151
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Human Leukocyte Antigen (HLA) System: Genetics and Association with Bacterial and Viral Infections. J Immunol Res 2022; 2022:9710376. [PMID: 35664353 PMCID: PMC9162874 DOI: 10.1155/2022/9710376] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/08/2022] [Indexed: 12/19/2022] Open
Abstract
The human leukocyte antigen (HLA) system is one of the most crucial host factors influencing disease progression in bacterial and viral infections. This review provides the basic concepts of the structure and function of HLA molecules in humans. Here, we highlight the main findings on the associations between HLA class I and class II alleles and susceptibility to important infectious diseases such as tuberculosis, leprosy, melioidosis, Staphylococcus aureus infection, human immunodeficiency virus infection, coronavirus disease 2019, hepatitis B, and hepatitis C in populations worldwide. Finally, we discuss challenges in HLA typing to predict disease outcomes in clinical implementation. Evaluation of the impact of HLA variants on the outcome of bacterial and viral infections would improve the understanding of pathogenesis and identify those at risk from infectious diseases in distinct populations and may improve the individual treatment.
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152
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Thammanichanond D, Tammakorn C, Ingsathit A, Worawichawong S, Sangkum P. Misidentification of preformed anti-HLA-DP antibodies leads to antibody-mediated kidney transplant rejection: a case report. BMC Nephrol 2022; 23:187. [PMID: 35581569 PMCID: PMC9115936 DOI: 10.1186/s12882-022-02807-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/28/2022] [Indexed: 11/25/2022] Open
Abstract
Background Patients who are HLA-sensitized are at high risk for early antibody-mediated rejection (AMR) and worse outcomes. Therefore, it is crucial to detect the presence of donor-specific antibodies (DSAs) using pretransplant antibody identification and crossmatch assays. An error in antibody identification can lead to disastrous clinical outcomes. We present a case of acute AMR associated with preformed HLA-DPα and HLA-DPβ DSAs that were not identified before transplantation. Case presentation A 27-year-old woman received a second kidney transplant from a deceased donor. Her pretransplant panel-reactive antibody level was 94%. The complement-dependent cytotoxicity crossmatch was negative for T and B cells at the time of transplantation. She experienced early acute AMR proven by a kidney biopsy. Single antigen bead testing of the patient’s serum at the time of rejection as well as the pre-second transplant serum revealed strong antibodies against the DPA1*01:03 and DPB1*02:01 alleles in the second donor. These antibodies were not identified by phenotypic bead assay during the patient’s time on the waiting list. The patient was treated with plasmapheresis and anti-thymocyte globulin. However, she experienced abdominal pain on day 37 post-transplantation. Surgical exploration revealed a laceration on the transplanted kidney, which was then repaired. Subsequently, infected hematoma was suspected and the transplanted kidney was removed. Conclusion The present case highlights the clinical significance of preformed HLA-DPα and HLA-DPβ DSAs. Accuracy in determination of HLA antibodies before transplantattion is critical for transplant outcome. HLA-DP typing and single antigen bead testing are recommended for a precise antibody interpretation, especially in highly sensitized patients. Careful interpretation of antibody testing results is essential for the success of organ transplantation.
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Affiliation(s)
- Duangtawan Thammanichanond
- Histocompatibility and Immunogenetics Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.
| | - Chutima Tammakorn
- Histocompatibility and Immunogenetics Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Atiporn Ingsathit
- Division of Nephrology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suchin Worawichawong
- Immunopathology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Premsant Sangkum
- Division of Urology, Department of Surgery, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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153
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Design of Vaccine Targeting Zika Virus Polyprotein by Immunoinformatics Technique. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10409-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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154
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Khor SS, Omae Y, Tokunaga K. Discovery of a novel HLA-B*40 allele, HLA-B*40:02:01:30 in a Japanese individual. HLA 2022; 100:368-369. [PMID: 35524970 DOI: 10.1111/tan.14654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 11/27/2022]
Abstract
HLA-B*40:02:01:30 differs from HLA-B*40:02:01:01 by one nucleotide in 3'UTR at position 2869. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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155
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- *Correspondence: Katherine Kedzierska,
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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156
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Alnaqbi H, Tay GK, Chehadeh SEH, Alsafar H. Characterizing the diversity of MHC conserved extended haplotypes using families from the United Arab Emirates. Sci Rep 2022; 12:7165. [PMID: 35504942 PMCID: PMC9065074 DOI: 10.1038/s41598-022-11256-y] [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: 01/25/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to characterize CEHs in the United Arab Emirates (UAE) population through segregation analysis of high-resolution, pedigree-phased, MHC haplotypes derived from 41 families. Twenty per cent (20.5%) of the total haplotype pool derived from this study cohort were identified as putative CEHs in the UAE population. These consisted of CEHs that have been previously detected in other ethnic groups, including the South Asian CEH 8.2 [HLA- C*07:02-B*08:01-DRB1*03:01-DQA1*05:01-DQB1*02:01 (H.F. 0.094)] and the common East Asian CEH 58.1 [HLA- C*03:02-B*58:01-DRB1*03:01- DQA1*05:01-DQB1*02:01 (H.F. 0.024)]. Additionally, three novel CEHs were identified in the current cohort, including HLA- C*15:02-B*40:06-DRB1*16:02-DQB1*05:02 (H.F. 0.035), HLA- C*16:02-B*51:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.029), and HLA- C*03:02-B*58:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.024). Overall, the results indicate a substantial gene flow with neighbouring ethnic groups in the contemporary UAE population including South Asian, East Asian, African, and European populations. Importantly, alleles and haplotypes that have been previously associated with autoimmune diseases (e.g., Type 1 Diabetes) were also present. In this regard, this study emphasizes that an appreciation for ethnic differences can provide insights into subpopulation-specific disease-related polymorphisms, which has remained a difficult endeavour.
