Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1).
Identifieur interne : 000171 ( PubMed/Corpus ); précédent : 000170; suivant : 000172Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1).
Auteurs : Liye Chen ; Hui Shi ; Danai Koftori ; Takuya Sekine ; Annalisa Nicastri ; Nicola Ternette ; Paul BownessSource :
- Molecular & cellular proteomics : MCP [ 1535-9484 ] ; 2020.
Abstract
Human leukocyte antigen (HLA) B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are strongly genetically associated with Behçet's disease (BD). Previous studies have defined two subgroups of HLA-B*51 peptidome containing Proline (Pro) or Alanine (Ala) at position 2 (P2). Little is known about the unconventional non-Pro/Ala2 HLA-B*51-bound peptides. We aimed to study the features of this novel sub-peptidome, and investigate its regulation by ERAP1. CRISPR-Cas9 was used to generate an HLA-ABC-triple knockout HeLa cell line (HeLa.ABC-KO), which was subsequently transduced to express HLA-B*51:01 (HeLa.ABC-KO.B51). ERAP1 was silenced using lentiviral shRNA. Peptides bound to HLA-B*51:01 were eluted and analyzed by Mass Spectrometry. The characteristics of non-Pro/Ala2, Pro2 and Ala2 peptides, and their alteration by ERAP1 silencing were investigated. Effects of ERAP1 silencing on cell surface expression of HLA-B*51:01 were studied using flow cytometry. More than 20% of peptides eluted from HLA-B*51:01 lacked Proline or Alanine at P2. This unconventional group of HLA-B*51:01-bound peptides was relatively enriched for 8-mers (with relatively fewer 9-mers) compared to the Pro2 and Ala2 sub-peptidomes, and had similar N-terminal and C-terminal residue usages to Ala2 peptides (with the exception of the less abundant Leucine at position Ω). Knockdown of ERAP1 increased the percentage of non-Pro/Ala2 from 20% to approximately 40%, increased the percentage of longer (10-mer and 11-mer) peptides eluted from HLA-B*51:01 complexes, and abrogated the predominance of Leucine at P1. Interestingly knockdown of ERAP1 altered the length and N-terminal residue usage of non-Ala2&Pro2 and Ala2 but not the Pro2 peptides. Finally, ERAP1 silencing regulated the expression levels of cell surface HLA-B*51 in a cell type-dependent manner. In conclusion, we have used a novel methodology to identify an unconventional but surprisingly abundant non-Pro/Ala2 HLA-B*51:01 sub-peptidome. It is increased by knockdown of ERAP1, a gene affecting the risk of developing BD. This has implications for theories of disease pathogenesis.
DOI: 10.1074/mcp.RA119.001617
PubMed: 32161166
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1).</title><author><name sortKey="Chen, Liye" sort="Chen, Liye" uniqKey="Chen L" first="Liye" last="Chen">Liye Chen</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom liyechen2009@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Shi, Hui" sort="Shi, Hui" uniqKey="Shi H" first="Hui" last="Shi">Hui Shi</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Koftori, Danai" sort="Koftori, Danai" uniqKey="Koftori D" first="Danai" last="Koftori">Danai Koftori</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Sekine, Takuya" sort="Sekine, Takuya" uniqKey="Sekine T" first="Takuya" last="Sekine">Takuya Sekine</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Nicastri, Annalisa" sort="Nicastri, Annalisa" uniqKey="Nicastri A" first="Annalisa" last="Nicastri">Annalisa Nicastri</name><affiliation><nlm:affiliation>Target Discovery Institute, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Ternette, Nicola" sort="Ternette, Nicola" uniqKey="Ternette N" first="Nicola" last="Ternette">Nicola Ternette</name><affiliation><nlm:affiliation>Jenner Institute, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Bowness, Paul" sort="Bowness, Paul" uniqKey="Bowness P" first="Paul" last="Bowness">Paul Bowness</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32161166</idno><idno type="pmid">32161166</idno><idno type="doi">10.1074/mcp.RA119.001617</idno><idno type="wicri:Area/PubMed/Corpus">000171</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000171</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1).