared with frequency data on healthy Koreans from the allelic frequency databases, and 4-digit characteristics of HLA genotyping were used. Associations were assessed by two-tailed Fischer’s exact test with correction for multiple comparisons. Variants previously associated with sarcoidosis risk (HLA-C*03:04, HLA-DRB1*12:01, HLA-DRB1*14:54) and a known protective variant HLA-DPB1*04:01, were associated with sarcoidosis in Koreans. Further, we suggest new HLA variants associated with sarcoidosis risk (e.g., HLA-DQA1*05:08) and novel protective variants HLA-DQB1*03:02 and HLA-DQA1*01:02 in Koreans. This first study of HLA variation in Korean patients with sarcoidosis by precise genotyping methodology reports data that could serve future meta-analyses on HLA variation’s role in sarcoidosis.
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Affiliation(s)
- Kateřina Sikorová
- Department of Pathological Physiology & Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Su-Jin Moon
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hee-Young Yoon
- Division of Allergy and Respiratory Diseases, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Adam Strnad
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Jin Woo Song
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Martin Petrek
- Department of Pathological Physiology & Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.
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9
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Moyer AM, Gandhi MJ. Human Leukocyte Antigen (HLA) Testing in Pharmacogenomics. Methods Mol Biol 2022; 2547:21-45. [PMID: 36068459 DOI: 10.1007/978-1-0716-2573-6_2] [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] [Indexed: 06/15/2023]
Abstract
The genetic region on the short arm of chromosome 6 where the human leukocyte antigen (HLA) genes are located is the major histocompatibility complex. The genes in this region are highly polymorphic, and some loci have a high degree of homology with other genes and pseudogenes. Histocompatibility testing has traditionally been performed in the setting of transplantation and involves determining which specific alleles are present. Several HLA alleles have been associated with disease risk or increased risk of adverse drug reaction (ADR) when treated with certain medications. Testing for these applications differs from traditional histocompatibility in that the desired result is simply presence or absence of the allele of interest, rather than determining which allele is present. At present, the majority of HLA typing is done by molecular methods using commercially available kits. A subset of pharmacogenomics laboratories has developed their own methods, and in some cases, query single nucleotide variants associated with certain HLA alleles rather than directly testing for the allele. In this chapter, a brief introduction to the HLA system is provided, followed by an overview of a variety of testing technologies including those specifically used in pharmacogenomics, and the chapter concludes with details regarding specific HLA alleles associated with ADR.
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Affiliation(s)
- Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Manish J Gandhi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Lee KH, Kang DY, Kim HH, Kim YJ, Kim HJ, Kim JH, Song EY, Yun J, Kang H. Reducing severe cutaneous adverse and type B adverse drug reactions using pre-stored human leukocyte antigen genotypes. Clin Transl Allergy 2022; 12:e12098. [PMID: 35070271 PMCID: PMC8760506 DOI: 10.1002/clt2.12098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/26/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Several type B adverse drug reactions (ADRs), especially severe cutaneous adverse reactions (SCARs), are associated with particular human leukocyte antigen (HLA) genotypes. However, pre-stored HLA information obtained from other clinical workups has not been used to prevent ADRs. We aimed to simulate the preemptive use of pre-stored HLA information in electronic medical records to evaluate whether this information can prevent ADRs. METHODS We analyzed the incidence and the risk of ADRs for selected HLA alleles (HLA-B*57:01, HLA-B*58:01, HLA-A*31:01, HLA-B*15:02, HLA-B*15:11, HLA-B*13:01, HLA-B*59:01, and HLA-A*32:01) and seven drugs (abacavir, allopurinol, carbamazepine, oxcarbazepine, dapsone, methazolamide, and vancomycin) using pre-stored HLA information of transplant patients based on the Pharmacogenomics Knowledge Base guidelines and experts' consensus. RESULTS Among 11,988 HLA-tested transplant patients, 4092 (34.1%) had high-risk HLA alleles, 4583 (38.2%) were prescribed risk drugs, and 580 (4.8%) experienced type B ADRs. Patients with HLA-B*58:01 had a significantly higher incidence of type B ADR and SCARs associated with allopurinol use than that of patients without HLA-B*58:01 (17.2% vs. 11.9%, odds ratio [OR] 1.53 [95% confidence interval {CI} 1.09-2.13], p = 0.001, 2.3% versus 0.3%, OR 7.13 [95% CI 2.19-22.69], p < 0.001). Higher risks of type B ADR and SCARs were observed in patients taking carbamazepine or oxcarbazepine if they had one of HLA-A*31:01, HLA-B*15:02, or HLA-B*15:11 alleles. Vancomycin and dapsone use in HLA-A*32:01 and HLA-B*13:01 carriers, respectively, showed trends toward increased risk of type B ADRs. CONCLUSION Utilization of pre-stored HLA data can prevent type B ADRs including SCARs by screening high-risk patients.
