Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands
Identifieur interne : 000401 ( Pmc/Checkpoint ); précédent : 000400; suivant : 000402Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands
Auteurs : Marta A. S. Perez [Suisse] ; Michal Bassani-Sternberg [Suisse] ; George Coukos [Suisse] ; David Gfeller [Suisse] ; Vincent Zoete [Suisse]Source :
- Frontiers in Immunology [ 1664-3224 ] ; 2019.
Abstract
Recent clinical developments in antitumor immunotherapy involving T-cell related therapeutics have led to a renewed interest for
Url:
DOI: 10.3389/fimmu.2019.02731
PubMed: 31824508
PubMed Central: 6883762
Affiliations:
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<author><name sortKey="Bassani Sternberg, Michal" sort="Bassani Sternberg, Michal" uniqKey="Bassani Sternberg M" first="Michal" last="Bassani-Sternberg">Michal Bassani-Sternberg</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands</title>
<author><name sortKey="Perez, Marta A S" sort="Perez, Marta A S" uniqKey="Perez M" first="Marta A. S." last="Perez">Marta A. S. Perez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne</institution>
,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
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<country xml:lang="fr">Suisse</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Swiss Institute of Bioinformatics</institution>
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,<country>Switzerland</country>
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<country xml:lang="fr">Suisse</country>
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<author><name sortKey="Bassani Sternberg, Michal" sort="Bassani Sternberg, Michal" uniqKey="Bassani Sternberg M" first="Michal" last="Bassani-Sternberg">Michal Bassani-Sternberg</name>
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,<addr-line>Lausanne</addr-line>
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<author><name sortKey="Coukos, George" sort="Coukos, George" uniqKey="Coukos G" first="George" last="Coukos">George Coukos</name>
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,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
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<country xml:lang="fr">Suisse</country>
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<author><name sortKey="Gfeller, David" sort="Gfeller, David" uniqKey="Gfeller D" first="David" last="Gfeller">David Gfeller</name>
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<author><name sortKey="Zoete, Vincent" sort="Zoete, Vincent" uniqKey="Zoete V" first="Vincent" last="Zoete">Vincent Zoete</name>
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<country xml:lang="fr">Suisse</country>
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<series><title level="j">Frontiers in Immunology</title>
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<front><div type="abstract" xml:lang="en"><p>Recent clinical developments in antitumor immunotherapy involving T-cell related therapeutics have led to a renewed interest for <bold>h</bold>
uman <bold>l</bold>
eukocyte <bold>a</bold>
ntigen class <bold>I</bold>
(HLA-I) binding peptides, given their potential use as peptide vaccines. Databases of HLA-I binding peptides hold therefore information on therapeutic targets essential for understanding immunity. In this work, we use in depth and accurate HLA-I peptidomics datasets determined by mass-spectrometry (MS) and analyze properties of the HLA-I binding peptides with structure-based computational approaches. HLA-I binding peptides are studied grouping all alleles together or in allotype-specific contexts. We capitalize on the increasing number of structurally determined proteins to (1) map the 3D structure of HLA-I binding peptides into the source proteins for analyzing their secondary structure and solvent accessibility in the protein context, and (2) search for potential differences between these properties in HLA-I binding peptides and in a reference dataset of HLA-I motif-like peptides. This is performed by an <italic>in-house</italic>
developed heuristic search that considers peptides across all the human proteome and converges to a collection of peptides that exhibit exactly the same motif as the HLA-I peptides. Our results, based on 9-mers matched to protein 3D structures, clearly show enriched sampling for HLA-I presentation of helical fragments in the source proteins. This enrichment is significant, as compared to 9-mer HLA-I motif-like peptides, and is not entirely explained by the helical propensity of the preferred residues in the HLA-I motifs. We give possible hypothesis for the secondary structure biases observed in HLA-I peptides. This contribution is of potential interest for researchers working in the field of antigen presentation and proteolysis. This knowledge refines the understanding of the rules governing antigen presentation and could be added to the parameters of the current peptide-MHC class I binding predictors to increase their antigen predictive ability.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Immunol</journal-id>
<journal-id journal-id-type="iso-abbrev">Front Immunol</journal-id>
<journal-id journal-id-type="publisher-id">Front. Immunol.</journal-id>
<journal-title-group><journal-title>Frontiers in Immunology</journal-title>
</journal-title-group>
<issn pub-type="epub">1664-3224</issn>
<publisher><publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">31824508</article-id>
<article-id pub-id-type="pmc">6883762</article-id>
<article-id pub-id-type="doi">10.3389/fimmu.2019.02731</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Immunology</subject>
<subj-group><subject>Hypothesis and Theory</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Perez</surname>
<given-names>Marta A. S.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/688176/overview"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Bassani-Sternberg</surname>
<given-names>Michal</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/83326/overview"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Coukos</surname>