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Affiliation(s)
- Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Division of Psychiatry, UWA Medical School, The University of Western Australia, Perth, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Sarah El Hajj Chehadeh
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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157
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Khor SS, Omae Y, Tokunaga K. HLA-B*13:01:01:09, a variant of HLA-B*13:01:01:01, detected in a Japanese individual. HLA 2022; 100:263-264. [PMID: 35484931 DOI: 10.1111/tan.14647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022]
Abstract
HLA-B*13:01:01:09 differs from HLA-B*13:01:01:01 by one nucleotide in intron 4 at positions 1913. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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158
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Aisagbonhi O, Morris GP. Human Leukocyte Antigens in Pregnancy and Preeclampsia. Front Genet 2022; 13:884275. [PMID: 35571013 PMCID: PMC9093604 DOI: 10.3389/fgene.2022.884275] [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: 02/26/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
Preeclampsia is a pregnancy-induced hypertensive disorder, the pathophysiology of which includes underlying maternal cardiovascular disease, deficient spiral artery remodeling during placenta development, and inflammatory immune responses at the maternal-fetal interface. Human leukocyte antigens (HLA) are major histocompatibility complex molecules essential for the recognition of foreign antigens that is central to immune defense against pathogens and critical determinants for the immune system discriminating between self and non-self tissues, such as in transplantation. Pregnancy represents a naturally existing “transplantation”, where the maternal immune system must be immunologically tolerant to the developing fetus which is 50% allogeneic. It is then unsurprising that HLA also influence normal pregnancy and pregnancy complications including preeclampsia. Here we review the role of classical and non-classical HLA molecules in influencing normal physiologic function during pregnancy and describe the association of HLA with pathophysiology in preeclampsia.
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159
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Margulies DH, Taylor DK, Jiang J, Boyd LF, Ahmad J, Mage MG, Natarajan K. Chaperones and Catalysts: How Antigen Presentation Pathways Cope With Biological Necessity. Front Immunol 2022; 13:859782. [PMID: 35464465 PMCID: PMC9022212 DOI: 10.3389/fimmu.2022.859782] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Immune recognition by T lymphocytes and natural killer (NK) cells is in large part dependent on the identification of cell surface MHC molecules bearing peptides generated from either endogenous (MHC I) or exogenous (MHC II) dependent pathways. This review focuses on MHC I molecules that coordinately fold to bind self or foreign peptides for such surface display. Peptide loading occurs in an antigen presentation pathway that includes either the multimolecular peptide loading complex (PLC) or a single chain chaperone/catalyst, TAP binding protein, related, TAPBPR, that mimics a key component of the PLC, tapasin. Recent structural and dynamic studies of TAPBPR reveal details of its function and reflect on mechanisms common to tapasin. Regions of structural conservation among species suggest that TAPBPR and tapasin have evolved to satisfy functional complexities demanded by the enormous polymorphism of MHC I molecules. Recent studies suggest that these two chaperone/catalysts exploit structural flexibility and dynamics to stabilize MHC molecules and facilitate peptide loading.
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Affiliation(s)
- David H Margulies
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Daniel K Taylor
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Jiansheng Jiang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Lisa F Boyd
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Javeed Ahmad
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Michael G Mage
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Kannan Natarajan
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
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160
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Loeser E, Hallensleben M, Bernheiden M, Rakhmanov M, Emmerich F. The novel HLA-DQB1*06 null allele, HLA-DQB1*06:423N, identified in a volunteer blood donor. HLA 2022; 100:186-188. [PMID: 35439352 DOI: 10.1111/tan.14641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/29/2022]
Abstract
A single nucleotide exchange in exon 2 at position 370 (C -> T) generates a preterminal STOP encoding a C-terminally truncated protein. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Evelyn Loeser
- Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Hallensleben
- Institute for Transfusion Medicine and Transplant Engineering, Hanover Medical School, Hanover, Germany
| | - Martin Bernheiden
- Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mirzokhid Rakhmanov
- Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Florian Emmerich
- Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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161
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Khor S, Omae Y, Tokunaga K. Characterization of the novel
HLA‐A
allele
, A*24:02:01:111
in a Japanese individual. HLA 2022; 100:148-149. [DOI: 10.1111/tan.14635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Seik‐Soon Khor
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan
| | - Yosuke Omae
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan
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162
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Scavuzzi BM, van Drongelen V, Holoshitz J. HLA-G and the MHC Cusp Theory. Front Immunol 2022; 13:814967. [PMID: 35281038 PMCID: PMC8913506 DOI: 10.3389/fimmu.2022.814967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigens (HLA) are significant genetic risk factors in a long list of diseases. However, the mechanisms underlying these associations remain elusive in many cases. The best-characterized function of classical major histocompatibility complex (MHC) antigens is to allow safe presentation of antigenic peptides via a self/non-self-discrimination process. Therefore, most hypotheses to date have posited that the observed associations between certain HLA molecules and human diseases involve antigen presentation (AP). However, these hypotheses often represent inconsistencies with current knowledge. To offer answers to the inconsistencies, a decade ago we have invoked the MHC Cusp theory, postulating that in addition to its main role in AP, the MHC codes for allele-specific molecules that act as ligands in a conformationally-conserved cusp-like fold, which upon interaction with cognate receptors can trigger MHC-associated diseases. In the ensuing years, we have provided empirical evidence that substantiates the theory in several HLA-Class II-associated autoimmune diseases. Notably, in a recent study we have demonstrated that HLA-DRB1 alleles known to protect against several autoimmune diseases encode a protective epitope at the cusp region, which activates anti-inflammatory signaling leading to transcriptional and functional modulatory effects. Relevant to the topic of this session, cusp ligands demonstrate several similarities to the functional effects of HLA-G. The overall goal of this opinion article is to delineate the parallels and distinctive features of the MHC Cusp theory with structural and functional aspects of HLA-G molecules.
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Affiliation(s)
| | - Vincent van Drongelen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Joseph Holoshitz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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163
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 208] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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164
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Pyke RM, Mellacheruvu D, Dea S, Abbott CW, McDaniel L, Bhave DP, Zhang SV, Levy E, Bartha G, West J, Snyder MP, Chen RO, Boyle SM. A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity. Nat Commun 2022; 13:1925. [PMID: 35414054 PMCID: PMC9005524 DOI: 10.1038/s41467-022-29203-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
Human leukocyte antigen loss of heterozygosity (HLA LOH) allows cancer cells to escape immune recognition by deleting HLA alleles, causing the suppressed presentation of tumor neoantigens. Despite its importance in immunotherapy response, few methods exist to detect HLA LOH, and their accuracy is not well understood. Here, we develop DASH (Deletion of Allele-Specific HLAs), a machine learning-based algorithm to detect HLA LOH from paired tumor-normal sequencing data. With cell line mixtures, we demonstrate increased sensitivity compared to previously published tools. Moreover, our patient-specific digital PCR validation approach provides a sensitive, robust orthogonal approach that could be used for clinical validation. Using DASH on 610 patients across 15 tumor types, we find that 18% of patients have HLA LOH. Moreover, we show inflated HLA LOH rates compared to genome-wide LOH and correlations between CD274 (encodes PD-L1) expression and microsatellite instability status, suggesting the HLA LOH is a key immune resistance strategy. Human leukocyte antigen loss of heterozygosity (HLA LOH) is an important mechanism of immune escape in patients with cancer. Here the authors design and validate a machine learning algorithm with subclonal sensitivity for the identification of HLA LOH from paired tumor-normal sequencing data.