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Affiliation(s)
- Kye Hwa Lee
- Department of Information MedicineAsan Medical CenterSeoulSouth Korea
| | - Dong Yoon Kang
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
| | - Hyun Hwa Kim
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
| | - Yi Jun Kim
- Institute of Convergence MedicineEwha Womans University Mokdong HospitalSeoulSouth Korea
| | - Hyo Jung Kim
- Department of Digital HealthSamsung Advanced Institute for Health Science and TechnologySungkyunkwan UniversitySeoulSouth Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics and Systems Biomedical Informatics Research CenterDivision of Biomedical InformaticsSeoul National University College of MedicineSeoulSouth Korea
| | - Eun Young Song
- Department of Molecular Medicine and Biopharmaceutical SciencesGraduate School of Convergence Science and Technology and College of MedicineMedical Research CenterSeoul National UniversitySeoulSouth Korea
| | - James Yun
- Department of Immunology and RheumatologyNepean HospitalSydneyNew South WalesAustralia
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Hye‐Ryun Kang
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
- Institute of Allergy and Clinical ImmunologySeoul National University Medical Research CenterSeoul National University College of MedicineSeoulSouth Korea
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11
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Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, COMET C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Poller W, Borodina T, Pa-COVID SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine 2021; 40:101099. [PMID: 34490415 PMCID: PMC8410317 DOI: 10.1016/j.eclinm.2021.101099] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing. METHODS We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany (n = 135), Spain (n = 133), Switzerland (n = 20) and the United States (n = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID-19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS). FINDINGS We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted p-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles. INTERPRETATION HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2. FUNDING Funded by Roche Sequencing Solutions, Inc.
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Affiliation(s)
- January Weiner
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics Berlin, DE 10178, Germany
| | - Phillip Suwalski
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
- Berliner Simulations- und Trainingszentrum, Charite, Berlin, DE 10117, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Alexander Rakitko
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Charlotte Thibeault
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Melina Müller
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Dimitri Patriki
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Claudia Quedenau
- Max Delbrueck Center for Molecular Medicine Berlin, DE 13125, Germany
| | - Ulrike Krüger
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Valery Ilinsky
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Iaroslav Popov
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Joseph Balnis
- Department of Molecular and Cellular Physiology, Albany Medical College, NY, USA
| | - Ariel Jaitovich
- Department of Molecular and Cellular Physiology, Albany Medical College, NY, USA
| | - Elisa T Helbig
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Lena J Lippert
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Paula Stubbemann
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Luis M Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Juan Macías
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Juan A Pineda
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Marta Fernandez-Fuertes
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Xiaomin Wang
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Zehra Karadeniz
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Jacopo Saccomanno
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Jan-Moritz Doehn
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Ralf-Harto Hübner
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | | | | | - Anja Blueher
- Roche Sequencing Solutions Pleasanton, USA 94588
| | | | - Stjepan Jurisic
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Juerg H. Beer
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Jonas Rutishauser
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Benedikt Wiggli
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Hansruedi Schmid
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Kathrin Danninger
- Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria
| | - Ronald Binder
- Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria
| | - Victor M Corman
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Barbara Mühlemann
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Rao Arjun Arkal
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Gabriela K. Fragiadakis
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Consortium COMET
- COMET (COVID-19 Multiphenotyping for Effective Therapies) Consortium members are listed in the Supplementary Appendix 1
| | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - David J. Erle
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- COMET (COVID-19 Multiphenotyping for Effective Therapies) Consortium members are listed in the Supplementary Appendix 1
- Lung Biology Center, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Carolyn M. Hendrickson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Matthew F. Krummel
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Urmila Venkataramani
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Federico García
- Hospital Universitario Clínico San Cecilio, Instituto de Investigación Ibs. Granada, Spain
| | - Joanna Zyla
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Christian Drosten
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Braun Alice
- Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 d-10117 Berlin, DE 10117, Germany
| | - Terry C Jones
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
- German Center for Infection Research (DZIF), Associated Partner Site, 10117 Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ, U.K
| | - Norbert Suttorp
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Martin Witzenrath
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Stefan Hippenstiel
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Carsten Skurk
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Wolfgang Poller
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Tatiana Borodina
- Max Delbrueck Center for Molecular Medicine Berlin, DE 13125, Germany
| | | | - Stephan Ripke
- Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 d-10117 Berlin, DE 10117, Germany
- Massachusetts General Hospital, Analytic and Translational Genetics, Boston, MA 02114, USA
- Stanley Center for Psychiatry Research, Broad Institute of MIT and Harvard Cambridge MA 02142, USA
| | - Leif E Sander
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics Berlin, DE 10178, Germany
| | - Ulf Landmesser
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
- Berlin Institute of Health at Charité, Berlin, Germany
| | | | - Florian Kurth
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Bettina Heidecker
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
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12
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Narcolepsy genetic marker HLA DQB1*06:02 and excessive daytime sleepiness in Parkinson disease patients treated with dopaminergic agents. J Neurol 2021; 269:2430-2439. [PMID: 34559298 DOI: 10.1007/s00415-021-10813-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To determine whether narcolepsy Human Leukocyte Antigen (HLA) risk allele DQB1*0602 is associated with excessive daytime sleepiness (EDS) and inappropriate sleep in patients with Parkinson disease (PD). BACKGROUND EDS is a common and disabling non-motor manifestation of PD, affecting quality of life and driving performance. DQB1*0602 is an HLA risk allele for narcolepsy. It is present in 12-30% of the general population. We hypothesize that DQB1*0602 is associated with an increased risk of EDS and inappropriate sleep in PD patients. METHODS This was a cross-sectional observational study of 150 PD individuals on dopaminergic agents. Main outcome measures were DQB1*0602 status and the modified Epworth Sleepiness Scale. Individuals with dementia, loss of independence, narcolepsy and untreated sleep apnea were excluded. Confounding variables for EDS were assessed using Parkinson Disease Sleep Scale, Mayo Sleep Questionnaire, Unified PD Rating Scale, Hoehn and Yahr scale. RESULTS DQB1*06:02 positive PD patients were approximately three times more likely to experience EDS and fall asleep inappropriately during activities that required sustained alertness (e.g. driving, eating, attending work etc.). Exploratory post hoc analysis showed a dopaminergic drug dose- and type- dependent effect on daytime sleepiness in DQB1*06:02 positive individuals. No significant differences were found in confounding variables. CONCLUSION PD individuals are more likely to experience EDS and fall asleep inappropriately during activities if DQB1*0602 positive. Genetic vulnerability may explain EDS risk in PD.
