Abstract
Identification of a natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune response. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by antigen processing in live cells. In infected cells, in addition to this complex HLA ligandome, a minority of peptides from degradation of the few proteins encoded by the viral genome are also bound to HLA class I molecules. In this study, the standard immunopeptidomics strategy was modified to include the classical acid stripping treatment after virus infection to enrich the HLA ligandome in virus ligands. Complexes of HLA-B*27:05-bound peptide pools were isolated from vaccinia virus (VACV)-infected cells treated with acid stripping after virus infection. The HLA class I ligandome was identified using high throughput mass spectrometry analyses, yielding 37 and 51 natural peptides processed and presented untreated and after acid stripping treatment VACV-infected human cells, respectively. Most of these virus ligands were identified in both conditions, but exclusive VACV ligands detected by mass spectrometry detected on acid stripping treatment doubled the number of those identified in the untreated VACV-infected condition. Theoretical binding affinity prediction of the VACV HLA-B*27:05 ligands and acute antiviral T cell response characterization in the HLA transgenic mice model showed no differences between HLA ligands identified under the two conditions: untreated and under acid stripping condition. These findings indicated that acid stripping treatment could be useful to identify HLA class I ligands from virus-infected cells.
Highlights
Proteasomes and other cytosolic peptidases degrade self and pathogenic proteins, generating an extremely varied pool of peptides, both in sequence and in length
The human leukocyte antigen (HLA)-B*27:05-bound peptide pools were isolated from large numbers of aciduntreated and either uninfected or vaccinia virus (VACV)-infected cells
Eighteen different VACV proteins (3BHS, A31, B18, C10, D2, E8, F7, F11, F12, F17, I1, K1, MCE, RP19, RP22, RP35, VGF, and VLTF1) displayed individual ligands bound to HLA-B*27:05 molecules (Table 1)
Summary
Proteasomes and other cytosolic peptidases degrade self and pathogenic proteins, generating an extremely varied pool of peptides, both in sequence and in length. Some of these degradation products are translocated to the endoplasmic reticulum (ER) lumen by the transporter associated with antigen-processing (TAP) molecules [1]. The peptides with the correct length (8 to 12 residues) and strong interactions with specific residues of the antigen recognition site of the HLA class I molecule [2], usually at position 2 (P2) as an anchor residue motif and auxiliary amino acids at the C-terminus [3,4], can stabilize their binding to HLA class I molecules.
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