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Affiliation(s)
| | | | | | | | | | | | | | - Eric Levy
- Personalis, Inc, Menlo Park, CA, USA
| | | | - John West
- Personalis, Inc, Menlo Park, CA, USA
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165
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Sim MJW, Sun PD. T Cell Recognition of Tumor Neoantigens and Insights Into T Cell Immunotherapy. Front Immunol 2022; 13:833017. [PMID: 35222422 PMCID: PMC8867076 DOI: 10.3389/fimmu.2022.833017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022] Open
Abstract
In cancer, non-synonymous DNA base changes alter protein sequence and produce neoantigens that are detected by the immune system. For immune detection, neoantigens must first be presented on class I or II human leukocyte antigens (HLA) followed by recognition by peptide-specific receptors, exemplified by the T-cell receptor (TCR). Detection of neoantigens represents a unique challenge to the immune system due to their high similarity with endogenous ‘self’ proteins. Here, we review insights into how TCRs detect neoantigens from structural studies and delineate two broad mechanistic categories: 1) recognition of mutated ‘self’ peptides and 2) recognition of novel ‘non-self’ peptides generated through anchor residue modifications. While mutated ‘self’ peptides differ only by a single amino acid from an existing ‘self’ epitope, mutations that form anchor residues generate an entirely new epitope, hitherto unknown to the immune system. We review recent structural studies that highlight these structurally distinct mechanisms and discuss how they may lead to differential anti-tumor immune responses. We discuss how T cells specific for neoantigens derived from anchor mutations can be of high affinity and provide insights to their use in adoptive T cell transfer-based immunotherapy.
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Affiliation(s)
- Malcolm J W Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
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166
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Hernández Mejía DG, Camacho Ramírez N, Mosquera Martínez M, Cendales PA, Camacho BA. The novel HLA-A*30:172 allele identified in a donor from the Colombian bone marrow donor registry. HLA 2022; 100:155-156. [PMID: 35393737 DOI: 10.1111/tan.14627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
HLA-A*30:172 differs from HLA-A*30:01:01:01 by a single nucleotide in codon 153 in exon 3. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | | | | | - Paola Andrea Cendales
- Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud - IDCBIS, Bogotá, Colombia
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167
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Cargou M, Elsermans V, Top I, Wojciechowski E, Visentin J. Characterization of the novel HLA-B*44:03:62 allele by sequencing-based typing. HLA 2022; 100:158-160. [PMID: 35343094 DOI: 10.1111/tan.14616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/30/2022]
Abstract
HLA-B*44:03:62 differs from HLA-B*44:03:01:01 by one nucleotide substitution in codon 127 in exon 3. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Vincent Elsermans
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Isabelle Top
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat, Bordeaux, France
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168
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Cargou M, Elsermans V, Top I, Guidicelli G, Visentin J. Characterization of the novel HLA-DQB1*02:197 allele by sequencing-based typing. HLA 2022; 100:184-186. [PMID: 35343106 DOI: 10.1111/tan.14614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
HLA-DQB1*02:197 differs from HLA-DQB1*02:01:01:01 by one nucleotide substitution in codon 18 in exon 2. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Vincent Elsermans
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Isabelle Top
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat, Bordeaux, France
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169
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Allelic imbalance of HLA-B expression in human lung cells infected with coronavirus and other respiratory viruses. Eur J Hum Genet 2022; 30:922-929. [PMID: 35322240 PMCID: PMC8940983 DOI: 10.1038/s41431-022-01070-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/09/2022] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
The human leucocyte antigen (HLA) loci have been widely characterized to be associated with viral infectious diseases using either HLA allele frequency-based association or in silico predicted studies. However, there is less experimental evidence to link the HLA alleles with COVID-19 and other respiratory infectious diseases, particularly in the lung cells. To examine the role of HLA alleles in response to coronavirus and other respiratory viral infections in disease-relevant cells, we designed a two-stage study by integrating publicly accessible RNA-seq data sets, and performed allelic expression (AE) analysis on heterozygous HLA genotypes. We discovered an increased AE pattern accompanied with overexpression of HLA-B gene in SARS-CoV-2-infected human lung epithelial cells. Analysis of independent data sets verified the respiratory virus-induced AE of HLA-B gene in lung cells and tissues. The results were further experimentally validated in cultured lung cells infected with SARS-CoV-2. We further uncovered that the antiviral cytokine IFNβ contribute to AE of the HLA-B gene in lung cells. Our analyses provide a new insight into allelic influence on the HLA expression in association with SARS-CoV-2 and other common viral infectious diseases.
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170
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Zhang LQ, Rozemuller E, Wang D, Liu XJ, Cai JP. Characterization of a novel HLA-A*11:335 allele resulting from a rare interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles with nanopore sequencing, in a volunteer from the China Marrow Donor Program. BMC Med Genomics 2022; 15:58. [PMID: 35296321 PMCID: PMC8925214 DOI: 10.1186/s12920-022-01176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) in humans includes three classical class I loci (A, B, and C), which are important biomarkers for the transplantation of organs and hematopoietic stem cells. In the MHC, polymorphism is known to be extremely high while interlocus recombination is rare. We report a rare interlocus recombination between HLA-A and HLA-H, which was analyzed using next generation sequencing and nanopore sequencing. METHODS In the sample, the genotypes of HLA-A, B, C, DRB1, and DQB1 were firstly determined using the methods of sequence-specific primer, sequence-specific oligonucleotide, Sanger's sequencing, and NGS; however, HLA-A could not be phased. Nanopore sequencing was finally utilized to distinguish the sequence of the novel allele. RESULTS Finally, the novel HLA-A*11:335 allele was identified as an interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles; this was mainly achieved by nanopore sequencing. CONCLUSIONS The identification of the interlocus recombination indicated that nanopore sequencing can be helpful in the characterization of novel alleles with complex rearrangements. Interlocus recombination has been identified as one of the mechanisms involved in the generation of novel HLA alleles.
