{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T23:51:23Z","timestamp":1780098683903,"version":"3.54.0"},"reference-count":67,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T00:00:00Z","timestamp":1712534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Antibodies are generated with great diversity in nature resulting in a set of molecules, each optimized to bind a specific target. Taking advantage of their diversity and specificity, antibodies make up for a large part of recently developed biologic drugs. For therapeutic use antibodies need to fulfill several criteria to be safe and efficient. Polyspecific antibodies can bind structurally unrelated molecules in addition to their main target, which can lead to side effects and decreased efficacy in a therapeutic setting, for example via reduction of effective drug levels. Therefore, we created a neural-network-based model to predict polyspecificity of antibodies using the heavy chain variable region sequence as input. We devised a strategy for enriching antibodies from an immunization campaign either for antigen-specific or polyspecific binding properties, followed by generation of a large sequencing data set for training and cross-validation of the model. We identified important physico-chemical features influencing polyspecificity by investigating the behaviour of this model. This work is a machine-learning-based approach to polyspecificity prediction and, besides increasing our understanding of polyspecificity, it might contribute to therapeutic antibody development.<\/jats:p>","DOI":"10.3389\/fbinf.2023.1286883","type":"journal-article","created":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T08:10:06Z","timestamp":1712563806000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Prediction of polyspecificity from antibody sequence data by machine learning"],"prefix":"10.3389","volume":"3","author":[{"given":"Szabolcs","family":"\u00c9li\u00e1s","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemens","family":"Wrzodek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte M.","family":"Deane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain C.","family":"Tissot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Klostermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Ros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,4,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1046\/j.1365-2567.2001.01159.x","article-title":"Molecular structure of eight human autoreactive monoclonal antibodies","volume":"102","author":"Aguilera","year":"2001","journal-title":"Immunology"},{"key":"B2","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"B3","doi-asserted-by":"publisher","first-page":"316ra192\u2014316ra192","DOI":"10.1126\/scitranslmed.aad0522","article-title":"Immune history profoundly affects broadly protective B cell responses to influenza","volume":"7","author":"Andrews","year":"2015","journal-title":"Sci. Transl. Med."},{"key":"B4","doi-asserted-by":"publisher","first-page":"4624","DOI":"10.1073\/pnas.86.12.4624","article-title":"Two murine natural polyreactive autoantibodies are encoded by nonmutated germ-line genes","volume":"86","author":"Baccala","year":"1989","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B5","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B Methodol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1111\/j.1399-3011.1988.tb01258.x","article-title":"Positional flexibilities of amino acid residues in globular proteins","volume":"32","author":"Bhaskaran","year":"1988","journal-title":"Int. J. Peptide Protein Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"146","DOI":"10.3233\/hab-1997-8306","article-title":"Heavy chain variable gene usage by human B-1 lymphocytes and polyreactive autoantibodies","volume":"8","author":"Bhat","year":"1997","journal-title":"Hum. Antibodies"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1016\/j.jmb.2008.01.093","article-title":"The intrinsic contributions of tyrosine, serine, Glycine and arginine to the affinity and specificity of antibodies","volume":"377","author":"Birtalan","year":"2008","journal-title":"J. Mol. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1002\/prot.24756","article-title":"Prediction of VH-VL domain orientation for antibody variable domain modeling","volume":"83","author":"Bujotzek","year":"2015","journal-title":"Proteins"},{"key":"B10","doi-asserted-by":"publisher","first-page":"eaan6619","DOI":"10.1126\/science.aan6619","article-title":"Natural polyreactive IgA antibodies coat the intestinal microbiota","volume":"358","author":"Bunker","year":"2017","journal-title":"Science"},{"key":"B11","doi-asserted-by":"publisher","first-page":"11937","DOI":"10.1073\/pnas.0904191106","article-title":"Design of therapeutic proteins with enhanced stability","volume":"106","author":"Chennamsetty","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1016\/j.molimm.2007.07.043","article-title":"The acquisition of narrow binding specificity by polyspecific natural IgM antibodies in a semi-physiological environment","volume":"45","author":"Chu","year":"2008","journal-title":"Mol. Immunol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1046\/j.1365-2249.2000.01096.x","article-title":"Molecular determinants of polyreactive antibody binding: HCDR3 and cyclic peptides","volume":"119","author":"Deng","year":"2000","journal-title":"Clin. Exp. Immunol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1016\/j.bbrc.2010.06.073","article-title":"Heterogeneous antigen recognition behavior of induced polyspecific antibodies","volume":"398","author":"Dimitrov","year":"2010","journal-title":"Biochem. Biophysical Res. Commun."