Large-scale analysis of HLA peptides presented by HLA-Cw4

Buchsbaum, Samuel; Barnea, Eilon; Dassau, Lior; Beer, Ilan; Milner, Elena; Admon, Arie

doi:10.1007/s00251-003-0570-0

Cited by 20 publications

(21 citation statements)

References 19 publications

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“…Database searching on the peptidome data allowed the identification of 7375 unique peptides at a FDR Ͻ 1% (supplemental Data S1). Of them, 70 (1%), 214 (3%) and 6674 (91%) were classified as B*35, C*04 or B*40 ligands, respectively, according to the binding motif reported for these molecules (8,(33)(34)(35). Only 417 sequences (6%) could not be confidently assigned to any allotype.…”

Section: Resultsmentioning

confidence: 99%

“…A total of 1128 unique peptides of eight to 13 residues long were identified at a FDR Յ 1% at the peptide level (supplemental Data S5). Of them, 953 (84%) had His or Arg at P2, the canonical binding motif of this allele (14, 38) whereas 14 (1%) and 53 (5%) matched respectively the binding motifs of HLA-B*35 (33) and HLA-C*04 (34,35). The remaining 108 sequences (10%) could not be confidently assigned to any allotype.…”

Section: Structures Of Hla-b*40 In Complex With An Endogenous Phosphomentioning

confidence: 99%

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A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Alpízar

Marino

Ramos-Fernández

et al. 2017

Molecular & Cellular Proteomics

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Section: Resultsmentioning

confidence: 99%

Section: Structures Of Hla-b*40 In Complex With An Endogenous Phosphomentioning

confidence: 99%

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Alpízar

Marino

Ramos-Fernández

et al. 2017

Molecular & Cellular Proteomics

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“…Arginine was selected for SILAC isotope labeling because it is a dominant "anchor" amino acid at position 2 (P2) of HLA-B27 peptide ligands (26-28), whereas it is not an anchor residue for the other alleles expressed (HLA-Cw*04 and HLA-B*35), albeit at low levels, in C1R cells (29)(30)(31). We first looked for evidence of extended versions of peptides identified in either ERAP1-silenced cells or ERAP1-competent cells.…”

Section: Erap1 In Hla-b27 Peptide Presentation 287mentioning

confidence: 99%

Critical Role of Endoplasmic Reticulum Aminopeptidase 1 in Determining the Length and Sequence of Peptides Bound and Presented by HLA–B27

Chen

Fischer

Peng

et al. 2014

Arthritis & Rheumatology

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Objective. HLA-B27 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are the two strongest genetic factors predisposing to ankylosing spondylitis (AS). A key aminopeptidase in class I major histocompatibility complex presentation, ERAP1 potentially contributes to the pathogenesis of AS by altering HLA-B27 peptide presentation. The aim of this study was to analyze the effects of ERAP1 on the HLA-B27 peptide repertoire and peptide presentation to cytotoxic T lymphocytes (CTLs).Methods. ERAP1-silenced and -competent HeLa.B27 and C1R.B27 cells were isotope-labeled, mixed, lysed, and then immunoprecipitated using W6/32 or ME1 antibodies. Peptides bound to HLA-B27 were eluted and analyzed by tandem mass spectrometry. Selected peptides were synthesized and tested for HLA-B27 binding ability. The effect of ERAP1 silencing/ mutation on presentation of an immunodominant viral HLA-B27 epitope, KK10, to CTLs was also studied.Results. In both HeLa.B27 and C1R.B27 cells, the proportion of 9-mer HLA-B27-bound peptides was decreased by ERAP1 silencing, whereas the percentages of longer peptides (11-13 mer) were increased. Surprisingly, following ERAP1 silencing, C-terminally extended peptides were readily identified. These were better able to bind to HLA-B27 than were N-terminally extended peptides lacking an arginine at position 2. In both HeLa.B27 cells and mouse fibroblasts expressing HLA-B27, the absence of ERAP1 reduced peptide recognition by HLA-B27-restricted KK10-specific CTLs following infection with recombinant vaccinia virus or transfection with minigenes expressing KK10 precursors. Presence of an AS-protective variant of ERAP1, K528R, as compared to wild-type ERAP1, reduced the peptide recognition by KK10 CTLs following transfection with extended KK10 minigenes.Conclusion. These results show that ERAP1 directly alters peptide binding and presentation by HLA-B27, thus demonstrating a potential pathogenic mechanism in AS. Inhibition of ERAP1 could potentially be used for treatment of AS and other ERAP1-associated diseases.The human leukocyte antigen HLA-B27 is very strongly associated with development of the common inflammatory rheumatic disease ankylosing spondylitis (AS). However, the pathogenic mechanism remains unclear. Recent genome-wide association studies have identified additional AS-associated genes, of which the strongest association is with endoplasmic reticulum aminopeptidase 1 (ERAP1) (1). The strong genetic association of AS with ERAP1 single-nucleotide polymorphisms has been confirmed in different populations (2-7).