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Affiliation(s)
- Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China
| | | | - Dan Wang
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Xiang-Jun Liu
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China.
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171
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Wojciechowski E, Cargou M, Guidicelli G, Ralazamahaleo M, Visentin J. Characterization of the novel HLA-C*12:354 allele by sequencing-based typing. HLA 2022; 100:88-90. [PMID: 35261184 DOI: 10.1111/tan.14594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 01/24/2023]
Abstract
HLA-C*12:354 differs from HLA-C*12:03:01:01 by one nucleotide substitution in codon 240 in exon 4. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France
| | - Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France
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172
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Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil. Nat Commun 2022; 13:1004. [PMID: 35246524 PMCID: PMC8897431 DOI: 10.1038/s41467-022-28648-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS. Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
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173
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Pontarotti P, Paganini J. COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution. Int J Mol Sci 2022; 23:ijms23052665. [PMID: 35269808 PMCID: PMC8910380 DOI: 10.3390/ijms23052665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
We propose a new hypothesis that explains the maintenance and evolution of MHC polymorphism. It is based on two phenomena: the constitution of the repertoire of naive T lymphocytes and the evolution of the pathogen and its impact on the immune memory of T lymphocytes. Concerning the latter, pathogen evolution will have a different impact on reinfection depending on the MHC allomorph. If a mutation occurs in a given region, in the case of MHC allotypes, which do not recognize the peptide in this region, the mutation will have no impact on the memory repertoire. In the case where the MHC allomorph binds to the ancestral peptides and not to the mutated peptide, that individual will have a higher chance of being reinfected. This difference in fitness will lead to a variation of the allele frequency in the next generation. Data from the SARS-CoV-2 pandemic already support a significant part of this hypothesis and following up on these data may enable it to be confirmed. This hypothesis could explain why some individuals after vaccination respond less well than others to variants and leads to predict the probability of reinfection after a first infection depending upon the variant and the HLA allomorph.
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Affiliation(s)
- Pierre Pontarotti
- Evolutionary Biology Team, MEPHI, Aix Marseille Université, IRD, APHM, IHU MI, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- SNC 5039 CNRS, 13005 Marseille, France
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
| | - Julien Paganini
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
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174
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Okada M, Shimizu K, Fujii SI. Identification of Neoantigens in Cancer Cells as Targets for Immunotherapy. Int J Mol Sci 2022; 23:ijms23052594. [PMID: 35269735 PMCID: PMC8910406 DOI: 10.3390/ijms23052594] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
The clinical benefits of immune checkpoint blockage (ICB) therapy have been widely reported. In patients with cancer, researchers have demonstrated the clinical potential of antitumor cytotoxic T cells that can be reinvigorated or enhanced by ICB. Compared to self-antigens, neoantigens derived from tumor somatic mutations are believed to be ideal immune targets in tumors. Candidate tumor neoantigens can be identified through immunogenomic or immunopeptidomic approaches. Identification of neoantigens has revealed several points of the clinical relevance. For instance, tumor mutation burden (TMB) may be an indicator of immunotherapy. In various cancers, mutation rates accompanying neoantigen loads may be indicative of immunotherapy. Furthermore, mismatch repair-deficient tumors can be eradicated by T cells in ICB treatment. Hence, immunotherapies using vaccines or adoptive T-cell transfer targeting neoantigens are potential innovative strategies. However, significant efforts are required to identify the optimal epitopes. In this review, we summarize the recent progress in the identification of neoantigens and discussed preclinical and clinical studies based on neoantigens. We also discuss the issues remaining to be addressed before clinical applications of these new therapeutic strategies can be materialized.
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Affiliation(s)
- Masahiro Okada
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
- Program for Drug Discovery and Medical Technology Platforms, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-45-503-7062
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175
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López D. Predicted HLA Class I and Class II Epitopes From Licensed Vaccines Are Largely Conserved in New SARS-CoV-2 Omicron Variant of Concern. Front Immunol 2022; 13:832889. [PMID: 35154154 PMCID: PMC8831693 DOI: 10.3389/fimmu.2022.832889] [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: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
The potential effect of emerging SARS-CoV-2 variants on vaccine efficacy is an issue of critical importance. In this study, the possible impact of mutations that facilitate virus escape from the cytotoxic and the helper cellular immune responses in the new SARS-CoV-2 Omicron variant of concern was analyzed for the 551 and 41 most abundant HLA class I and II alleles, respectively. Computational prediction showed that almost all of these 592 alleles, which cover >90% of the human population, contain enough epitopes without escape mutations in the emerging SARS-CoV-2 Omicron variant of concern. These data suggest that both cytotoxic and helper cellular immune protection elicited by currently licensed vaccines are virtually unaffected by the highly contagious SARS-CoV-2 Omicron variant of concern.