},{"key":"B15","doi-asserted-by":"publisher","first-page":"993","DOI":"10.4049\/jimmunol.1300880","article-title":"Antibody polyreactivity in health and disease: statu variabilis","volume":"191","author":"Dimitrov","year":"2013","journal-title":"J. Immunol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"17767","DOI":"10.1074\/jbc.m114.556266","article-title":"A cryptic polyreactive antibody recognizes distinct clades of HIV-1 glycoprotein 120 by an identical binding mechanism","volume":"289","author":"Dimitrov","year":"2014","journal-title":"J. Biol. Chem."},{"key":"B17","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.addr.2016.11.004","article-title":"The state-of-play and future of antibody therapeutics","volume":"122","author":"Elgundi","year":"2016","journal-title":"Adv. drug Deliv. Rev."},{"key":"B18","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1046\/j.1365-3083.1997.d01-397.x","article-title":"Polyreactive binding of antibodies generated by polyclonal B cell activation. I. Polyreactivity could be caused by differential glycosylation of immunoglobulins","volume":"45","author":"Fern\u00e1ndez","year":"","journal-title":"Scand. J. Immunol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1046\/j.1365-3083.1997.d01-398.x","article-title":"Polyreactive binding of antibodies generated by polyclonal B cell activation. II. Crossreactive and monospecific antibodies can be generated from an identical Ig rearrangement by differential glycosylation","volume":"45","author":"Fern\u00e1ndez","year":"","journal-title":"Scand. J. Immunol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"177","DOI":"10.48550\/arXiv.1801.01489","article-title":"All models are wrong, but many are useful: learning a variable\u2019s importance by studying an entire class of prediction models simultaneously","volume":"20","author":"Fisher","year":"2019","journal-title":"J. Mach. Learn. Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"12","DOI":"10.3390\/antib9020012","article-title":"A review of deep learning methods for antibodies","volume":"9","author":"Graves","year":"2020","journal-title":"Antibodies (Basel)"},{"key":"B22","doi-asserted-by":"publisher","first-page":"7554","DOI":"10.1038\/s41467-022-35276-4","article-title":"An in silico method to assess antibody fragment polyreactivity","volume":"13","author":"Harvey","year":"2022","journal-title":"Nat. Commun."},{"key":"B23","first-page":"515","article-title":"Rapid, reliable ligation-independent cloning of PCR products using modified plasmid vectors","volume":"13","author":"Haun","year":"1992","journal-title":"BioTechniques"},{"key":"B24","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1084\/jem.180.3.885","article-title":"Analysis of the structural correlates for antibody polyreactivity by multiple reassortments of chimeric human immunoglobulin heavy and light chain V segments","volume":"180","author":"Ichiyoshi","year":"1994","journal-title":"J. Exp. Med."},{"key":"B25","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1073\/pnas.1616408114","article-title":"Biophysical properties of the clinical-stage antibody landscape","volume":"114","author":"Jain","year":"2017","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B26","doi-asserted-by":"publisher","first-page":"413","DOI":"10.3389\/fimmu.2018.00413","article-title":"Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification","volume":"9","author":"Jeliazkov","year":"2018","journal-title":"Front. Immunol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"780","DOI":"10.24297\/jbt.v6i1.4013","article-title":"A graph-theoretic model of single point mutations in the cystic fibrosis transmembrane conductance regulator","volume":"6","author":"Kakraba","year":"2016","journal-title":"J. Adv. Biotechnol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"D202","DOI":"10.1093\/nar\/gkm998","article-title":"AAindex: amino acid index database, progress report 2008","volume":"36","author":"Kawashima","year":"2007","journal-title":"Nucleic acids Res."