</title><author><name sortKey="Chen, Liye" sort="Chen, Liye" uniqKey="Chen L" first="Liye" last="Chen">Liye Chen</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom liyechen2009@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Shi, Hui" sort="Shi, Hui" uniqKey="Shi H" first="Hui" last="Shi">Hui Shi</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Koftori, Danai" sort="Koftori, Danai" uniqKey="Koftori D" first="Danai" last="Koftori">Danai Koftori</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Sekine, Takuya" sort="Sekine, Takuya" uniqKey="Sekine T" first="Takuya" last="Sekine">Takuya Sekine</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Nicastri, Annalisa" sort="Nicastri, Annalisa" uniqKey="Nicastri A" first="Annalisa" last="Nicastri">Annalisa Nicastri</name><affiliation><nlm:affiliation>Target Discovery Institute, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Ternette, Nicola" sort="Ternette, Nicola" uniqKey="Ternette N" first="Nicola" last="Ternette">Nicola Ternette</name><affiliation><nlm:affiliation>Jenner Institute, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Bowness, Paul" sort="Bowness, Paul" uniqKey="Bowness P" first="Paul" last="Bowness">Paul Bowness</name><affiliation><nlm:affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular & cellular proteomics : MCP</title><idno type="eISSN">1535-9484</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Human leukocyte antigen (HLA) B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are strongly genetically associated with Behçet's disease (BD). Previous studies have defined two subgroups of HLA-B*51 peptidome containing Proline (Pro) or Alanine (Ala) at position 2 (P2). Little is known about the unconventional non-Pro/Ala2 HLA-B*51-bound peptides. We aimed to study the features of this novel sub-peptidome, and investigate its regulation by ERAP1. CRISPR-Cas9 was used to generate an HLA-ABC-triple knockout HeLa cell line (HeLa.ABC-KO), which was subsequently transduced to express HLA-B*51:01 (HeLa.ABC-KO.B51). ERAP1 was silenced using lentiviral shRNA. Peptides bound to HLA-B*51:01 were eluted and analyzed by Mass Spectrometry. The characteristics of non-Pro/Ala2, Pro2 and Ala2 peptides, and their alteration by ERAP1 silencing were investigated. Effects of ERAP1 silencing on cell surface expression of HLA-B*51:01 were studied using flow cytometry. More than 20% of peptides eluted from HLA-B*51:01 lacked Proline or Alanine at P2. This unconventional group of HLA-B*51:01-bound peptides was relatively enriched for 8-mers (with relatively fewer 9-mers) compared to the Pro2 and Ala2 sub-peptidomes, and had similar N-terminal and C-terminal residue usages to Ala2 peptides (with the exception of the less abundant Leucine at position Ω). Knockdown of ERAP1 increased the percentage of non-Pro/Ala2 from 20% to approximately 40%, increased the percentage of longer (10-mer and 11-mer) peptides eluted from HLA-B*51:01 complexes, and abrogated the predominance of Leucine at P1. Interestingly knockdown of ERAP1 altered the length and N-terminal residue usage of non-Ala2&Pro2 and Ala2 but not the Pro2 peptides. Finally, ERAP1 silencing regulated the expression levels of cell surface HLA-B*51 in a cell type-dependent manner. In conclusion, we have used a novel methodology to identify an unconventional but surprisingly abundant non-Pro/Ala2 HLA-B*51:01 sub-peptidome. It is increased by knockdown of ERAP1, a gene affecting the risk of developing BD. This has implications for theories of disease pathogenesis.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32161166</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>12</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1535-9484</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>11</Day></PubDate></JournalIssue><Title>Molecular & cellular proteomics : MCP</Title><ISOAbbreviation>Mol. Cell Proteomics</ISOAbbreviation></Journal><ArticleTitle>Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1).