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Affiliation(s)
- Daniel López
- Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
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176
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Wojciechowski E, Milhes J, Ralazamahaleo M, Cargou M, Visentin J. Characterization of the novel
HLA‐B
*44:
544 N
allele by sequencing‐based typing. HLA 2022; 99:631-633. [DOI: 10.1111/tan.14581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon Bordeaux France
- Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat Bordeaux France
| | - Jean Milhes
- CHU de Toulouse, Laboratoire d'immunologie, Hôpital Purpan, 330 Av de Grande Bretagne TSA 70034, 31059 Toulouse France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon Bordeaux France
| | - Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon Bordeaux France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon Bordeaux France
- Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat Bordeaux France
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177
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Bastos M, Alcoceba M, Chillón MC, García‐Sanz R, Boix F. Identification of the novel
HLA‐A
*23:01:01:27
allele in an acute myeloid patient and related donor. HLA 2022; 100:62-64. [DOI: 10.1111/tan.14579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Miguel Bastos
- Department of Haematology University Hospital of Salamanca (HUS‐IBSAL) , CIBERONC, and Cancer Research Institute of Salamanca‐IBMCC (CSIC‐USAL University) Salamanca Spain
| | - Miguel Alcoceba
- Department of Haematology University Hospital of Salamanca (HUS‐IBSAL) , CIBERONC, and Cancer Research Institute of Salamanca‐IBMCC (CSIC‐USAL University) Salamanca Spain
| | - M. Carmen Chillón
- Department of Haematology University Hospital of Salamanca (HUS‐IBSAL) , CIBERONC, and Cancer Research Institute of Salamanca‐IBMCC (CSIC‐USAL University) Salamanca Spain
| | - Ramón García‐Sanz
- Department of Haematology University Hospital of Salamanca (HUS‐IBSAL) , CIBERONC, and Cancer Research Institute of Salamanca‐IBMCC (CSIC‐USAL University) Salamanca Spain
| | - Francisco Boix
- Department of Haematology University Hospital of Salamanca (HUS‐IBSAL) , CIBERONC, and Cancer Research Institute of Salamanca‐IBMCC (CSIC‐USAL University) Salamanca Spain
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178
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Wojciechowski E, Thevenin CR, Bonafoux B, Ralazamahaleo M, Visentin J. Characterization of the novel HLA-A*24:564 allele by sequencing-based typing. HLA 2022; 99:623-625. [PMID: 35122405 DOI: 10.1111/tan.14576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
HLA-A*24:564 differs from HLA-A*24:02:01:01 by one nucleotide substitution in codon 240 in exon 4. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat, Bordeaux, France
| | - Celine Rene Thevenin
- CHU de Montpellier, Service d'Immunologie, 191 av. du Doyen Giraud, Montpellier, France
| | - Beatrice Bonafoux
- CHU de Montpellier, Service d'Immunologie, 191 av. du Doyen Giraud, Montpellier, France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 146 rue Léo Saignat, Bordeaux, France
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179
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Foix A, López D, Díez-Fuertes F, McConnell MJ, Martín-Galiano AJ. Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1009726. [PMID: 35143484 PMCID: PMC8830725 DOI: 10.1371/journal.pcbi.1009726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
The massive assessment of immune evasion due to viral mutations that increase COVID-19 susceptibility can be computationally facilitated. The adaptive cytotoxic T response is critical during primary infection and the generation of long-term protection. Here, potential HLA class I epitopes in the SARS-CoV-2 proteome were predicted for 2,915 human alleles of 71 families using the netMHCIpan EL algorithm. Allele families showed extreme epitopic differences, underscoring genetic variability of protective capacity between humans. Up to 1,222 epitopes were associated with any of the twelve supertypes, that is, allele clusters covering 90% population. Next, from all mutations identified in ~118,000 viral NCBI isolates, those causing significant epitope score reduction were considered epitope escape mutations. These mutations mainly involved non-conservative substitutions at the second and C-terminal position of the ligand core, or total ligand removal by large recurrent deletions. Escape mutations affected 47% of supertype epitopes, which in 21% of cases concerned isolates from two or more sub-continental areas. Some of these changes were coupled, but never surpassed 15% of evaded epitopes for the same supertype in the same isolate, except for B27. In contrast to most supertypes, eight allele families mostly contained alleles with few SARS-CoV-2 ligands. Isolates harboring cytotoxic escape mutations for these families co-existed geographically within sub-Saharan and Asian populations enriched in these alleles according to the Allele Frequency Net Database. Collectively, our findings indicate that escape mutation events have already occurred for half of HLA class I supertype epitopes. However, it is presently unlikely that, overall, it poses a threat to the global population. In contrast, single and double mutations for susceptible alleles may be associated with viral selective pressure and alarming local outbreaks. The integration of genomic, geographical and immunoinformatic information eases the surveillance of variants potentially affecting the global population, as well as minority subpopulations.
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Affiliation(s)
- Anna Foix
- European Bioinformatic Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Daniel López
- Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Michael J. McConnell
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
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180
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Vita R, Mody A, Overton JA, Buus S, Haley ST, Sette A, Mallajosyula V, Davis MM, Long DL, Willis RA, Peters B, Altman JD. Minimal Information about MHC Multimers (MIAMM). JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:531-537. [PMID: 35042788 PMCID: PMC8830768 DOI: 10.4049/jimmunol.2100961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
With the goal of improving the reproducibility and annotatability of MHC multimer reagent data, we present the establishment of a new data standard: Minimal Information about MHC Multimers (https://miamm.lji.org/). Multimers are engineered reagents composed of a ligand and a MHC, which can be represented in a standardized format using ontology terminology. We provide an online Web site to host the details of the standard, as well as a validation tool to assist with the adoption of the standard. We hope that this publication will bring increased awareness of Minimal Information about MHC Multimers and drive acceptance, ultimately improving the quality and documentation of multimer data in the scientific literature.
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Affiliation(s)
- Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA;
| | - Apurva Mody
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | | | - Soren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Dale L Long
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Richard A Willis
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
| | - John D Altman
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA
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181
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Minervina AA, Pogorelyy MV, Kirk AM, Crawford JC, Allen EK, Chou CH, Mettelman RC, Allison KJ, Lin CY, Brice DC, Zhu X, Vegesana K, Wu G, Trivedi S, Kottapalli P, Darnell D, McNeely S, Olsen SR, Schultz-Cherry S, Estepp JH, McGargill MA, Wolf J, Thomas PG. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.07.12.21260227. [PMID: 34341799 PMCID: PMC8328067 DOI: 10.1101/2021.07.12.21260227] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although mRNA vaccine efficacy against severe COVID-19 remains high, variant emergence and breakthrough infections have changed vaccine policy to include booster immunizations. However, the effect of diverse and repeated antigen exposures on SARS-CoV-2 memory T cells is poorly understood. Here, we utilize DNA-barcoded MHC-multimers combined with scRNAseq and scTCRseq to capture the ex vivo profile of SARS-CoV-2-responsive T cells within a cohort of individuals with one, two, or three antigen exposures, including vaccination, primary infection, and breakthrough infection. We found that the order of exposure determined the relative distribution between spike- and non-spike-specific responses, with vaccination after infection leading to further expansion of spike-specific T cells and differentiation to a CCR7-CD45RA+ effector phenotype. In contrast, individuals experiencing a breakthrough infection mount vigorous non-spike-specific responses. In-depth analysis of over 4,000 epitope-specific T cell receptor sequences demonstrates that all types of exposures elicit diverse repertoires characterized by shared, dominant TCR motifs, with no evidence for repertoire narrowing from repeated exposure. Our findings suggest that breakthrough infections diversify the T cell memory repertoire and that current vaccination protocols continue to expand and differentiate spike-specific memory responses.