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13
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Nilsson JB, Grifoni A, Tarke A, Sette A, Nielsen M. PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage. Front Immunol 2021; 12:728936. [PMID: 34484239 PMCID: PMC8416060 DOI: 10.3389/fimmu.2021.728936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
The use of minimal peptide sets offers an appealing alternative for design of vaccines and T cell diagnostics compared to conventional whole protein approaches. T cell immunogenicity towards peptides is contingent on binding to human leukocyte antigen (HLA) molecules of the given individual. HLA is highly polymorphic, and each variant typically presents a different repertoire of peptides. This polymorphism combined with pathogen diversity challenges the rational selection of peptide sets with broad immunogenic potential and population coverage. Here we propose PopCover-2.0, a simple yet highly effective method, for resolving this challenge. The method takes as input a set of (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and pathogen strain annotation together with information on HLA allele frequencies, and identifies peptide sets with optimal pathogen and HLA (class I and II) coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was confirmed by experimentally validating the peptide pools for T cell responses in a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an effective method for rational selection of peptide subsets with broad HLA and pathogen coverage. The tool is available at https://services.healthtech.dtu.dk/service.php?PopCover-2.0.
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Affiliation(s)
- Jonas Birkelund Nilsson
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Internal Medicine, University of Genoa, Genoa, Italy
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
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14
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Batool H, Batool S, Mahmood MS, Mushtaq N, Khan AU, Ali M, Sahibzada KI, Ashraf NM. Prediction of putative epitope-based vaccine against all corona virus strains for the Chinese population: Approach toward development of vaccine. Microbiol Immunol 2021; 65:154-160. [PMID: 33295677 DOI: 10.1111/1348-0421.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/13/2020] [Accepted: 12/05/2020] [Indexed: 11/30/2022]
Abstract
Currently, the whole world is facing the coronavirus disease-19 pandemic. As of now, approximately 0.15 million people around the globe are infected with the novel coronavirus. In the last decade, two strains of the coronavirus family, severe acute respiratory syndrome-related coronavirus and Middle East respiratory syndrome coronavirus, also resulted in epidemics in south Asian and the Middle Eastern countries with high mortality rate. This scenario demands the development of a putative vaccine which may provide immunity against all current and new evolving coronavirus strains. In this study, we designed an epitope-based vaccine using an immunoinformatic approach. This vaccine may protect against all coronavirus strains. The vaccine is developed by considering the geographical distribution of coronavirus strains and host genetics (Chinese population). Nine experimentally validated epitopes sequences from coronavirus strains were used to derive the variants considering the conservancy in all strains. Further, the binding affinities of all derived variants were checked with most abundant human leukocyte antigen alleles in the Chinese population. Three major histocompatibility complex (MHC) Class I epitopes from spike glycoprotein and nucleoprotein showed sufficient binding while one MHC Class II epitope from spike glycoprotein was found to be an effective binder. A cocktail of these epitopes gave more than 95% population coverage in the Chinese population. Moreover, molecular dynamics simulation supported the aforementioned predictions. Further, in vivo studies are needed to confirm the immunogenic potential of these vaccines.
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Affiliation(s)
- Hina Batool
- Department of Life Science, School of Science, University of Management Technology, Lahore, Pakistan
| | - Sana Batool
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Malik Siddique Mahmood
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.,Department of Biochemistry, NUR International University, Lahore, Pakistan
| | - Nada Mushtaq
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Azmat Ullah Khan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Kashif Iqbal Sahibzada
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.,Division of Viral Hepatitis, CDC, Atlanta, Georgia, USA
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
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15
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Closa L, Vidal F, Herrero MJ, Caro JL. High-throughput genotyping of HLA-G, HLA-F, MICA, and MICB and analysis of frequency distributions in healthy blood donors from Catalonia. HLA 2021; 97:420-427. [PMID: 33599111 DOI: 10.1111/tan.14221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022]
Abstract
Similarly to HLA class I molecules, certain non-classical HLA class I genes and MHC class I polypeptide-related sequences A and B (MICA and MICB) act as ligands for KIR and NKG2D natural killer receptors. Although these genes are less polymorphic than HLA class I, few studies have analyzed their association with diseases. Information on allele frequencies in healthy donors is needed to map their distribution worldwide. This study is the first to analyze high-resolution HLA-G, HLA-F, MICA, and MICB allele frequencies using a novel high-throughput next generation-sequencing method. We analyzed DNA samples from 96 unrelated blood donors resident in Catalonia, Spain, and registered in the Barcelona Blood and Tissue Bank. Using the first two fields of the HLA nomenclature, we detected six HLA-G and two HLA-F alleles. The most frequent alleles were HLA-G*01:01 (77.08%) and HLA-F*01:01(84.90%). When the four fields were analyzed, we detected 16 and 10 alleles, respectively. Nineteen alleles were detected for MICA and 10 for MICB. The most frequent alleles in these cases were MICA*008:01 (16.15%) and MICB*005:02 (46.84%). All frequencies were in Hardy Weinberg equilibrium except MICA. We also estimated maximum-likelihood haplotype frequencies and calculated corresponding linkage disequilibrium (LD) values and found that few allele pairs were in disequilibrium. Strong LD between MICA and HLA-B (using data from a previous study) was observed. Our findings will be useful for guiding further research evaluating the functional role of these genes in different diseases and populations.