<given-names>George</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gfeller</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/474112/overview"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Zoete</surname>
<given-names>Vincent</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="c001"><sup>*</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/87459/overview"></uri>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup>
<institution>Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne</institution>
,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
</aff>
<aff id="aff2"><sup>2</sup>
<institution>Swiss Institute of Bioinformatics</institution>
,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
</aff>
<aff id="aff3"><sup>3</sup>
<institution>Human Integrated Tumor Immunology Discovery Engine, Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne</institution>
,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
</aff>
<aff id="aff4"><sup>4</sup>
<institution>Computational Cancer Biology, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne</institution>
,<addr-line>Lausanne</addr-line>
,<country>Switzerland</country>
</aff>
<author-notes><fn fn-type="edited-by"><p>Edited by: Shahram Kordasti, King's College London, United Kingdom</p>
</fn>
<fn fn-type="edited-by"><p>Reviewed by: Denis Colum Shields, University College Dublin, Ireland; Reno Debets, Erasmus Medical Center, Netherlands</p>
</fn>
<corresp id="c001">*Correspondence: Vincent Zoete <email>vincent.zoete@unil.ch</email>
</corresp>
<fn fn-type="other" id="fn001"><p>This article was submitted to Cancer Immunity and Immunotherapy, a section of the journal Frontiers in Immunology</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>22</day>
<month>11</month>
<year>2019</year>
</pub-date>
<pub-date pub-type="collection"><year>2019</year>
</pub-date>
<volume>10</volume>
<elocation-id>2731</elocation-id>
<history><date date-type="received"><day>18</day>
<month>2</month>
<year>2019</year>
</date>
<date date-type="accepted"><day>07</day>
<month>11</month>
<year>2019</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2019 Perez, Bassani-Sternberg, Coukos, Gfeller and Zoete.</copyright-statement>
<copyright-year>2019</copyright-year>
<copyright-holder>Perez, Bassani-Sternberg, Coukos, Gfeller and Zoete</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p>
</license>
</permissions>
<abstract><p>Recent clinical developments in antitumor immunotherapy involving T-cell related therapeutics have led to a renewed interest for <bold>h</bold>
uman <bold>l</bold>
eukocyte <bold>a</bold>
ntigen class <bold>I</bold>
(HLA-I) binding peptides, given their potential use as peptide vaccines. Databases of HLA-I binding peptides hold therefore information on therapeutic targets essential for understanding immunity. In this work, we use in depth and accurate HLA-I peptidomics datasets determined by mass-spectrometry (MS) and analyze properties of the HLA-I binding peptides with structure-based computational approaches. HLA-I binding peptides are studied grouping all alleles together or in allotype-specific contexts. We capitalize on the increasing number of structurally determined proteins to (1) map the 3D structure of HLA-I binding peptides into the source proteins for analyzing their secondary structure and solvent accessibility in the protein context, and (2) search for potential differences between these properties in HLA-I binding peptides and in a reference dataset of HLA-I motif-like peptides. This is performed by an <italic>in-house</italic>
developed heuristic search that considers peptides across all the human proteome and converges to a collection of peptides that exhibit exactly the same motif as the HLA-I peptides. Our results, based on 9-mers matched to protein 3D structures, clearly show enriched sampling for HLA-I presentation of helical fragments in the source proteins. This enrichment is significant, as compared to 9-mer HLA-I motif-like peptides, and is not entirely explained by the helical propensity of the preferred residues in the HLA-I motifs. We give possible hypothesis for the secondary structure biases observed in HLA-I peptides. This contribution is of potential interest for researchers working in the field of antigen presentation and proteolysis. This knowledge refines the understanding of the rules governing antigen presentation and could be added to the parameters of the current peptide-MHC class I binding predictors to increase their antigen predictive ability.</p>
</abstract>
<kwd-group><kwd>human leukocyte antigen</kwd>
<kwd>HLA-I ligand presentation</kwd>
<kwd>computational immunology</kwd>
<kwd>3D structure</kwd>
<kwd>heuristic search</kwd>
<kwd>HLA-I motif-like peptides</kwd>
</kwd-group>
<counts><fig-count count="8"></fig-count>
<table-count count="1"></table-count>
<equation-count count="4"></equation-count>
<ref-count count="78"></ref-count>
<page-count count="18"></page-count>
<word-count count="12576"></word-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Suisse</li>
</country>
</list>
<tree><country name="Suisse"><noRegion><name sortKey="Perez, Marta A S" sort="Perez, Marta A S" uniqKey="Perez M" first="Marta A. S." last="Perez">Marta A. S. Perez</name>
</noRegion>
<name sortKey="Bassani Sternberg, Michal" sort="Bassani Sternberg, Michal" uniqKey="Bassani Sternberg M" first="Michal" last="Bassani-Sternberg">Michal Bassani-Sternberg</name>
<name sortKey="Coukos, George" sort="Coukos, George" uniqKey="Coukos G" first="George" last="Coukos">George Coukos</name>
<name sortKey="Gfeller, David" sort="Gfeller, David" uniqKey="Gfeller D" first="David" last="Gfeller">David Gfeller</name>
<name sortKey="Gfeller, David" sort="Gfeller, David" uniqKey="Gfeller D" first="David" last="Gfeller">David Gfeller</name>
<name sortKey="Perez, Marta A S" sort="Perez, Marta A S" uniqKey="Perez M" first="Marta A. S." last="Perez">Marta A. S. Perez</name>
<name sortKey="Zoete, Vincent" sort="Zoete, Vincent" uniqKey="Zoete V" first="Vincent" last="Zoete">Vincent Zoete</name>
<name sortKey="Zoete, Vincent" sort="Zoete, Vincent" uniqKey="Zoete V" first="Vincent" last="Zoete">Vincent Zoete</name>
</country>
</tree>
</affiliations>
</record>
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