Unusual Placement of an EBV Epitope into the Groove of the Ankylosing Spondylitis-Associated HLA-B27 Allele Allows CD8+ T Cell Activation

Abstract

The human leukocyte antigen HLA-B27 is a strong risk factor for Ankylosing Spondylitis (AS), an immune-mediated disorder affecting axial skeleton and sacroiliac joints. Additionally, evidence exists sustaining a strong protective role for HLA-B27 in viral infections. These two aspects could stem from common molecular mechanisms. Recently, we have found that the HLA-B*2705 presents an EBV epitope (pEBNA3A-RPPIFIRRL), lacking the canonical B27 binding motif but known as immunodominant in the HLA-B7 context of presentation. Notably, 69% of B*2705 carriers, mostly patients with AS, possess B*2705-restricted, pEBNA3A-specific CD8+ T cells. Contrarily, the non-AS-associated B*2709 allele, distinguished from the B*2705 by the single His116Asp polymorphism, is unable to display this peptide and, accordingly, B*2709 healthy subjects do not unleash specific T cell responses. Herein, we investigated whether the reactivity towards pEBNA3A could be a side effect of the recognition of the natural longer peptide (pKEBNA3A) having the classical B27 consensus (KRPPIFIRRL). The stimulation of PBMC from B*2705 positive patients with AS in parallel with both pEBNA3A and pKEBNA3A did not allow to reach an unambiguous conclusion since the differences in the magnitude of the response measured as percentage of IFNγ-producing CD8+ T cells were not statistically significant. Interestingly, computational analysis suggested a structural shift of pEBNA3A as well as of pKEBNA3A into the B27 grooves, leaving the A pocket partially unfilled. To our knowledge this is the first report of a viral peptide: HLA-B27 complex recognized by TCRs in spite of a partially empty groove. This implies a rethinking of the actual B27 immunopeptidome crucial for viral immune-surveillance and autoimmunity.

Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions

“…The latter, which essentially describes the pockets shapes, confirms the geometrical shape similarity for all the binding grooves ( Figure S6). Contrary to our previous results [10], this might suggest a quite-rigid conformation of the pMHC pocket, which seems to be unaffected by the sequence of the peptide.…”

“…In fact, the hydrogen bonds between the same residues of the binding groove and the residue P1-P2 and P8-P9 of the peptide are always maintained. Curiously, these h-bonds were found in our previous work on two HLA-B*27 subtypes [10], suggesting that, independently by the peptide sequence and the HLA type, the two ends of the ligand establish a similar interaction with conserved pocket residues. On the other hand, the hydrogen bonds between the peptide and the TCRs are specific of the complexes (Table 2 and Table S1): in the case of the 1G4-ESO9C, the peptide forms one and three h-bonds with the alpha and beta chains.…”

“…Moreover, recent NMR investigations of soluble αβ dimer ectodomain alone has suggested that TCR-CD3 signaling is governed by allosteric regulation upon pMHC binding [8,9]. Combining experimental and theoretical studies, we recently found that the bound peptide can affect the conformation of the MHC I binding groove, suggesting a different presentation of the antigens, which seems to be related to different CTLs responses [10]. However, in that study we did not provide a modelling of the pMHC interacting with the TCR.…”

“…USA). Combining experimental and theoretical studies, we recently found that the bound peptide can affect the conformation of the MHC I binding groove, suggesting a different presentation of the antigens, which seems to be related to different CTLs responses [10]. However, in that study we did not provide a modelling of the pMHC interacting with the TCR.…”

Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study

“…The results of this study revealed a high mobility of the CDR-loops of the TCR as well as the presence of two conformational clusters in the peptide’s structure, underlying the backbone flexibility of the peptide. Very recently, Tedeschi et al [17] used MD simulations to complement their experimental studies on an unusual placement of an EBV epitope in the binding groove of an ankylosing spondylitis (AS)-associated HLA-B27 allele that allowed CD8+ T cell activation and inferred from computational analysis that the strongest risk factor for AS, i.e., B*2705, is able to elicit anti-viral T cell immune-responses even when the binding groove might be partially occupied by the epitope. In the present study, we performed MD simulations of bound and unbound TCR-pMHC configurations of a LC13-HLA-B*44:05-pEEYLQAFTY complex in order to evaluate if and how intramolecular domain movements and relative orientations (namely between TCR V α and TCR V β , and MHC α1 and MHC α2) change due to complexation of TCR with pMHC molecules.…”