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Affiliation(s)
- Laia Closa
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusional Medicine Group, Vall d'Hebron Research Institute-Autonomous University of Barcelona (VHIR-UAB), Barcelona, Spain
| | - Francisco Vidal
- Transfusional Medicine Group, Vall d'Hebron Research Institute-Autonomous University of Barcelona (VHIR-UAB), Barcelona, Spain.,Congenital Coagulopathy Laboratory, Blood and Tissue Bank, Barcelona, Spain.,CIBER of Cardiovascular Diseases, Barcelona, Spain
| | - Maria J Herrero
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank, Barcelona, Spain
| | - Jose L Caro
- Department of Immunology, Hospital Clínic, Barcelona, Spain
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16
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Wang F, Huang S, Gao R, Zhou Y, Lai C, Li Z, Xian W, Qian X, Li Z, Huang Y, Tang Q, Liu P, Chen R, Liu R, Li X, Tong X, Zhou X, Bai Y, Duan G, Zhang T, Xu X, Wang J, Yang H, Liu S, He Q, Jin X, Liu L. Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility. Cell Discov 2020; 6:83. [PMID: 33298875 PMCID: PMC7653987 DOI: 10.1038/s41421-020-00231-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/03/2020] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic has accounted for millions of infections and hundreds of thousand deaths worldwide in a short-time period. The patients demonstrate a great diversity in clinical and laboratory manifestations and disease severity. Nonetheless, little is known about the host genetic contribution to the observed interindividual phenotypic variability. Here, we report the first host genetic study in the Chinese population by deeply sequencing and analyzing 332 COVID-19 patients categorized by varying levels of severity from the Shenzhen Third People's Hospital. Upon a total of 22.2 million genetic variants, we conducted both single-variant and gene-based association tests among five severity groups including asymptomatic, mild, moderate, severe, and critical ill patients after the correction of potential confounding factors. Pedigree analysis suggested a potential monogenic effect of loss of function variants in GOLGA3 and DPP7 for critically ill and asymptomatic disease demonstration. Genome-wide association study suggests the most significant gene locus associated with severity were located in TMEM189-UBE2V1 that involved in the IL-1 signaling pathway. The p.Val197Met missense variant that affects the stability of the TMPRSS2 protein displays a decreasing allele frequency among the severe patients compared to the mild and the general population. We identified that the HLA-A*11:01, B*51:01, and C*14:02 alleles significantly predispose the worst outcome of the patients. This initial genomic study of Chinese patients provides genetic insights into the phenotypic difference among the COVID-19 patient groups and highlighted genes and variants that may help guide targeted efforts in containing the outbreak. Limitations and advantages of the study were also reviewed to guide future international efforts on elucidating the genetic architecture of host-pathogen interaction for COVID-19 and other infectious and complex diseases.
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Affiliation(s)
- Fang Wang
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Shujia Huang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Rongsui Gao
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Yuwen Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China
| | - Changxiang Lai
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Zhichao Li
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China
| | - Wenjie Xian
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Xiaobo Qian
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China
| | - Zhiyu Li
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Yushan Huang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China
| | - Qiyuan Tang
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Panhong Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China
| | - Ruikun Chen
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Rong Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xuan Li
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Xin Tong
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xuan Zhou
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Yong Bai
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Gang Duan
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- James D. Watson Institute of Genome Science, Hangzhou, Zhejiang, 310008, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- James D. Watson Institute of Genome Science, Hangzhou, Zhejiang, 310008, China
| | - Siyang Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.
| | - Qing He
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China.
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
| | - Lei Liu
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China.
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17
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Jawdat D, Uyar FA, Alaskar A, Müller CR, Hajeer A. HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 Allele and Haplotype Frequencies of 28,927 Saudi Stem Cell Donors Typed by Next-Generation Sequencing. Front Immunol 2020; 11:544768. [PMID: 33193311 PMCID: PMC7643328 DOI: 10.3389/fimmu.2020.544768] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 08/18/2020] [Indexed: 11/21/2022] Open
Abstract
Human leukocyte antigen (HLA) allele and haplotype frequency distribution varies widely between different ethnicities and geographical areas. Matching for HLA alleles is essential for successful related and unrelated stem cell transplantation. Among the Saudi population, data on HLA alleles and haplotypes are limited. A cross-sectional study was performed on 28,927 bone marrow donors. The most frequent HLA alleles were HLA-A*02:01:01G (20.2%), A*24:02:01G (7.5%); B*51:01:01G (19.0%), B*50:01:01G (12.3%); C*06:02:01G (16.7%), C*07:02:01G (12.2%); DRB1*07:01:01 (15.7%), DRB1*03:01:01G (13.3%); DQB1*02:01:01G (29.9%), DQB1*03:02:01G (13.2%); and DPB1*04:01:01G (35.2%), DPB1*02:01:02G (21.8%). The most frequent HLA-A~C~B~DRB1~DQB1 haplotypes were A*02:01:01G~C*06:02:01G~B*50:01:01G~DRB1*07:01:01G~DQB1*02:01:01G (1.9%) and A*02:05:01G~C*06:02:01G~B*50:01:01G~DRB1*07:01:01G~DQB1*02:01:01G (1.6%). The most frequent HLA-A~C~B~DRB1~DQB1~DPB1 haplotypes were A*02:01:01G~C*15:02:01G~B*51:01:01G~DRB1*04:02~DQB1*03:02:01G~DPB1*04:01:0G (1%) and A*02:01:01G~C*07:02:01G~B*07:02:01G~DRB1*15:01:01G~DQB1*06:02:01G~ DPB1*04:01:01G (0.9%). Based on these haplotype frequencies, we provide forecasts for the fraction of patients with full matching and single mismatched donors for 3 to 6 loci depending on the registry size. With one million donors, about 50% of the patients would find an 8/8 match and 90% a 7/8 match. These data are essential for registry planning, finding unrelated stem cell donors, population genetic studies, and HLA disease associations.
