The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27
Identifieur interne : 001168 ( Pmc/Checkpoint ); précédent : 001167; suivant : 001169The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27
Auteurs : Luke Hecht [Royaume-Uni] ; Anton Dormer [États-Unis]Source :
- Bioinformation [ 0973-8894 ] ; 2013.
Abstract
Url:
DOI: 10.6026/97320630009315
PubMed: 23745018
PubMed Central: 3607191
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:3607191Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27</title>
<author><name sortKey="Hecht, Luke" sort="Hecht, Luke" uniqKey="Hecht L" first="Luke" last="Hecht">Luke Hecht</name>
<affiliation wicri:level="4"><nlm:aff id="A2">Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT</nlm:aff>
<orgName type="university">Université d'Édimbourg</orgName>
<country>Royaume-Uni</country>
<placeName><settlement type="city">Édimbourg</settlement>
<region type="country">Écosse</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dormer, Anton" sort="Dormer, Anton" uniqKey="Dormer A" first="Anton" last="Dormer">Anton Dormer</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Washington Adventist University, Department of Biology, 7600 Flower Avenue Takoma Park, Maryland 20721</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Maryland</region>
</placeName>
<wicri:cityArea>Washington Adventist University, Department of Biology, 7600 Flower Avenue Takoma Park</wicri:cityArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">23745018</idno>
<idno type="pmc">3607191</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607191</idno>
<idno type="RBID">PMC:3607191</idno>
<idno type="doi">10.6026/97320630009315</idno>
<date when="2013">2013</date>
<idno type="wicri:Area/Pmc/Corpus">000B26</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B26</idno>
<idno type="wicri:Area/Pmc/Curation">000B26</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B26</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001168</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001168</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27</title>
<author><name sortKey="Hecht, Luke" sort="Hecht, Luke" uniqKey="Hecht L" first="Luke" last="Hecht">Luke Hecht</name>
<affiliation wicri:level="4"><nlm:aff id="A2">Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT</nlm:aff>
<orgName type="university">Université d'Édimbourg</orgName>
<country>Royaume-Uni</country>
<placeName><settlement type="city">Édimbourg</settlement>
<region type="country">Écosse</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dormer, Anton" sort="Dormer, Anton" uniqKey="Dormer A" first="Anton" last="Dormer">Anton Dormer</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Washington Adventist University, Department of Biology, 7600 Flower Avenue Takoma Park, Maryland 20721</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Maryland</region>
</placeName>
<wicri:cityArea>Washington Adventist University, Department of Biology, 7600 Flower Avenue Takoma Park</wicri:cityArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Bioinformation</title>
<idno type="ISSN">0973-8894</idno>
<idno type="eISSN">0973-2063</idno>
<imprint><date when="2013">2013</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p><italic>In silico</italic>
tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This
perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV.
Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database
were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27.
Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for
ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that
consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to
pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less
immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding,
of an arginine residue at the 2<sup>nd</sup>
position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with
HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that
has much relevance for the creation of personalized therapeutics for HIV treatment.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pandit, A" uniqKey="Pandit A">A Pandit</name>
</author>
<author><name sortKey="Sinha, S" uniqKey="Sinha S">S Sinha</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Middleton, D" uniqKey="Middleton D">D Middleton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grene, E" uniqKey="Grene E">E Grene</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tang, J" uniqKey="Tang J">J Tang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brander, C" uniqKey="Brander C">C Brander</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ammaranond, P" uniqKey="Ammaranond P">P Ammaranond</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shankarkumar, U" uniqKey="Shankarkumar U">U Shankarkumar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schneidewind, A" uniqKey="Schneidewind A">A Schneidewind</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wyatt, R" uniqKey="Wyatt R">R Wyatt</name>
</author>
<author><name sortKey="Sodroski, J" uniqKey="Sodroski J">J Sodroski</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kwong, Pd" uniqKey="Kwong P">PD Kwong</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brander, C" uniqKey="Brander C">C Brander</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bazykin, Ga" uniqKey="Bazykin G">GA Bazykin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Oliveira, T" uniqKey="De Oliveira T">T de Oliveira</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chenna, R" uniqKey="Chenna R">R Chenna</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Reche, Pa" uniqKey="Reche P">PA Reche</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Drummond, Aj" uniqKey="Drummond A">AJ Drummond</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Wu, X" uniqKey="Wu X">X Wu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Munier, Cm" uniqKey="Munier C">CM Munier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kim, Jh" uniqKey="Kim J">JH Kim</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Van Regenmortel, Mhv" uniqKey="Van Regenmortel M">MHV Van Regenmortel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Van Regenmortel, Mh" uniqKey="Van Regenmortel M">MH Van Regenmortel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rozera, G" uniqKey="Rozera G">G Rozera</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, Cc" uniqKey="Huang C">CC Huang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mester, B" uniqKey="Mester B">B Mester</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Seyed, N" uniqKey="Seyed N">N Seyed</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, Z" uniqKey="Li Z">Z Li</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xu, W" uniqKey="Xu W">W Xu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Warren, Rl" uniqKey="Warren R">RL Warren</name>
