Computer‐aided design of T‐cell epitope‐based vaccines: addressing population coverage
Identifieur interne : 000797 ( Istex/Corpus ); précédent : 000796; suivant : 000798Computer‐aided design of T‐cell epitope‐based vaccines: addressing population coverage
Auteurs : P. Oyarzun ; B. KobeSource :
- International Journal of Immunogenetics [ 1744-3121 ] ; 2015-10.
Abstract
Epitope‐based vaccines (EVs) make use of short antigen‐derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. EVs potentially allow for precise control over the immune response activation by focusing on the most relevant – immunogenic and conserved – antigen regions. Experimental screening of large sets of peptides is time‐consuming and costly; therefore, in silico methods that facilitate T‐cell epitope mapping of protein antigens are paramount for EV development. The prediction of T‐cell epitopes focuses on the peptide presentation process by proteins encoded by the major histocompatibility complex (MHC). Because different MHCs have different specificities and T‐cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T‐cell epitopes are restricted by MHC proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the MHC proteins, EVs could fail to adequately cover the target population. This article reviews state‐of‐the‐art algorithms and computational tools to guide EV design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.
Url:
DOI: 10.1111/iji.12214
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ISTEX:0D19E4B76AB50CEA901283D95F02946C14C3D9B5Le document en format XML
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Tel: +61 7 3365 2132; Fax: +61 3365 4699; E‐mail:</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: patricio.oyarzun@uss.clb.kobe@uq.edu.au</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">International Journal of Immunogenetics</title><title level="j" type="alt">INTERNATIONAL JOURNAL OF IMMUNOGENETICS</title><idno type="ISSN">1744-3121</idno><idno type="eISSN">1744-313X</idno><imprint><biblScope unit="vol">42</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="313">313</biblScope><biblScope unit="page" to="321">321</biblScope><biblScope unit="page-count">9</biblScope><date type="published" when="2015-10">2015-10</date></imprint><idno type="ISSN">1744-3121</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1744-3121</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">Epitope‐based vaccines (EVs) make use of short antigen‐derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. 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Therefore, without careful consideration of the specificity and prevalence of the MHC proteins, EVs could fail to adequately cover the target population. This article reviews state‐of‐the‐art algorithms and computational tools to guide EV design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>P. Oyarzun</name><affiliations><json:string>Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción, Chile</json:string><json:string>Correspondence: Patricio Oyarzun, Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Campus Las Tres Pascualas, Lientur 1457, Concepción, Chile. 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Because different <hi rend="fc">MHC</hi>s have different specificities and T‐cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T‐cell epitopes are restricted by <hi rend="fc">MHC</hi> proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the <hi rend="fc">MHC</hi> proteins, <hi rend="fc">EV</hi>s could fail to adequately cover the target population. This article reviews state‐of‐the‐art algorithms and computational tools to guide <hi rend="fc">EV</hi> design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.</p></abstract><textClass><keywords rend="articleCategory"><term>Review</term></keywords><keywords rend="tocHeading1"><term>REVIEW ARTICLE</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-WQWBT8SM-K/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component type="serialArticle" version="2.0" xml:id="iji12214" xml:lang="en"><header><publicationMeta level="product"><doi origin="wiley" registered="yes">10.1111/(ISSN)1744-313X</doi><issn type="print">1744-3121</issn><issn type="electronic">1744-313X</issn><idGroup><id type="product" value="IJI"></id></idGroup><titleGroup><title sort="INTERNATIONAL JOURNAL OF IMMUNOGENETICS" type="main">International Journal of Immunogenetics</title><title type="short">Int J Immunogenet</title></titleGroup></publicationMeta><publicationMeta level="part" position="50"><doi origin="wiley">10.1111/iji.2015.42.issue-5</doi><copyright ownership="publisher">Copyright © 2015 John Wiley & Sons Ltd</copyright><numberingGroup><numbering type="journalVolume" number="42">42</numbering><numbering type="journalIssue">5</numbering></numberingGroup><coverDate startDate="2015-10">October 2015</coverDate></publicationMeta><publicationMeta level="unit" position="10" status="forIssue" type="reviewArticle"><doi>10.1111/iji.12214</doi><idGroup><id type="unit" value="IJI12214"></id></idGroup><countGroup><count number="9" type="pageTotal"></count></countGroup><titleGroup><title type="articleCategory">Review</title><title type="tocHeading1">REVIEW ARTICLE</title></titleGroup><copyright ownership="publisher">© 2015 John Wiley & Sons Ltd</copyright><eventGroup><event date="2015-03-19" type="manuscriptReceived"></event><event date="2015-04-28" type="manuscriptRevised"></event><event date="2015-05-25" type="manuscriptAccepted"></event><event agent="SPS" date="2015-06-03" type="xmlCreated"></event><event type="publishedOnlineEarlyUnpaginated" date="2015-07-24"></event><event type="firstOnline" date="2015-07-24"></event><event type="publishedOnlineFinalForm" date="2015-08-25"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.7.5 mode:FullText" date="2016-01-23"></event></eventGroup><numberingGroup><numbering type="pageFirst">313</numbering><numbering type="pageLast">321</numbering></numberingGroup><correspondenceTo><lineatedText><line>Correspondence: Patricio Oyarzun, Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Campus Las Tres Pascualas, Lientur 1457, Concepción, Chile. Tel: +56 41 2487962; Fax: +56 41 400002; E‐mail: <email>patricio.oyarzun@uss.cl</email></line><line>Bostjan Kobe, School of Chemistry and Molecular Biosciences, University of Queeland, Brisbane, Qld 4072, Australia. Tel: +61 7 3365 2132; Fax: +61 3365 4699; E‐mail: <email>b.kobe@uq.edu.au</email></line></lineatedText></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:IJI.IJI12214.