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Affiliation(s)
- Dunia Jawdat
- Saudi Stem Cells Donor Registry, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - F. Aytül Uyar
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ahmed Alaskar
- Department of Oncology, King Abdulaziz Medical City - Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Carlheinz R. Müller
- ZKRD Zentrales Knochenmarkspender–Register für die Bundesrepublik Deutschland, Ulm, Germany
| | - Ali Hajeer
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City - Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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18
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Powlson J, Wright D, Zeltina A, Giza M, Nielsen M, Rampling T, Venkatrakaman N, Bowden TA, Hill AVS, Ewer KJ. Characterization of Antigenic MHC-Class-I-Restricted T Cell Epitopes in the Glycoprotein of Ebolavirus. Cell Rep 2020; 29:2537-2545.e3. [PMID: 31775024 PMCID: PMC6899439 DOI: 10.1016/j.celrep.2019.10.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/20/2019] [Accepted: 10/25/2019] [Indexed: 11/05/2022] Open
Abstract
Ebolavirus causes highly lethal hemorrhagic fever in humans. The envelope-displayed viral glycoprotein (GP) is the primary target of humoral immunity induced by natural exposure and vaccination. No T cell epitopes in the GP have been characterized in humans. A phase I clinical trial of a heterologous prime-boost vaccination regime with viral vectors encoding filovirus antigens elicits humoral and T cell responses in vaccinees. The most frequently recognized peptide pools are deconvoluted to identify the minimal epitopes recognized by antigen-specific T cells. We characterize nine immunogenic epitopes on the Ebolavirus GP. Histocompatibility leukocyte antigen (HLA) typing with in silico epitope analysis determines the likely MHC class I restriction elements. Thirteen HLA-A and -B alleles are predicted to present the identified CD8+ T cell epitopes, suggesting promiscuous recognition and a broad immune response. Delivery of the Ebolavirus GP antigen by using a heterologous prime-boost approach is immunogenic in genetically diverse human populations, with responses against multiple epitopes. Vaccination induces high T cell responses to the Ebola virus glycoprotein in humans Eight CD8+ epitopes were defined, recognized through multiple MHC class I alleles Responses match those observed in Ebola survivors and could boost vaccine efficacy
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Affiliation(s)
- Jonathan Powlson
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Daniel Wright
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mark Giza
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Morten Nielsen
- Department of Health Technology, The Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs Lyngby, Denmark
| | - Tommy Rampling
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Navin Venkatrakaman
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Katie J Ewer
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK.
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19
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Hajjej A, Abdrakhmanova S, Turganbekova A, Almawi WY. Distribution of
HLA Class I and Class II
alleles and haplotypes in
German
and
Uzbek
minorities in
Kazakhstan
, and relationship to other populations. HLA 2020; 96:615-620. [DOI: 10.1111/tan.14057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics National Blood Transfusion Center Tunis Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion Kazakhstan Ministry of Health Astana Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion Kazakhstan Ministry of Health Astana Kazakhstan
| | - Wassim Y. Almawi
- Department of Biomedical Sciences, School of Medicine Nazarbayev University Astana Kazakhstan
- College of Health Sciences, Abu Dhabi University Abu Dhabi United Arab Emirates
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20
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Petzl-Erler ML. Beyond the HLA polymorphism: A complex pattern of genetic susceptibility to pemphigus. Genet Mol Biol 2020; 43:e20190369. [PMID: 32639508 PMCID: PMC7341728 DOI: 10.1590/1678-4685-gmb-2019-0369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pemphigus is a group of autoimmune bullous skin diseases that result in
significant morbidity. As for other multifactorial autoimmune disorders,
environmental factors may trigger the disease in genetically susceptible
individuals. The goals of this review are to summarize the state of knowledge
about the genetic variation that may affect the susceptibility and pathogenesis
of pemphigus vulgaris and pemphigus foliaceus – both the endemic and the
sporadic forms –, to compare and discuss the possible meaning of the
associations reported, and to propose recommendations for new research
initiatives. Understanding how genetic variants translate into pathogenic
mechanisms and phenotypes remains a mystery for most of the polymorphisms that
contribute to disease susceptibility. However, genetic studies provide a strong
foundation for further developments in this field by generating testable
hypotheses. Currently, results still have limited influence on disease
prevention and prognosis, drug development, and clinical practice, although the
perspectives for future applications for the benefit of patients are
encouraging. Recommendations for the continued advancement of our understanding
as to the impact of genetic variation on pemphigus include these partially
overlapping goals: (1) Querying the functional effect of genetic variants on the
regulation of gene expression through their impact on the nucleotide sequence of
cis regulatory DNA elements such as promoters and enhancers, the splicing of
RNA, the structure of regulatory RNAs and proteins, binding of these regulatory
molecules to regulatory DNA elements, and alteration of epigenetic marks; (2)
identifying key cell types and cell states that are implicated in pemphigus
pathogenesis and explore their functional genomes; (3) integrating structural
and functional genomics data; (4) performing disease-progression longitudinal
studies to disclose the causal relationships between genetic and epigenetic
variation and intermediate disease phenotypes; (5) understanding the influence
of genetic and epigenetic variation in the response to treatment and the
severity of the disease; (6) exploring gene-gene and genotype-environment
interactions; (7) developing improved pemphigus-prone and non-prone animal
models that are appropriate for research about the mechanisms that link
genotypes to pemphigus. Achieving these goals will demand larger samples of
patients and controls and multisite collaborations.
