[{"has_accepted_license":"1","publication":"Frontiers in Immunology","oa_version":"Published Version","article_number":"965446","month":"09","keyword":["Immunology","Immunology and Allergy","COVID-19","SARS-CoV-2","synthetic library","RBD","neutralization nanobody","VHH"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-16T00:00:00Z","publication_identifier":{"issn":["1664-3224"]},"oa":1,"file":[{"file_name":"2022_FrontiersImmunology_Dormeshkin.pdf","content_type":"application/pdf","date_updated":"2023-01-30T09:22:26Z","file_size":5695892,"checksum":"f8f5d8110710033d0532e7e08bf9dad4","date_created":"2023-01-30T09:22:26Z","creator":"dernst","file_id":"12443","access_level":"open_access","relation":"main_file","success":1}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","_id":"12252","author":[{"last_name":"Dormeshkin","first_name":"Dmitri","full_name":"Dormeshkin, Dmitri"},{"full_name":"Shapira, Michail","first_name":"Michail","last_name":"Shapira"},{"full_name":"Dubovik, Simon","last_name":"Dubovik","first_name":"Simon"},{"first_name":"Anton","last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","id":"4968f7ad-eb97-11eb-a6c2-8ed382e8912c"},{"full_name":"Katsin, Mikalai","last_name":"Katsin","first_name":"Mikalai"},{"first_name":"Alexandr","last_name":"Migas","full_name":"Migas, Alexandr"},{"full_name":"Meleshko, Alexander","first_name":"Alexander","last_name":"Meleshko"},{"last_name":"Semyonov","first_name":"Sergei","full_name":"Semyonov, Sergei"}],"department":[{"_id":"LeSa"}],"date_created":"2023-01-16T09:56:57Z","article_processing_charge":"No","publication_status":"published","intvolume":"        13","title":"Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library","quality_controlled":"1","file_date_updated":"2023-01-30T09:22:26Z","publisher":"Frontiers Media","article_type":"original","year":"2022","citation":{"apa":"Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas, A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>","ama":"Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>","chicago":"Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library,” <i>Frontiers in Immunology</i>, vol. 13. Frontiers Media, 2022.","short":"D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas, A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).","mla":"Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>, vol. 13, 965446, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>.","ista":"Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13, 965446."},"date_updated":"2023-08-04T09:49:24Z","external_id":{"isi":["000862479100001"]},"isi":1,"day":"16","doi":"10.3389/fimmu.2022.965446","abstract":[{"text":"The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 10<jats:sup>11</jats:sup> diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\\ml and 9.6 ng\\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.","lang":"eng"}],"volume":13,"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.","ddc":["570"]},{"has_accepted_license":"1","publication":"Frontiers in Immunology","article_number":"2153","month":"09","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2019-09-20T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1664-3224"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_id":"6984","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2019_FrontiersImmonology_Kelemen.pdf","date_updated":"2020-07-14T12:47:46Z","file_size":2083061,"checksum":"68d1708f7aa412544159b498ef17a6b9","date_created":"2019-11-04T15:54:00Z"}],"author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","first_name":"Réka K","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281"},{"full_name":"Rajakaruna, H","first_name":"H","last_name":"Rajakaruna"},{"first_name":"IA","last_name":"Cockburn","full_name":"Cockburn, IA"},{"last_name":"Ganusov","first_name":"VV","full_name":"Ganusov, VV"}],"scopus_import":"1","_id":"6983","pmid":1,"intvolume":"        10","title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","department":[{"_id":"BeVi"}],"article_processing_charge":"No","date_created":"2019-11-04T15:50:06Z","publication_status":"published","file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","article_type":"original","publisher":"Frontiers","external_id":{"isi":["000487187000001"],"pmid":["31616407"]},"isi":1,"citation":{"ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. 2019;10. doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., &#38; Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” <i>Frontiers in Immunology</i>, vol. 10. Frontiers, 2019.","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>.","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>, vol. 10, 2153, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>.","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153."},"year":"2019","date_updated":"2023-08-30T07:18:23Z","abstract":[{"text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.","lang":"eng"}],"day":"20","doi":"10.3389/fimmu.2019.02153","ddc":["570"],"volume":10},{"language":[{"iso":"eng"}],"quality_controlled":"1","article_type":"original","publisher":"Frontiers","author":[{"full_name":"Ilieva, Kristina M.","last_name":"Ilieva","first_name":"Kristina M."},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Achkova, Daniela Y.","last_name":"Achkova","first_name":"Daniela Y."},{"full_name":"Dodev, Tihomir S.","last_name":"Dodev","first_name":"Tihomir S."},{"first_name":"Silvia","last_name":"Mele","full_name":"Mele, Silvia"},{"last_name":"Crescioli","first_name":"Silvia","full_name":"Crescioli, Silvia"},{"full_name":"Bax, Heather J.","first_name":"Heather J.","last_name":"Bax"},{"first_name":"Anthony","last_name":"Cheung","full_name":"Cheung, Anthony"},{"full_name":"Karagiannis, Panagiotis","first_name":"Panagiotis","last_name":"Karagiannis"},{"full_name":"Correa, Isabel","last_name":"Correa","first_name":"Isabel"},{"last_name":"Figini","first_name":"Mariangela","full_name":"Figini, Mariangela"},{"full_name":"Marlow, Rebecca","last_name":"Marlow","first_name":"Rebecca"},{"first_name":"Debra H.","last_name":"Josephs","full_name":"Josephs, Debra H."},{"first_name":"Andrew J.","last_name":"Beavil","full_name":"Beavil, Andrew J."},{"full_name":"Maher, John","last_name":"Maher","first_name":"John"},{"full_name":"Spicer, James F.","first_name":"James F.","last_name":"Spicer"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"},{"full_name":"Tutt, Andrew N.","first_name":"Andrew N.","last_name":"Tutt"},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"}],"publication":"Frontiers in Immunology","_id":"8237","month":"09","title":"Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields","article_number":"1112","intvolume":"         8","publication_status":"published","oa_version":"Published Version","date_created":"2020-08-10T11:53:32Z","article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":8,"main_file_link":[{"url":"https://doi.org/10.3389/fimmu.2017.01112","open_access":"1"}],"date_published":"2017-09-11T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:17:39Z","year":"2017","citation":{"chicago":"Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev, Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” <i>Frontiers in Immunology</i>. Frontiers, 2017. <a href=\"https://doi.org/10.3389/fimmu.2017.01112\">https://doi.org/10.3389/fimmu.2017.01112</a>.","ieee":"K. M. Ilieva <i>et al.</i>, “Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields,” <i>Frontiers in Immunology</i>, vol. 8. Frontiers, 2017.","ama":"Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. <i>Frontiers in Immunology</i>. 2017;8. doi:<a href=\"https://doi.org/10.3389/fimmu.2017.01112\">10.3389/fimmu.2017.01112</a>","apa":"Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli, S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2017.01112\">https://doi.org/10.3389/fimmu.2017.01112</a>","ista":"Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J, Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 8, 1112.","short":"K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli, H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs, A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis, Frontiers in Immunology 8 (2017).","mla":"Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” <i>Frontiers in Immunology</i>, vol. 8, 1112, Frontiers, 2017, doi:<a href=\"https://doi.org/10.3389/fimmu.2017.01112\">10.3389/fimmu.2017.01112</a>."},"abstract":[{"lang":"eng","text":"Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells."}],"oa":1,"doi":"10.3389/fimmu.2017.01112","day":"11","publication_identifier":{"issn":["1664-3224"]}}]