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Affiliation(s)
| | - Mikhail V. Pogorelyy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Allison M. Kirk
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | | | - E. Kaitlynn Allen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Robert C. Mettelman
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Kim J. Allison
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Chun-Yang Lin
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - David C. Brice
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Xun Zhu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Kasi Vegesana
- Information Services, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Sanchit Trivedi
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Pratibha Kottapalli
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Suzanne McNeely
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Scott R. Olsen
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Jeremie H. Estepp
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN USA
| | | | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
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182
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Stuart PE, Tsoi LC, Nair RP, Ghosh M, Kabra M, Shaiq PA, Raja GK, Qamar R, Thelma B, Patrick MT, Parihar A, Singh S, Khandpur S, Kumar U, Wittig M, Degenhardt F, Tejasvi T, Voorhees JJ, Weidinger S, Franke A, Abecasis GR, Sharma VK, Elder JT. Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide. HGG ADVANCES 2022; 3:100069. [PMID: 34927100 PMCID: PMC8682265 DOI: 10.1016/j.xhgg.2021.100069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/24/2021] [Indexed: 02/06/2023] Open
Abstract
Because transethnic analysis may facilitate prioritization of causal genetic variants, we performed a genomewide association study (GWAS) of psoriasis in South Asians (SAS), consisting of 2,590 cases and 1,720 controls. Comparison with our existing European-origin (EUR) GWAS showed that effect sizes of known psoriasis signals were highly correlated in SAS and EUR (Spearman ρ = 0.78; p < 2 × 10-14). Transethnic meta-analysis identified two non-MHC psoriasis loci (1p36.22 and 1q24.2) not previously identified in EUR, which may have regulatory roles. For these two loci, the transethnic GWAS provided higher genetic resolution and reduced the number of potential causal variants compared to using the EUR sample alone. We then explored multiple strategies to develop reference panels for accurately imputing MHC genotypes in both SAS and EUR populations and conducted a fine-mapping of MHC psoriasis associations in SAS and the largest such effort for EUR. HLA-C*06 was the top-ranking MHC locus in both populations but was even more prominent in SAS based on odds ratio, disease liability, model fit and predictive power. Transethnic modeling also substantially boosted the probability that the HLA-C*06 protein variant is causal. Secondary MHC signals included coding variants of HLA-C and HLA-B, but also potential regulatory variants of these two genes as well as HLA-A and several HLA class II genes, with effects on both chromatin accessibility and gene expression. This study highlights the shared genetic basis of psoriasis in SAS and EUR populations and the value of transethnic meta-analysis for discovery and fine-mapping of susceptibility loci.
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Affiliation(s)
- Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI, USA
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Manju Ghosh
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Pakeeza A. Shaiq
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Ghazala K. Raja
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Raheel Qamar
- COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - B.K. Thelma
- Department of Genetics, University of Delhi South Campus, 110021 New Delhi, India
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita Parihar
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sonam Singh
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sujay Khandpur
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Michael Wittig
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - John J. Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephan Weidinger
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Goncalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vinod K. Sharma
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
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183
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Dholakia D, Kalra A, Misir BR, Kanga U, Mukerji M. HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts. BMC Genomics 2022; 23:10. [PMID: 34991484 PMCID: PMC8740486 DOI: 10.1186/s12864-021-08239-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ~ 146,000 studies on HLA reported from diverse locations. Currently, IPD-IMGT/HLA (Robinson et al., Nucleic Acids Research 48:D948-D955, 2019) database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ~ 28 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 109 countries and 40 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/ . This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.
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Affiliation(s)
- Dhwani Dholakia
- Institute of Genomics and Integrative Biology-Council of Scientific and Industrial Research, New Delhi, 110025, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
| | - Ankit Kalra
- Netaji Subhas University of Technology, New Delhi, 110078, India
| | - Bishnu Raman Misir
- Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR- IGIB, Delhi, 110007, India
| | - Uma Kanga
- All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Mitali Mukerji
- Institute of Genomics and Integrative Biology-Council of Scientific and Industrial Research, New Delhi, 110025, India.
- Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR- IGIB, Delhi, 110007, India.
- Present Address: Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India.
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184
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Hernández DG, Camacho Ramírez N, Mosquera Martínez M, Cendales PA, Camacho BA. Characterization of the novel HLA-DRB1*04:315 allele by next-generation sequencing. HLA 2022; 99:654-655. [PMID: 34978763 DOI: 10.1111/tan.14534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 11/27/2022]
Abstract
HLA-DRB1*04:315 differs from HLA-DRB1*04:07:01:02 by a single nucleotide substitution in codon 147 of exon 3.
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Affiliation(s)
| | | | | | - Paola Andrea Cendales
- Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud - IDCBIS, Bogotá, Colombia
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185
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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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186
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Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V. Structural Prediction of Peptide-MHC Binding Modes. Methods Mol Biol 2022; 2405:245-282. [PMID: 35298818 DOI: 10.1007/978-1-0716-1855-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The immune system is constantly protecting its host from the invasion of pathogens and the development of cancer cells. The specific CD8+ T-cell immune response against virus-infected cells and tumor cells is based on the T-cell receptor recognition of antigenic peptides bound to class I major histocompatibility complexes (MHC) at the surface of antigen presenting cells. Consequently, the peptide binding specificities of the highly polymorphic MHC have important implications for the design of vaccines, for the treatment of autoimmune diseases, and for personalized cancer immunotherapy. Evidence-based machine-learning approaches have been successfully used for the prediction of peptide binders and are currently being developed for the prediction of peptide immunogenicity. However, understanding and modeling the structural details of peptide/MHC binding is crucial for a better understanding of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D structures of peptide/MHC (pMHC) complexes in the Protein Data Bank only covers a small fraction of the possibilities. Consequently, there is a growing need for rapid and efficient approaches to predict 3D structures of pMHC complexes. Here, we review the key characteristics of the 3D structure of pMHC complexes before listing databases and other sources of information on pMHC structures and MHC specificities. Finally, we discuss some of the most prominent pMHC docking software.
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Affiliation(s)
- Marta A S Perez
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel A Cuendet
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland.
| | - Vincent Zoete
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne, Switzerland.