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Affiliation(s)
- Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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21
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Wang G, Wan H, Jian X, Li Y, Ouyang J, Tan X, Zhao Y, Lin Y, Xie L. INeo-Epp: A Novel T-Cell HLA Class-I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence-Related Amino Acid Features. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5798356. [PMID: 32626747 PMCID: PMC7315274 DOI: 10.1155/2020/5798356] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/23/2020] [Indexed: 12/30/2022]
Abstract
In silico T-cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g., proteasomal cleavage, transporter associated with antigen processing (TAP), and major histocompatibility complex (MHC) combination. To date, however, the mechanism for the immunogenicity of epitopes remains unclear. It is generally agreed upon that T-cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties, and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA-I T-cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including the amino acid physicochemical property of the epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score, and frequency score for an immunogenic peptide. Subsequently, a random forest classifier for T-cell immunogenic HLA-I presenting antigen epitopes and neoantigens was constructed. The classification results for the antigen epitopes outperformed the previous research (the optimal AUC = 0.81, external validation data set AUC = 0.77). As mutational epitopes generated by the coding region contain only the alterations of one or two amino acids, we assume that these characteristics might also be applied to the classification of the endogenic mutational neoepitopes also called "neoantigens." Based on mutation information and sequence-related amino acid characteristics, a prediction model of a neoantigen was established as well (the optimal AUC = 0.78). Further, an easy-to-use web-based tool "INeo-Epp" was developed for the prediction of human immunogenic antigen epitopes and neoantigen epitopes.
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Affiliation(s)
- Guangzhi Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Huihui Wan
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xingxing Jian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education and Key Laboratory of Carcinogenesis, National Health and Family Planning Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuyu Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Xiaoxiu Tan
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yong Lin
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lu Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
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22
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Association of HLA-DRB1*04:05 allele with drug-induced interstitial lung disease in Japanese population. THE PHARMACOGENOMICS JOURNAL 2020; 20:823-830. [PMID: 32467566 DOI: 10.1038/s41397-020-0172-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/23/2022]
Abstract
Drug-induced interstitial lung disease (DILD) is a life-threatening adverse reaction. The Japanese population is more susceptible to DILD as compared with other populations, suggesting its pathogenesis could vary depending on ethnic genetic background. We conducted case-control studies to elucidate the association between DILD and HLA alleles in the Japanese. The 177 clinically diagnosed DILD patients and 3002 healthy controls for exploration and 55 DILD patients and 201 healthy controls for validation were genotyped for four HLA genes. HLA-DRB1*04:05 was significantly associated with DILD (corrected p = 0.014); this was also validated in the other set of patients/controls. Chemical drugs other than protein therapeutics showed this association (p = 1.7 × 10-4) . The Japanese population showed a higher HLA-DRB1*04:05 frequency than most other populations. In conclusion, HLA-DRB1*04:05 could be associated with DILD susceptibility in Japanese individuals, and its high general frequency may explain the high reported incidence of DILD in Japanese.
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23
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Nakamura R, Ozeki T, Hirayama N, Sekine A, Yamashita T, Mashimo Y, Mizukawa Y, Shiohara T, Watanabe H, Sueki H, Ogawa K, Asada H, Kaniwa N, Tsukagoshi E, Matsunaga K, Niihara H, Yamaguchi Y, Aihara M, Mushiroda T, Saito Y, Morita E. Association of HLA-A*11:01 with Sulfonamide-Related Severe Cutaneous Adverse Reactions in Japanese Patients. J Invest Dermatol 2020; 140:1659-1662.e6. [PMID: 31981579 DOI: 10.1016/j.jid.2019.12.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/03/2019] [Accepted: 12/28/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Ryosuke Nakamura
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Takeshi Ozeki
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Noriaki Hirayama
- Institute of Advanced Biosciences, Tokai University, Kanagawa, Japan
| | - Akihiro Sekine
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Taiki Yamashita
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Yoichi Mashimo
- Center for Preventive Medical Science, Chiba University, Chiba, Japan
| | - Yoshiko Mizukawa
- Department of Dermatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Tetsuo Shiohara
- Department of Dermatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Hideaki Watanabe
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Hirohiko Sueki
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Kohei Ogawa
- Department of Dermatology, Nara Medical University, Nara, Japan
| | - Hideo Asada
- Department of Dermatology, Nara Medical University, Nara, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Eri Tsukagoshi
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Kayoko Matsunaga
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Aichi, Japan
| | - Hiroyuki Niihara
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane, Japan
| | - Yukie Yamaguchi
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Michiko Aihara
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan.