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“…Variable modifications included phosphorylation of serine, threonine, and tyrosine; oxidation of methionine; and pyroglutamic acid formation from N-terminal glutamine. Peptide sequences that matched the HLA-C*04:01 binding motif, Phe or Tyr at P2 and Asp at P3 (27), were discarded. Estimation of the false discovery rate (FDR) was carried out by decoy hit counting as previously described (28,29), and only those matches with an FDR Ͻ 5% at the peptide level were considered.…”

Section: Ms/ms Ion Search and Peptidementioning

confidence: 99%

Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue

Marcilla

Alpízar

Lombardía

et al. 2014

Molecular & Cellular Proteomics

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Human leukocyte antigen (HLA) class I molecules bind peptides derived from the intracellular degradation of endogenous proteins and present them to cytotoxic T lymphocytes, allowing the immune system to detect transformed or virally infected cells. It is known that HLA class I-associated peptides may harbor posttranslational modifications. In particular, phosphorylated ligands have raised much interest as potential targets for cancer immunotherapy. By combining affinity purification with highresolution mass spectrometry, we identified more than 2000 unique ligands bound to HLA-B40. Sequence analysis revealed two major anchor motifs: aspartic or glutamic acid at peptide position 2 (P2) and methionine, phenylalanine, or aliphatic residues at the C terminus. The use of immobilized metal ion and TiO 2 affinity chromatography allowed the characterization of 85 phosphorylated ligands. We further confirmed every sequence belonging to this subset by comparing its experimental MS2 spectrum with that obtained upon fragmentation of the corresponding synthetic peptide. Remarkably, three phospholigands lacked a canonical anchor residue at P2, containing phosphoserine instead. Binding assays showed that these peptides bound to HLA-B40 with high affinity. Together, our data demonstrate that the peptidome of a given HLA allotype can be broadened by the presentation of peptides with posttranslational modifications at major anchor positions. We suggest that ligands with phosphorylated residues at P2 might be optimal targets for T-cell-based cancer immunotherapy. Molecular & Cellular Proteomics 13: 10.1074/mcp.M113.034314, 462-474, 2014. Major histocompatibility complex (MHC)1 class I molecules are cell surface glycoproteins that are expressed on almost every nucleated cell in vertebrates. They result from the noncovalent interaction of a polymorphic heavy chain, a constant light chain (␤-2-microglobulin (␤2m)), and a peptide ligand (1). The extracellular region of the heavy chain encompasses three domains, ␣ 1 , ␣ 2 , and ␣ 3 , with ␣ 1 and ␣ 2 forming a groove that accommodates a peptide ligand of, typically, 8 to 11 amino acid residues. The binding of the ligand to the groove is governed by the interaction of the side chains of certain peptide residues, called anchor positions, with several pockets of the heavy chain named A to F (1, 2). The size and chemical nature of these pockets impose restrictions on the peptide repertoire that can be associated with a particular class I antigen. It is reckoned that the ligandome of a given class I allotype may comprise up to 10,000 different peptides (3), although recent reports suggest that this number may be underestimated (4).Peptides displayed by MHC class I molecules derive from the intracellular degradation of endogenous proteins in the nucleus and cytosol and reach the lumen of the endoplasmic reticulum by means of the transporter associated with antigen processing. Inside the endoplasmic reticulum, peptides bind to the heavy chain and ␤2m in a multistep process involving several c...

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Large-scale analysis of HLA peptides presented by HLA-Cw4

Cited by 20 publications

References 19 publications

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Critical Role of Endoplasmic Reticulum Aminopeptidase 1 in Determining the Length and Sequence of Peptides Bound and Presented by HLA–B27

Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue

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