},{"key":"B29","volume-title":"Adam: a method for stochastic optimization","author":"Kingma","year":"2017"},{"key":"B30","volume-title":"Deep sequencing based analysis of ig repertoire in humanized mice","author":"Klostermann","year":"2015"},{"key":"B31","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.molimm.2019.06.012","article-title":"Sequence features of variable region determining physicochemical properties and polyreactivity of therapeutic antibodies","volume":"112","author":"Lecerf","year":"2019","journal-title":"Mol. Immunol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.dci.2004.07.003","article-title":"IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains","volume":"29","author":"Lefranc","year":"2005","journal-title":"Dev. Comp. Immunol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/nmeth1010","article-title":"Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC","volume":"4","author":"Li","year":"2007","journal-title":"Nat. Methods"},{"key":"B34","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Mago\u010d","year":"2011","journal-title":"Bioinformatics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1016\/j.cels.2023.04.009","article-title":"Simplifying complex antibody engineering using machine learning","volume":"14","author":"Makowski","year":"","journal-title":"cels"},{"key":"B36","doi-asserted-by":"publisher","first-page":"3788","DOI":"10.1038\/s41467-022-31457-3","article-title":"Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space","volume":"13","author":"Makowski","year":"2022","journal-title":"Nat. Commun."},{"key":"B37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41551-023-01074-6","article-title":"Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning","author":"Makowski","year":"","journal-title":"Nat. Biomed. Eng."},{"key":"B38","doi-asserted-by":"publisher","first-page":"9823","DOI":"10.1074\/jbc.REV120.010181","article-title":"How repertoire data are changing antibody science","volume":"295","author":"Marks","year":"2020","journal-title":"J. Biol. Chem."},{"key":"B39","doi-asserted-by":"publisher","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"UMAP: Uniform Manifold approximation and projection","volume":"3","author":"McInnes","year":"2018","journal-title":"J. Open Source Softw."},{"key":"B40","doi-asserted-by":"publisher","first-page":"9727","DOI":"10.1073\/pnas.0803644105","article-title":"Autoreactive IgG memory antibodies in patients with systemic lupus erythematosus arise from nonreactive and polyreactive precursors","volume":"105","author":"Mietzner","year":"2008","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B41","doi-asserted-by":"publisher","first-page":"224","DOI":"10.3389\/fimmu.2018.00224","article-title":"Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires","volume":"9","author":"Miho","year":"2018","journal-title":"Front. Immunol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1021\/bi801901d","article-title":"Association energetics of cross-reactive and specific antibodies","volume":"48","author":"Mohan","year":"2009","journal-title":"Biochemistry"},{"key":"B43","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/nature09385","article-title":"Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation","volume":"467","author":"Mouquet","year":"2010","journal-title":"Nature"},{"key":"B44","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1126\/science.286.5447.2156","article-title":"Control of early viral and bacterial distribution and disease by natural antibodies","volume":"286","author":"Ochsenbein","year":"1999","journal-title":"Science"},{"key":"B45","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1002\/eji.200424936","article-title":"Somatic mutations can lead to a loss of superantigenic and polyreactive binding","volume":"34","author":"Oppezzo","year":"2004","journal-title":"Eur. J. Immunol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1016\/j.celrep.2019.03.032","article-title":"HIV-1 envelope recognition by polyreactive and cross-reactive intestinal B cells","volume":"27","author":"Planchais","year":"2019","journal-title":"Cell Rep."},{"key":"B47","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.cimid.2017.08.002","article-title":"Development, phenotype, and function of non-conventional B cells","volume":"54","author":"Prieto","year":"2017","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"B48","doi-asserted-by":"publisher","first-page":"2568","DOI":"10.1016\/j.celrep.2018.04.101","article-title":"Conformational plasticity in broadly neutralizing HIV-1 antibodies triggers polyreactivity","volume":"23","author":"Prigent","year":"2018","journal-title":"Cell Rep."