| | - Eishin Morita
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane, Japan
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24
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Closa L, Vidal F, Herrero MJ, Caro JL. Distribution of human killer cell immunoglobulin‐like receptors and ligands among blood donors of Catalonia. HLA 2019; 95:179-188. [DOI: 10.1111/tan.13754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/17/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Laia Closa
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank Barcelona Spain
- Department of Immunology, Hospital Clínic, Transfusional Medicine Group, Vall d'Hebron Research InstituteAutonomous University of Barcelona (VHIR‐UAB) Barcelona Spain
| | - Francisco Vidal
- Department of Immunology, Hospital Clínic, Transfusional Medicine Group, Vall d'Hebron Research InstituteAutonomous University of Barcelona (VHIR‐UAB) Barcelona Spain
- Congenital Coagulopathy Laboratory, Blood and Tissue Bank Barcelona Spain
- CIBER of Cardiovascular Diseases Barcelona Spain
| | - Maria J. Herrero
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank Barcelona Spain
| | - Jose L. Caro
- Department of Immunology, Hospital Clínic, Transfusional Medicine Group, Vall d'Hebron Research InstituteAutonomous University of Barcelona (VHIR‐UAB) Barcelona Spain
- Department of ImmunologyHospital Clínic Barcelona Spain
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25
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Shen M, Lim JME, Chia C, Ren EC. CD39 + regulatory T cells modulate the immune response to carbamazepine in HLA-B*15:02 carriers. Immunobiology 2019; 225:151868. [PMID: 31784043 DOI: 10.1016/j.imbio.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/31/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
The HLA-B*15:02 allele is associated with an increased risk of developing carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Many studies, however, have demonstrated that a large majority of HLA-B*15:02 individuals are unlikely to develop the adverse drug reaction while on CBZ. This phenomenon suggests that other factors that modulate the allergic immune response, such as regulatory T cells (Tregs), might contribute to an uncontrolled immune response in SJS/TEN. Peripheral blood mononuclear cells (PBMCs) from 15 healthy HLA-B*15:02 carriers were isolated to investigate the role of Tregs in controlling the immune response towards CBZ. Recognition of CBZ was assessed using enzyme linked immunosorbent spot (ELISPOT) assay for IFN-γ, and the donor T-cell profiles were quantified by flow cytometry to differentiate CBZ responders from non-responders. As CD39 expression on Tregs promotes immune tolerance, we investigated the mechanisms of Treg suppression using inhibitors targeting the CD39/adenosinergic pathway. PBMCs from seven donors (responders) produced high levels of IFN-γ when re-exposed to CBZ, while eight donors (non-responders) did not. Flow cytometric analysis revealed that non-responders produced significantly higher frequencies of CD4+CD25+CD127loCD39+FoxP3+ Tregs compared to responders. CD39 inhibition using POM-1 inhibitor converted five of the eight non-responders into responders (P < 0.05). Higher frequencies of CD4+CD25+CD127loCD39+FoxP3+ Tregs was correlated with lower production of IFN-γ (P < 0.01). Our data suggest that CD4+CD25+CD127loCD39+FoxP3+ Tregs may play a role in promoting CBZ tolerance in HLA-B*15:02 carriers. The CD39/adenosinergic axis can be a potential target to alleviate the uncontrolled immune response during this adverse drug event.
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Affiliation(s)
- Meixin Shen
- Singapore Immunology Network (SIgN), A*STAR, Singapore
| | | | - Cheryl Chia
- Singapore Immunology Network (SIgN), A*STAR, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network (SIgN), A*STAR, Singapore; Department of Microbiology and Immunology, National University of Singapore (NUS), Singapore, Singapore.
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Andreani M, Gaspari S, Locatelli F. Human leucocyte antigen diversity: A biological gift to escape infections, no longer a barrier for haploidentical Hemopoietic Stem Cell Transplantation. Int J Immunogenet 2019; 47:34-40. [PMID: 31657118 DOI: 10.1111/iji.12459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/10/2019] [Accepted: 10/05/2019] [Indexed: 11/29/2022]
Abstract
Since the beginning of life, every multicellular organism appeared to have a complex innate immune system although the adaptive immune system, centred on lymphocytes bearing antigen receptors generated by somatic recombination, arose in jawed fish approximately 500 million years ago. The major histocompatibility complex MHC, named the Human leucocyte antigen (HLA) system in humans, represents a vital function structure in the organism by presenting pathogen-derived peptides to T cells as the main initial step of the adaptive immune response. The huge level of polymorphism observed in HLA genes definitely reflects selection, favouring heterozygosity at the individual or population level, in a pathogen-rich environment, although many are located in introns or in exons that do not code for the antigen-biding site of the HLA. Over the past three decades, the extent of allelic diversity at HLA loci has been well characterized using high-resolution HLA-DNA typing and the number of new HLA alleles, produced through next-generation sequencing methods, is even more rapidly increasing. The level of the HLA system polymorphism represents an obstacle to the search of potential compatible donors for patients affected by haematological disease proposed for a hematopoietic stem cell transplant (HSCT). Data reported in literature clearly show that antigenic and/or allelic mismatches between related or unrelated donors and patients influences the successful HSCT outcome. However, the recent development of the new transplant strategy based on the choice of haploidentical donors for HSCT is questioning the role of HLA compatibility, since the great HLA disparities present do not worsen the overall clinical outcome. Nowadays, NGS has contributed to define at allelic levels the HLA polymorphism and solve potential ambiguities. However, HLA functions and tissue typing probably need to be further investigated in the next future, to understand the reasons why in haploidentical transplants the presence of a whole mismatch haplotype between donors and recipients, both the survival rate and the incidence of acute GvHD or graft rejection are similar to those reported for unrelated HSCTs.