</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">mcp.RA119.001617</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1074/mcp.RA119.001617</ELocationID><Abstract><AbstractText>Human leukocyte antigen (HLA) B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are strongly genetically associated with Behçet's disease (BD). Previous studies have defined two subgroups of HLA-B*51 peptidome containing Proline (Pro) or Alanine (Ala) at position 2 (P2). Little is known about the unconventional non-Pro/Ala2 HLA-B*51-bound peptides. We aimed to study the features of this novel sub-peptidome, and investigate its regulation by ERAP1. CRISPR-Cas9 was used to generate an HLA-ABC-triple knockout HeLa cell line (HeLa.ABC-KO), which was subsequently transduced to express HLA-B*51:01 (HeLa.ABC-KO.B51). ERAP1 was silenced using lentiviral shRNA. Peptides bound to HLA-B*51:01 were eluted and analyzed by Mass Spectrometry. The characteristics of non-Pro/Ala2, Pro2 and Ala2 peptides, and their alteration by ERAP1 silencing were investigated. Effects of ERAP1 silencing on cell surface expression of HLA-B*51:01 were studied using flow cytometry. More than 20% of peptides eluted from HLA-B*51:01 lacked Proline or Alanine at P2. This unconventional group of HLA-B*51:01-bound peptides was relatively enriched for 8-mers (with relatively fewer 9-mers) compared to the Pro2 and Ala2 sub-peptidomes, and had similar N-terminal and C-terminal residue usages to Ala2 peptides (with the exception of the less abundant Leucine at position Ω). Knockdown of ERAP1 increased the percentage of non-Pro/Ala2 from 20% to approximately 40%, increased the percentage of longer (10-mer and 11-mer) peptides eluted from HLA-B*51:01 complexes, and abrogated the predominance of Leucine at P1. Interestingly knockdown of ERAP1 altered the length and N-terminal residue usage of non-Ala2&Pro2 and Ala2 but not the Pro2 peptides. Finally, ERAP1 silencing regulated the expression levels of cell surface HLA-B*51 in a cell type-dependent manner. In conclusion, we have used a novel methodology to identify an unconventional but surprisingly abundant non-Pro/Ala2 HLA-B*51:01 sub-peptidome. It is increased by knockdown of ERAP1, a gene affecting the risk of developing BD. This has implications for theories of disease pathogenesis.</AbstractText><CopyrightInformation>Published under license by The American Society for Biochemistry and Molecular Biology, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Liye</ForeName><Initials>L</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-1503-6017</Identifier><AffiliationInfo><Affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom liyechen2009@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Hui</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koftori</LastName><ForeName>Danai</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sekine</LastName><ForeName>Takuya</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nicastri</LastName><ForeName>Annalisa</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Target Discovery Institute, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ternette</LastName><ForeName>Nicola</ForeName><Initials>N</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-9283-0743</Identifier><AffiliationInfo><Affiliation>Jenner Institute, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bowness</LastName><ForeName>Paul</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Cell Proteomics</MedlineTA><NlmUniqueID>101125647</NlmUniqueID><ISSNLinking>1535-9476</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Antigen presentation</Keyword><Keyword MajorTopicYN="N">Behçet's disease</Keyword><Keyword MajorTopicYN="N">ERAP1</Keyword><Keyword MajorTopicYN="N">HLA-B*51:01</Keyword><Keyword MajorTopicYN="N">Immunoaffinity</Keyword><Keyword MajorTopicYN="N">Immunology*</Keyword><Keyword MajorTopicYN="N">Immunopeptidome</Keyword><Keyword MajorTopicYN="N">Mass Spectrometry</Keyword><Keyword MajorTopicYN="N">Peptides*</Keyword><Keyword MajorTopicYN="N">Tandem Mass Spectrometry</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>06</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>03</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32161166</ArticleId><ArticleId IdType="pii">RA119.001617</ArticleId><ArticleId IdType="doi">10.1074/mcp.RA119.001617</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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