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1021\/bi00405a042","article-title":"Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution","volume":"27","author":"Radzicka","year":"1988","journal-title":"Biochemistry"},{"key":"B50","doi-asserted-by":"publisher","first-page":"311","DOI":"10.4049\/jimmunol.2300136","article-title":"Defining and studying B cell receptor and TCR interactions","volume":"211","author":"Rappazzo","year":"2023","journal-title":"J. Immunol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1002\/jmr.2394","article-title":"Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition","volume":"27","author":"Regenmortel","year":"2014","journal-title":"J. Mol. Recognit. JMR"},{"key":"B52","doi-asserted-by":"publisher","first-page":"1846900","DOI":"10.1080\/19420862.2020.1846900","article-title":"Rabbits transgenic for human IgG genes recapitulating rabbit B-cell biology to generate human antibodies of high specificity and affinity","volume":"12","author":"Ros","year":"2020","journal-title":"MAbs"},{"key":"B53","doi-asserted-by":"publisher","first-page":"45","DOI":"10.3390\/antib8030045","article-title":"Back-to-Germline (B2G) procedure for antibody devolution","volume":"8","author":"Schrade","year":"2019","journal-title":"Antibodies (Basel)"},{"key":"B54","doi-asserted-by":"publisher","first-page":"e86184","DOI":"10.1371\/journal.pone.0086184","article-title":"A robust high throughput platform to generate functional recombinant monoclonal antibodies using rabbit B cells from peripheral blood","volume":"9","author":"Seeber","year":"2014","journal-title":"PLoS ONE"},{"key":"B55","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/bf00209287","article-title":"Molecular characterization of the variable regions of a mouse polyreactive IgG2b antibody with rheumatoid factor activity","volume":"36","author":"Sequeira","year":"1992","journal-title":"Immunogenetics"},{"key":"B56","doi-asserted-by":"publisher","first-page":"3300","DOI":"10.1016\/j.celrep.2019.08.056","article-title":"Affinity maturation enhances antibody specificity but compromises conformational stability","volume":"28","author":"Shehata","year":"2019","journal-title":"Cell Rep."},{"key":"B57","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1007\/bf01541346","article-title":"Half-life of polyreactive antibodies","volume":"14","author":"Sigounas","year":"1994","journal-title":"J. Clin. Immunol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"6335","DOI":"10.1073\/pnas.94.12.6335","article-title":"The epitopes for natural polyreactive antibodies are rich in proline","volume":"94","author":"Tchernychev","year":"1997","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B59","doi-asserted-by":"publisher","first-page":"1426","DOI":"10.1002\/pro.5560060707","article-title":"Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association","volume":"6","author":"Tsai","year":"1997","journal-title":"Protein Sci."},{"key":"B60","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-immunol-020711-075032","article-title":"Germinal centers","volume":"30","author":"Victora","year":"2012","journal-title":"Annu. Rev. Immunol."},{"key":"B61","doi-asserted-by":"publisher","first-page":"1374","DOI":"10.1126\/science.1086907","article-title":"Predominant autoantibody production by early human B cell precursors","volume":"301","author":"Wardemann","year":"2003","journal-title":"Science"},{"key":"B62","doi-asserted-by":"publisher","first-page":"e1003045","DOI":"10.1371\/journal.pcbi.1003045","article-title":"Human germline antibody gene segments encode polyspecific antibodies","volume":"9","author":"Willis","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"B63","doi-asserted-by":"publisher","first-page":"1761","DOI":"10.1084\/jem.20060075","article-title":"Light chain editing generates polyreactive antibodies in chronic graft-versus-host reaction","volume":"203","author":"Witsch","year":"2006","journal-title":"J. Exp. Med."},{"key":"B64","doi-asserted-by":"publisher","first-page":"2844","DOI":"10.1073\/pnas.75.6.2844","article-title":"\u201cPanning\u201d for lymphocytes: a method for cell selection","volume":"75","author":"Wysocki","year":"1978","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B65","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1093\/protein\/gzt047","article-title":"Addressing polyspecificity of antibodies selected from an in vitro yeast presentation system: a FACS-based, high-throughput selection and analytical tool","volume":"26","author":"Xu","year":"2013","journal-title":"Protein Eng. Des. Sel. PEDS"},{"key":"B66","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.jaut.2009.03.011","article-title":"Polyreactive autoantibodies in systemic lupus erythematosus have pathogenic potential","volume":"33","author":"Zhang","year":"2009","journal-title":"J. Autoimmun."},{"key":"B67","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.chom.2007.01.002","article-title":"The broad antibacterial activity of the natural antibody repertoire is due to polyreactive antibodies","volume":"1","author":"Zhou","year":"2007","journal-title":"Cell Host Microbe"}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1286883\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T08:10:12Z","timestamp":1712563812000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1286883\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,8]]},"references-count":67,"alternative-id":["10.3389\/fbinf.2023.1286883"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2023.1286883","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,8]]},"article-number":"1286883"}}