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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187
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Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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188
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Shkurnikov MY, Averinskaya DA, Komarov AG, Karbyshev IA, Speshilov GI, Shtinova IA, Doroshenko DA, Vechorko VI, Drapkina OM. Association of HLA Class I Genotype with Mortality in Patients with Diabetes Mellitus and COVID-19. DOKL BIOCHEM BIOPHYS 2022; 507:289-293. [PMID: 36786988 PMCID: PMC9926432 DOI: 10.1134/s1607672922060114] [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: 08/11/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 02/15/2023]
Abstract
Numerous studies showed that diabetes mellitus (DM) increases the risk of death from COVID-19 by five times. It is generally accepted that the high lethality of COVID-19 against the background of DM is due to the main complications of this disease: micro- and macroangiopathies, as well as heart and kidney failure. In addition, it was shown that acute respiratory viral infection increases the production of interferon gamma, increases muscle resistance to insulin, and modulates the activity of effector CD8+ T cells. The ability of CD8+ T cells to recognize SARS-CoV-2-infected cells depends not only on humoral factors but also on individual genetic characteristics, including the individual set of major histocompatibility complex class I (MHC-I) molecules. In this study, the relationship of the MHC-I genotype of patients with DM aged less than 60 years with the outcome of COVID-19 was studied using a sample of 222 patients. It was shown that lethal outcomes of COVID-19 in patients with DM are associated with the low affinity of the interaction of an individual set of MHC-I molecules with SARS-CoV-2 peptides.
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Affiliation(s)
- M. Yu. Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia ,Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - D. A. Averinskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - A. G. Komarov
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - I. A. Karbyshev
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - G. I. Speshilov
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - I. A. Shtinova
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - D. A. Doroshenko
- Moscow City Public Institution of Health Care Filatov City Clinical Hospital of Moscow Health Department, Moscow, Russia
| | - V. I. Vechorko
- Moscow City Public Institution of Health Care Filatov City Clinical Hospital of Moscow Health Department, Moscow, Russia
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
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189
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Mattei AE, Gutierrez AH, Martin WD, Terry FE, Roberts BJ, Rosenberg AS, De Groot AS. In silico Immunogenicity Assessment for Sequences Containing Unnatural Amino Acids: A Method Using Existing in silico Algorithm Infrastructure and a Vision for Future Enhancements. FRONTIERS IN DRUG DISCOVERY 2022; 2:952326. [PMID: 36945694 PMCID: PMC10026553 DOI: 10.3389/fddsv.2022.952326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The in silico prediction of T cell epitopes within any peptide or biologic drug candidate serves as an important first step for assessing immunogenicity. T cell epitopes bind human leukocyte antigen (HLA) by a well-characterized interaction of amino acid side chains and pockets in the HLA molecule binding groove. Immunoinformatics tools, such as the EpiMatrix algorithm, have been developed to screen natural amino acid sequences for peptides that will bind HLA. In addition to commonly occurring in synthetic peptide impurities, unnatural amino acids (UAA) are also often incorporated into novel peptide therapeutics to improve properties of the drug product. To date, the HLA binding properties of peptides containing UAA are not accurately estimated by most algorithms. Both scenarios warrant the need for enhanced predictive tools. The authors developed an in silico method for modeling the impact of a given UAA on a peptide's likelihood of binding to HLA and, by extension, its immunogenic potential. In silico assessment of immunogenic potential allows for risk-based selection of best candidate peptides in further confirmatory in vitro, ex vivo and in vivo assays, thereby reducing the overall cost of immunogenicity evaluation. Examples demonstrating in silico immunogenicity prediction for product impurities that are commonly found in formulations of the generic peptides teriparatide and semaglutide are provided. Next, this article discusses how HLA binding studies can be used to estimate the binding potentials of commonly encountered UAA and "correct" in silico estimates of binding based on their naturally occurring counterparts. As demonstrated here, these in vitro binding studies are usually performed with known ligands which have been modified to contain UAA in HLA anchor positions. An example using D-amino acids in relative binding position 1 (P1) of the PADRE peptide is presented. As more HLA binding data become available, new predictive models allowing for the direct estimation of HLA binding for peptides containing UAA can be established.
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190
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Bugada LF, Smith MR, Wen F. Rapid Identification of MHCII-Binding Peptides Through Microsphere-Assisted Peptide Screening (MAPS). Methods Mol Biol 2022; 2574:233-250. [PMID: 36087205 DOI: 10.1007/978-1-0716-2712-9_11] [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
CD4+ T cells play a vital role in the immune response, and their function requires T cell receptor (TCR) recognition of peptide epitopes presented in complex with MHC class II (MHCII) molecules. Consequently, rapidly identifying peptides that bind MHCII is critical to understanding and treating infectious disease, cancer, autoimmunity, allergy, and transplant rejection. Computational methods provide a fast, ultrahigh-throughput approach to predict MHCII-binding peptides but lack the accuracy of experimental methods. In contrast, experimental methods offer accurate, quantitative results at the expense of speed. To address the gap between these two approaches, we developed a high-throughput, semiquantitative experimental screening strategy termed microsphere-assisted peptide screening (MAPS). Here, we use the Zika virus envelope protein as an example to demonstrate the rapid identification of MHCII-binding peptides from a single pathogenic protein using MAPS. This process involves several key steps including peptide library design, peptide exchange into MHCII, peptide-MHCII loading onto microspheres, flow cytometry screening, and data analysis to identify peptides that bind to one or more MHCII alleles.
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Affiliation(s)
- Luke F Bugada
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Mason R Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
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191
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Hernández DG, Camacho Ramírez N, Mosquera Martínez M, Cendales PA, Camacho BA. Description of HLA-DRB1*14:02:09, a novel HLA allele identified in a Colombian donor. HLA 2021; 99:405-407. [PMID: 34951145 DOI: 10.1111/tan.14519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/26/2022]
Abstract
HLA-DRB1*14:02:09 differs from HLA-DRB1*14:02:01:02 by a single nucleotide substitution in codon 169 of exon 3. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | | | | | - Paola Andrea Cendales
- Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud - IDCBIS, Bogotá, Colombia
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192
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Kubanov AA, Chikin VV, Karamova AE, Znamenskaya LF, Artamonova OG, Verbenko DA. Genetic markers for psoriatic arthritis among patients with psoriasis. Part II: HLA genes. VESTNIK DERMATOLOGII I VENEROLOGII 2021. [DOI: 10.25208/vdv1269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Psoriatic arthritis often leads to the development of severe outcomes ankylosis, deformities of the affected joints with severe impairment of their functions and disability. Early identification of patients with psoriasis with an increased risk of developing psoriatic arthritis for the purpose of its timely diagnosis and early initiation of therapy can prevent the development of severe disease outcomes. It is believed that the genes of the HLA system make the greatest individual genetic contribution to the formation of a predisposition to hereditary diseases with polygenic inheritance. The literature review considers the polymorphisms of the genes of the HLA system, associated with the development of psoriatic arthritis, in patients with psoriasis. The HLA alleles that contribute to the development of psoriatic arthritis and its individual forms have been identified. HLA alleles have been identified, which have a protective effect against the development of psoriatic arthritis.
