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      Heterotypic immunity against vaccinia virus in an HLA-B*07:02 transgenic mousepox infection model

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          Abstract

          Vaccination with vaccinia virus (VACV) elicits heterotypic immunity to smallpox, monkeypox, and mousepox, the mechanistic basis for which is poorly understood. It is generally assumed that heterotypic immunity arises from the presentation of a wide array of VACV-derived, CD8 + T cell epitopes that share homology with other poxviruses. Herein this assumption was tested using a large panel of VACV-derived peptides presented by HLA-B*07:02 (B7.2) molecules in a mousepox/ectromelia virus (ECTV)-infection, B7.2 transgenic mouse model. Most dominant epitopes recognized by ECTV- and VACV-reactive CD8 + T cells overlapped significantly without altering immunodominance hierarchy. Further, several epitopes recognized by ECTV-reactive CD8 + T cells were not recognized by VACV-reactive CD8 + T cells, and vice versa. In one instance, the lack of recognition owed to a N72K variation in the ECTV C4R 70–78 variant of the dominant VACV B8R 70–78 epitope. C4R 70–78 does not bind to B7.2 and, hence, it was neither immunogenic nor antigenic. These findings provide a mechanistic basis for VACV vaccination-induced heterotypic immunity which can protect against Variola and Monkeypox disease. The understanding of how cross-reactive responses develop is essential for the rational design of a subunit-based vaccine that would be safe, and effectively protect against heterologous infection.

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          HLA class I supertypes: a revised and updated classification

          Background Class I major histocompatibility complex (MHC) molecules bind, and present to T cells, short peptides derived from intracellular processing of proteins. The peptide repertoire of a specific molecule is to a large extent determined by the molecular structure accommodating so-called main anchor positions of the presented peptide. These receptors are extremely polymorphic, and much of the polymorphism influences the peptide-binding repertoire. However, despite this polymorphism, class I molecules can be clustered into sets of molecules that bind largely overlapping peptide repertoires. Almost a decade ago we introduced this concept of clustering human leukocyte antigen (HLA) alleles and defined nine different groups, denominated as supertypes, on the basis of their main anchor specificity. The utility of this original supertype classification, as well several other subsequent arrangements derived by others, has been demonstrated in a large number of epitope identification studies. Results Following our original approach, in the present report we provide an updated classification of HLA-A and -B class I alleles into supertypes. The present analysis incorporates the large amount of class I MHC binding data and sequence information that has become available in the last decade. As a result, over 80% of the 945 different HLA-A and -B alleles examined to date can be assigned to one of the original nine supertypes. A few alleles are expected to be associated with repertoires that overlap multiple supertypes. Interestingly, the current analysis did not identify any additional supertype specificities. Conclusion As a result of this updated analysis, HLA supertype associations have been defined for over 750 different HLA-A and -B alleles. This information is expected to facilitate epitope identification and vaccine design studies, as well as investigations into disease association and correlates of immunity. In addition, the approach utilized has been made more transparent, allowing others to utilize the classification approach going forward.
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            Global analysis of protein folding using massively parallel design, synthesis, and testing

            Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.
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              Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism.

              Herein, we review the epitope approach to vaccine development, and discuss how knowledge of HLA supertypes might be used as a tool in the development of such vaccines. After reviewing the main structural features of the A2-, A3-, B7-, and B44- supertype alleles, and biological data demonstrating their immunological relevance, we analyze the frequency at which these supertype alleles are expressed in various ethnicities and discuss the relevance of those observations to vaccine development. Next, the existence of five new supertypes (A1, A24, B27, B58, and B62) is reported. As a result, it is possible to account for the predominance of all known HLA class I with only nine main functional binding specificities. The practical implications of this finding, as well as its relevance to understanding the functional implication of MHC polymorphism in humans, are discussed.
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                Author and article information

                Contributors
                sebastian.joyce@vumc.org
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                5 August 2020
                5 August 2020
                2020
                : 10
                : 13167
                Affiliations
                [1 ]ISNI 0000 0004 0420 4633, GRID grid.452900.a, Department of Veterans Affairs, , Tennessee Valley Healthcare System, ; Nashville, TN USA
                [2 ]ISNI 0000 0004 1936 9916, GRID grid.412807.8, Department of Pathology, Microbiology and Immunology, , Vanderbilt University Medical Centre, ; Nashville, TN USA
                [3 ]ISNI 0000 0001 2264 7217, GRID grid.152326.1, Department of Chemical and Biomolecular Engineering, , Vanderbilt University, ; Nashville, TN USA
                [4 ]ISNI 0000 0004 1936 9342, GRID grid.262962.b, Department of Molecular Microbiology and Immunology, , Saint Louis University School of Medicine, ; St. Louis, MO USA
                Author information
                http://orcid.org/0000-0003-2571-1290
                http://orcid.org/0000-0003-4874-2911
                http://orcid.org/0000-0002-9144-2634
                http://orcid.org/0000-0002-2191-6689
                http://orcid.org/0000-0002-1670-8041
                http://orcid.org/0000-0002-3183-1451
                Article
                69897
                10.1038/s41598-020-69897-w
                7406653
                32759969
                288093e9-b70d-44c5-96d0-7cd8c21809bd
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 February 2020
                : 13 July 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: AI121626
                Award ID: AI121626
                Award Recipient :
                Funded by: Saint Louis University
                Award ID: Start-up Funds
                Award Recipient :
                Funded by: VA Merit
                Award ID: BX001444
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                adaptive immunity,antigen processing and presentation,infection,vaccines,immunology
                Uncategorized
                adaptive immunity, antigen processing and presentation, infection, vaccines, immunology

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