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Affiliation(s)
- Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti, Polo di Ricerca di San Paolo, Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Stefania Gaspari
- Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Franco Locatelli
- Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
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27
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Bazmara S, Shadmani M, Ghasemnejad A, Aghazadeh H, Pooshang Bagheri K. In silico rational design of a novel tetra-epitope tetanus vaccine with complete population coverage using developed immunoinformatics and surface epitope mapping approaches. Med Hypotheses 2019; 130:109267. [PMID: 31383332 DOI: 10.1016/j.mehy.2019.109267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 01/01/2023]
Abstract
Presentation of many unwanted epitopes within tetanus toxoid vaccine to lymphocyte clones may lead to production of many unwanted antibodies. Moreover an ideal vaccine must cover all individuals in a population that is dependent to the kinds of human leukocyte antigen alleles. Concerning these issues, our study was aimed to in silico design of a multi-epitope tetanus vaccine (METV) in order to improve population coverage and protectivity of tetanus vaccine as well as reduction of complications. Concerning these issues, a novel rational filtration was implemented to design a novel METV using immunoinformatics and surface epitope mapping approaches. Prediction of epitopes for tetanus toxin was performed in the candidate country in which the frequency had been gathered from almost all geographical distributions. The most strong binder epitopes for major histocompatibility complex class II were selected and among them the surface epitopes of native toxin were selected. The population coverage of the selected epitopes was estimated. The final candidate epitopes had highly population coverage. Molecular docking was performed to prediction of binding affinity of our candidate epitopes to the HLA-DRB1 alleles. At first, 680 strong binder epitopes were predicted. Among them 11 epitopes were selected. Finally, 4 epitopes had the most population coverage and suggested as a tetra-epitope tetanus vaccine. 99.41% of inessential strong binders were deleted using our tree steps filtration. HLA-DP had the most roles in epitope presentation. Molecular docking analysis proved the strong binding affinity of candidate epitopes to the HLA-DRB1 alleles. In conclusion, we theoretically reduced 99.41% of unwanted antibodies using our novel filtration strategies. Our tetra-epitope tetanus vaccine showed 100% population coverage in the candidate country. Furthermore, it was demonstrated that HLA-DP and HLA-DQ had more potential in epitope presentation in comparison to HLA-DRB1.
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Affiliation(s)
- Samira Bazmara
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahsa Shadmani
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Ghasemnejad
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hossein Aghazadeh
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Wagner EK, Qerqez AN, Stevens CA, Nguyen AW, Delidakis G, Maynard JA. Human cytomegalovirus-specific T-cell receptor engineered for high affinity and soluble expression using mammalian cell display. J Biol Chem 2019; 294:5790-5804. [PMID: 30796163 PMCID: PMC6463697 DOI: 10.1074/jbc.ra118.007187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
T-cell receptors (TCR) have considerable potential as therapeutics and antibody-like reagents to monitor disease progression and vaccine efficacy. Whereas antibodies recognize only secreted and surface-bound proteins, TCRs recognize otherwise inaccessible disease-associated intracellular proteins when they are presented as processed peptides bound to major histocompatibility complexes (pMHC). TCRs have been primarily explored for cancer therapy applications but could also target infectious diseases such as cytomegalovirus (CMV). However, TCRs are more difficult to express and engineer than antibodies, and advanced methods are needed to enable their widespread use. Here, we engineered the human CMV-specific TCR RA14 for high-affinity and robust soluble expression. To achieve this, we adapted our previously reported mammalian display system to present TCR extracellular domains and used this to screen CDR3 libraries for clones with increased pMHC affinity. After three rounds of selection, characterized clones retained peptide specificity and activation when expressed on the surface of human Jurkat T cells. We obtained high yields of soluble, monomeric protein by fusing the TCR extracellular domains to antibody hinge and Fc constant regions, adding a stabilizing disulfide bond between the constant domains and disrupting predicted glycosylation sites. One variant exhibited 50 nm affinity for its cognate pMHC, as measured by surface plasmon resonance, and specifically stained cells presenting this pMHC. Our work has identified a human TCR with high affinity for the immunodominant CMV peptide and offers a new strategy to rapidly engineer soluble TCRs for biomedical applications.
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Affiliation(s)
- Ellen K Wagner
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ahlam N Qerqez
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Christopher A Stevens
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Annalee W Nguyen
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - George Delidakis
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A Maynard
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712.
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29
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Nemat-Gorgani N, Guethlein LA, Henn BM, Norberg SJ, Chiaroni J, Sikora M, Quintana-Murci L, Mountain JL, Norman PJ, Parham P. Diversity of KIR, HLA Class I, and Their Interactions in Seven Populations of Sub-Saharan Africans. THE JOURNAL OF IMMUNOLOGY 2019; 202:2636-2647. [PMID: 30918042 DOI: 10.4049/jimmunol.1801586] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022]
Abstract
HLA class I and KIR sequences were determined for Dogon, Fulani, and Baka populations of western Africa, Mbuti of central Africa, and Datooga, Iraqw, and Hadza of eastern Africa. Study of 162 individuals identified 134 HLA class I alleles (41 HLA-A, 60 HLA-B, and 33 HLA-C). Common to all populations are three HLA-C alleles (C1+C*07:01, C1+C*07:02, and C2+C*06:02) but no HLA-A or -B Unexpectedly, no novel HLA class I was identified in these previously unstudied and anthropologically distinctive populations. In contrast, of 227 KIR detected, 22 are present in all seven populations and 28 are novel. A high diversity of HLA A-C-B haplotypes was observed. In six populations, most haplotypes are represented just once. But in the Hadza, a majority of haplotypes occur more than once, with 2 having high frequencies and 10 having intermediate frequencies. The centromeric (cen) part of the KIR locus exhibits an even balance between cenA and cenB in all seven populations. The telomeric (tel) part has an even balance of telA to telB in East Africa, but this changes across the continent to where telB is vestigial in West Africa. All four KIR ligands (A3/11, Bw4, C1, and C2) are present in six of the populations. HLA haplotypes of the Iraqw and Hadza encode two KIR ligands, whereas the other populations have an even balance between haplotypes encoding one and two KIR ligands. Individuals in these African populations have a mean of 6.8-8.4 different interactions between KIR and HLA class I, compared with 2.9-6.5 for non-Africans.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, NY 11794
| | | | - Jacques Chiaroni
- UMR 7268-Anthropologie Bio-Culturelle, Droit, Éthique et Santé, Aix-Marseille Université, l'Etablissement Français du Sang, Centre National de la Recherche Scientifique, 13344 Marseille, France
| | - Martin Sikora
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | | | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO 80045; and.,Department of Immunology, University of Colorado, Denver, CO 80045
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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