</author>
<author><name sortKey="Holt, Ra" uniqKey="Holt R">RA Holt</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Groot, As" uniqKey="De Groot A">AS De Groot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Groot, As" uniqKey="De Groot A">AS De Groot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jain, Kk" uniqKey="Jain K">KK Jain</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Flynn, Bj" uniqKey="Flynn B">BJ Flynn</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformation</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformation</journal-id>
<journal-id journal-id-type="publisher-id">Bioinformation</journal-id>
<journal-title-group><journal-title>Bioinformation</journal-title>
</journal-title-group>
<issn pub-type="ppub">0973-8894</issn>
<issn pub-type="epub">0973-2063</issn>
<publisher><publisher-name>Biomedical Informatics</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23745018</article-id>
<article-id pub-id-type="pmc">3607191</article-id>
<article-id pub-id-type="publisher-id">97320630009315</article-id>
<article-id pub-id-type="doi">10.6026/97320630009315</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Hypothesis</subject>
</subj-group>
</article-categories>
<title-group><article-title>The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Hecht</surname>
<given-names>Luke</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dormer</surname>
<given-names>Anton</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
<aff id="A1"><label>1</label>
Washington Adventist University, Department of Biology, 7600 Flower Avenue Takoma Park, Maryland 20721</aff>
<aff id="A2"><label>2</label>
Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT</aff>
</contrib-group>
<author-notes><corresp id="COR1"><label>*</label>
Anton Dormer: <email>adormer@wau.edu</email>
Phone: 508 577-0756</corresp>
</author-notes>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>3</month>
<year>2013</year>
</pub-date>
<volume>9</volume>
<issue>6</issue>
<fpage>315</fpage>
<lpage>320</lpage>
<history><date date-type="received"><day>01</day>
<month>1</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>29</day>
<month>1</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>© 2013 Biomedical Informatics</copyright-statement>
<copyright-year>2013</copyright-year>
<license license-type="open-access"><license-p>This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p><italic>In silico</italic>
tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This
perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV.
Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database
were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27.
Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for
ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that
consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to
pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less
immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding,
of an arginine residue at the 2<sup>nd</sup>
position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with
HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that
has much relevance for the creation of personalized therapeutics for HIV treatment.</p>
</abstract>
<kwd-group><kwd>CLUSTALW</kwd>
<kwd>Geneious</kwd>
<kwd>Human Immunodeficiency Virus type 1</kwd>
<kwd>Human Leukocyte Antigen A*02</kwd>
<kwd>Human Leukocyte Antigen B*27</kwd>
<kwd>Mesquite</kwd>
<kwd>‘personalized therapeutics’</kwd>
<kwd>RANKPEP</kwd>
</kwd-group>
</article-meta>
</front>
<floats-group><fig id="F1" position="float"><label>Figure 1</label>
<caption><p>Geneious was used to catalogue the collected gp160 sequences from HIV clade A, B, C, and D in order to construct a
phylogenic tree. RANKPEP results consisted of key immunogenic peptides predicted to stimulate to T-cell HLA-A*2 and B*27
clone is presented along with their binding percentages.</p>
</caption>
<graphic xlink:href="97320630009315F1"></graphic>
</fig>
<fig id="F2" position="float"><label>Figure 2</label>
<caption><p>Based on the alignment and ancestral sequence
reconstruction, (ASR), there appear to have been two
independent deletions.</p>
</caption>
<graphic xlink:href="97320630009315F2"></graphic>
</fig>
<fig id="F3" position="float"><label>Figure 3</label>
<caption><p>Rozera <italic>et al</italic>
. developed individual phylogentic trees
of the V3 protein sequences from patients analyzed after longterm
suppression of viremia. The CD26-provirus is indicated in
red and represents monocytes that harbor proviral quasispecies.
The green circles represent the CD26-provirus proviral
quasispecies harbored in T-lymphocytes. The nucleotide
sequences obtained for this patient was translated in amino acid
sequences and then filtered.</p>
</caption>
<graphic xlink:href="97320630009315F3"></graphic>
</fig>
<fig id="F4" position="float"><label>Figure 4</label>
<caption><p>The development of a HIV vaccine has been elusive.
Using a personalized approach may be helpful in a treatment
that is designed to the individual patient. The possible protocol
could include: Massively parallel pyrosequencing; Use of in
silico tools predictive programs (MHC Class I and/or Class II);
Dendritic cell pulse with selected in vivo evolutionary
conserved peptide; Personalized HIV vaccine; Weaning of the
patient from conventional HIV drug therapy.</p>
</caption>
<graphic xlink:href="97320630009315F4"></graphic>
</fig>
</floats-group>
</pmc>
<affiliations><list><country><li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Maryland</li>
<li>Écosse</li>
</region>
<settlement><li>Édimbourg</li>
</settlement>
<orgName><li>Université d'Édimbourg</li>
</orgName>
</list>
<tree><country name="Royaume-Uni"><region name="Écosse"><name sortKey="Hecht, Luke" sort="Hecht, Luke" uniqKey="Hecht L" first="Luke" last="Hecht">Luke Hecht</name>
</region>
</country>
<country name="États-Unis"><region name="Maryland"><name sortKey="Dormer, Anton" sort="Dormer, Anton" uniqKey="Dormer A" first="Anton" last="Dormer">Anton Dormer</name>
</region>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001168 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 001168 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Pmc |étape= Checkpoint |type= RBID |clé= PMC:3607191 |texte= The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27 }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:23745018" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |