Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition

Abstract

Small structural changes in peptides presented by major histocompatibility complex (MHC) molecules often result in large changes in immunogenicity, supporting the notion that T cell receptors are exquisitely sensitive to antigen structure. Yet there are striking examples of TCR recognition of structurally dissimilar ligands. The resulting unpredictability of how T cells will respond to different or modified antigens impacts both our understanding of the physical bases for TCR specificity as well as efforts to engineer peptides for immunomodulation. In cancer immunotherapy, epitopes and variants derived from the MART-1/Melan-A protein are widely used as clinical vaccines. Two overlapping epitopes spanning amino acid residues 26 through 35 are of particular interest: numerous clinical studies have been performed using variants of the MART-1 26-35 decamer, although only the 27-35 nonamer has been found on the surface of targeted melanoma cells. Here, we show that the 26-35 and 27-35 peptides adopt strikingly different conformations when bound to HLA-A2. Nevertheless, clonally distinct MART-1 26/27-35 -reactive T cells show broad cross-reactivity towards these ligands. Simultaneously, however, many of the cross-reactive T cells remain unable to recognize anchor-modified variants with very subtle structural differences. These dichotomous observations challenge our thinking about how structural information on unligated peptide/MHC complexes should be best used when addressing questions of TCR specificity. Our findings also indicate that caution is warranted in the design of immunotherapeutics based on the MART-1 26/27-35 epitopes, as neither cross-reactivity nor selectivity is predictable based on the analysis of the structures alone. Keywordspeptide/MHC; crystal structure; cross-reactivity; specificity; Melan-A; MART-1 Although structural studies of peptide/major histocompatibility complex (MHC) molecules and their interactions with αβ T cell receptors have considerably advanced our understanding of the molecular details of cellular immunity, the relationships between peptide/MHC structure and TCR specificity and cross-reactivity remain elusive. Alterations to antigenic peptides that result in very minor structural changes often result in substantial changes in immunological NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript potency, 1-5 leading to the commonly-held notion that T cell receptors can be exquisitely sensitive to antigen structure. Yet there are striking exceptions to this observation. Lee et al. recently demonstrated efficient TCR recognition of native and variant HIV gag epitopes that have significant structural differences across the center of the peptide. 6 Gagnon et al. showed TCR cross-reactivity between the native HTLV-1 Tax [11][12][13][14][15][16][17][18][19] peptide and a variant with a modified P5 side-chain that imparts dramatic structural differences on the peptide. 7 More remarkably, Zhao et al. identified a murine T cell clone that recognizes the peptide p...

Modification of MHC Anchor Residues Generates Heteroclitic Peptides That Alter TCR Binding and T Cell Recognition

“…Structural evidence suggests that substitution of alanine to leucine at the p2 anchor residue does not substantially alter Melan-A/MART-1 [26][27][28][29][30][31][32][33][34][35] peptide conformation in the uncomplexed pHLA A p 0201 molecule (47,48). However, a number of recent studies have shown that peptide conformation can be substantially altered during TCR docking (49)(50)(51).…”

Limited Induction of Tumor Cross-Reactive T Cells without a Measurable Clinical Benefit in Early Melanoma Patients Vaccinated with Human Leukocyte Antigen Class I–Modified Peptides

“…In addition, we now consider modified peptides as a potential "false ally" in cancer vaccines because their increased immunogenicity does not necessarily result in enhanced antitumor T-cell reactivity. Although the level of cross-recognition may vary among peptides, the unpredictability of T-cell function (48,49) makes this approach suboptimal for the effective enhancement of tumor immunity.…”

How an alloreactive T-cell receptor achieves peptide and MHC specificity

“…In examining the structure of the HCV1406-NS3/A2 complex, we noted that the conformation of the NS3 peptide in the A2-binding groove is remarkably similar to the conformation of the decameric MART-1 tumor antigen (sequence ELAGIGILTV) bound to A2 (35,36) (Fig. 6A).…”