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193
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Sauerer T, Lischer C, Weich A, Berking C, Vera J, Dörrie J. Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Front Microbiol 2021; 12:785662. [PMID: 35003017 PMCID: PMC8727593 DOI: 10.3389/fmicb.2021.785662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencing via the Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
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Affiliation(s)
- Tatjana Sauerer
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christopher Lischer
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Adrian Weich
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Carola Berking
- Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Julio Vera
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Jan Dörrie
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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194
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Niemann M, Matern BM, Spierings E, Schaub S, Hönger G. Peptides Derived From Mismatched Paternal Human Leukocyte Antigen Predicted to Be Presented by HLA-DRB1, -DRB3/4/5, -DQ, and -DP Induce Child-Specific Antibodies in Pregnant Women. Front Immunol 2021; 12:797360. [PMID: 34992608 PMCID: PMC8725048 DOI: 10.3389/fimmu.2021.797360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Predicted Indirectly ReCognizable Human Leukocyte Antigen (HLA) Epitopes (PIRCHE) are known to be a significant risk factor for the development of donor HLA-specific antibodies after organ transplantation. Most previous studies on PIRCHE limited their analyses on the presentation of the HLA-DRB1 locus, although HLA-DRB3/4/5, -DQ, and -DP are also known for presenting allopeptides to CD4+ T cells. In this study, we analyzed the impact of predicted allopeptides presented by these additional loci on the incidence of HLA-specific antibodies after an immunization event. We considered pregnancy as a model system of an HLA immunization and observed child-specific HLA antibody (CSA) development of 231 mothers during pregnancy by samples being taken at delivery. Our data confirm that PIRCHE presented by HLA-DRB1 along with HLA-DRB3/4/5, -DQ, and -DP are significant predictors for the development of CSA. Although there was limited peptidome overlap observed within the mothers’ presenting HLA proteins, combining multiple presenting loci in a single predictor improved the model only marginally. Prediction performance of PIRCHE further improved when normalizing scores by the respective presenters’ binding promiscuity. Immunogenicity analysis of specific allopeptides could not identify significant drivers of an immune response in this small cohort, suggesting confirmatory studies.
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Affiliation(s)
- Matthias Niemann
- Research and Development, PIRCHE AG, Berlin, Germany
- *Correspondence: Matthias Niemann,
| | - Benedict M. Matern
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
- Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Gideon Hönger
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
- Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
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195
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Martín-Galiano AJ, Díez-Fuertes F, McConnell MJ, López D. Predicted Epitope Abundance Supports Vaccine-Induced Cytotoxic Protection Against SARS-CoV-2 Variants of Concern. Front Immunol 2021; 12:732693. [PMID: 34899692 PMCID: PMC8656262 DOI: 10.3389/fimmu.2021.732693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
The effect of emerging SARS-CoV-2 variants on vaccine efficacy is of critical importance. In this study, the potential impact of mutations that facilitate escape from the cytotoxic cellular immune response in these new virus variants for the 551 most abundant HLA class I alleles was analyzed. Computational prediction showed that most of these alleles, that cover >90% of the population, contain enough epitopes without escape mutations in the principal SARS-CoV-2 variants. These data suggest that the cytotoxic cellular immune protection elicited by vaccination is not greatly affected by emerging SARS-CoV-2 variants.
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Affiliation(s)
- Antonio J Martín-Galiano
- Intrahospital Infection Laboratory, National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Francisco Díez-Fuertes
- Acquired Immune Deficiency Syndrome (AIDS) Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Michael J McConnell
- Intrahospital Infection Laboratory, National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Daniel López
- Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
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196
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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197
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Cargou M, Andreani M, Galluccio T, Ralazamahaleo M, Visentin J. Characterization of the novel HLA-DQA1*05:49 allele by sequencing-based typing. HLA 2021; 99:140-141. [PMID: 34837666 DOI: 10.1111/tan.14500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/27/2022]
Abstract
HLA-DQA1*05:49 differs from HLA-DQA1*05:01:01:02 by one nucleotide substitution in codon 78 in exon 2.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Tiziana Galluccio
- Laboratorio d'Immunogenetica dei Trapianti, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France.,University of Bordeaux, CNRS, ImmunoConcEpT, Bordeaux, France
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198
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Cargou M, Elsermans V, Cambridge CA, Guidicelli G, Visentin J. Characterization of the novel HLA-DPB1*665:01:02 allele by sequencing-based typing. HLA 2021; 99:150-152. [PMID: 34837466 DOI: 10.1111/tan.14496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]
Abstract
HLA-DPB1*665:01:02 differs from HLA-DPB1*665:01:01 by one nucleotide substitution in codon 139 in exon 3.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | | | | | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France.,Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France
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199
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Cargou M, Andreani M, Troiano M, Wojciechowski E, Visentin J. Characterization of the novel HLA-DRB4*01:151 allele by sequencing-based typing. HLA 2021; 99:64-66. [PMID: 34837481 DOI: 10.1111/tan.14501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/03/2023]
Abstract
HLA-DRB4*01:151 differs from DRB4*01:01:01:01 by one nucleotide substitution in codon 178 in exon 3.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Maria Troiano
- Laboratorio d'Immunogenetica dei Trapianti, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,CNRS, ImmunoConcEpT, University of Bordeaux, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France.,CNRS, ImmunoConcEpT, University of Bordeaux, Bordeaux, France
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200
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Cargou M, Elsermans V, Top I, Guidicelli G, Visentin J. Characterization of the novel HLA-B*57:146 allele by sequencing-based typing. HLA 2021; 99:389-390. [PMID: 34837669 DOI: 10.1111/tan.14497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
HLA-B*57:146 differs from HLA-B*57:01:01:01 by one nucleotide substitution in codon 103 in exon 3.
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Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Vincent Elsermans
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Isabelle Top
- CHU de Lille, Institut d'Immunologie-HLA, Bd du Professeur Jules Leclercq, Lille, France
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France.,CNRS, ImmunoConcEpT, UMR 5164, Univ. Bordeaux, Bordeaux, France
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