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">Computer‐aided design of T‐cell epitope‐based vaccines: addressing population coverage</title><title type="shortAuthors">P. Oyarzun & B. Kobe</title></titleGroup><creators><creator affiliationRef="#iji12214-aff-0001" corresponding="yes" creatorRole="author" xml:id="iji12214-cr-0001"><idGroup><id type="orcid" value="http://orcid.org/0000-0001-7305-1632"></id></idGroup><personName><givenNames>P.</givenNames> <familyName>Oyarzun</familyName></personName></creator><creator affiliationRef="#iji12214-aff-0002" creatorRole="author" corresponding="yes" xml:id="iji12214-cr-0002"><personName><givenNames>B.</givenNames> <familyName>Kobe</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="CL" type="organization" xml:id="iji12214-aff-0001"><orgDiv>Biotechnology Centre</orgDiv> <orgDiv>Facultad de Ingeniería y Tecnología</orgDiv> <orgName>Universidad San Sebastián</orgName> <address><city>Concepción</city> <country>Chile</country></address></affiliation><affiliation countryCode="AU" type="organization" xml:id="iji12214-aff-0002"><orgDiv>School of Chemistry and Molecular Biosciences</orgDiv> <orgDiv>Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre</orgDiv> <orgName>University of Queensland</orgName> <address><city>Brisbane</city> <countryPart>QLD</countryPart> <country>Australia</country></address></affiliation></affiliationGroup><fundingInfo><fundingAgency>National Health and Medical Research Council (NHMRC, Australia)</fundingAgency><fundingNumber>1003325</fundingNumber></fundingInfo><abstractGroup><abstract type="main" xml:id="iji12214-abs-0001"><title type="main">Summary</title><p>Epitope‐based vaccines (<fc>EV</fc>s) make use of short antigen‐derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. <fc>EV</fc>s potentially allow for precise control over the immune response activation by focusing on the most relevant – immunogenic and conserved – antigen regions. Experimental screening of large sets of peptides is time‐consuming and costly; therefore, <i>in silico</i> methods that facilitate T‐cell epitope mapping of protein antigens are paramount for <fc>EV</fc> development. The prediction of T‐cell epitopes focuses on the peptide presentation process by proteins encoded by the major histocompatibility complex (<fc>MHC</fc>). Because different <fc>MHC</fc>s have different specificities and T‐cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T‐cell epitopes are restricted by <fc>MHC</fc> proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the <fc>MHC</fc> proteins, <fc>EV</fc>s could fail to adequately cover the target population. This article reviews state‐of‐the‐art algorithms and computational tools to guide <fc>EV</fc> design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Computer‐aided design of T‐cell epitope‐based vaccines: addressing population coverage</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Computer‐aided design of T‐cell epitope‐based vaccines: addressing population coverage</title></titleInfo><name type="personal"><namePart type="given">P.</namePart><namePart type="family">Oyarzun</namePart><affiliation>Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción, Chile</affiliation><affiliation>Correspondence: Patricio Oyarzun, Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Campus Las Tres Pascualas, Lientur 1457, Concepción, Chile. Tel: +56 41 2487962; Fax: +56 41 400002; E‐mail: Bostjan Kobe, School of Chemistry and Molecular Biosciences, University of Queeland, Brisbane, Qld 4072, Australia. Tel: +61 7 3365 2132; Fax: +61 3365 4699; E‐mail:</affiliation><affiliation>E-mail: patricio.oyarzun@uss.clb.kobe@uq.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">B.</namePart><namePart type="family">Kobe</namePart><affiliation>School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD, Brisbane, Australia</affiliation><affiliation>Correspondence: Patricio Oyarzun, Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Campus Las Tres Pascualas, Lientur 1457, Concepción, Chile. Tel: +56 41 2487962; Fax: +56 41 400002; E‐mail: Bostjan Kobe, School of Chemistry and Molecular Biosciences, University of Queeland, Brisbane, Qld 4072, Australia. Tel: +61 7 3365 2132; Fax: +61 3365 4699; E‐mail:</affiliation><affiliation>E-mail: patricio.oyarzun@uss.clb.kobe@uq.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="reviewArticle" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2015-10</dateIssued><dateCreated encoding="w3cdtf">2015-06-03</dateCreated><dateCaptured encoding="w3cdtf">2015-03-19</dateCaptured><dateValid encoding="w3cdtf">2015-05-25</dateValid><copyrightDate encoding="w3cdtf">2015</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract>Epitope‐based vaccines (EVs) make use of short antigen‐derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. EVs potentially allow for precise control over the immune response activation by focusing on the most relevant – immunogenic and conserved – antigen regions. Experimental screening of large sets of peptides is time‐consuming and costly; therefore, in silico methods that facilitate T‐cell epitope mapping of protein antigens are paramount for EV development. The prediction of T‐cell epitopes focuses on the peptide presentation process by proteins encoded by the major histocompatibility complex (MHC). Because different MHCs have different specificities and T‐cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T‐cell epitopes are restricted by MHC proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the MHC proteins, EVs could fail to adequately cover the target population. 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