A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry

Abstract

MHC restriction, which describes the binding of TCRs from CD4+ T cells to class II MHC proteins and TCRs from CD8+ T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+ T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.

Enhanced T cell receptor specificity through framework engineering

“…The differences in the positional scanning library responses were reflected in the fingerprint analysis, with the values for the G104βP/T96βK variant downshifted compared to those of the T96βK variant (i.e., more peptides received lower, weakly/non-stimulatory scores) ( Figure 6C ). In previous work, we identified peptides with TCR fingerprint scores of 0.8 or higher as those more likely to lead to some level of functional recognition, with higher scores associated with higher binding affinity and stronger responses ( 47 ). The T96βK variant had approximately 67 million peptides in the range of 0.8 and above, while G104βP/T96βK had approximately 10-fold fewer (6.6 million) ( Figure 6C , inset).…”

“…IL-2 values in the PSL co-cultures were used to generate a position weight matrix as performed previously ( 46 , 47 ), except that, based on the IL-2 production data, peptides potentially more potent than the WT SL9 peptide were permitted to score higher. All values for each cell in the PSL heat map were normalized by the IL-2 response for the WT SL9 peptide to generate the matrix.…”

Dichotomy in TCR V-domain dynamics binding the opposed inclined planes of pMHC-II and pMHC-I α-helices

“…Now that these parameters have been hypothesized, and some indeed estimated, the trajectories of V-domain dynamics might be targeted by techniques such as NMR [31], hydrogen-deuterium exchange MS [32], or possibly other biochemical and biophysical approaches [16, 17]. It will also be important to investigate ‘rare’ TCR that bind pMHC in ‘non-canonical’ fashions [33, 34], indeed for the H3t TCR, Vα appears to have rotated slightly beyond 45°, perhaps contributing to the MHC-class ‘mismatch’ recognition displayed by T-cells bearing this TCR [34].…”

T-cell virtuosity in ‘‘knowing thyself”

“…The different elevation of the MHC α-helices over the groove results in a characteristic tilting (or incident) angle between TCRαβ and ligand that can vary in different complexes (0°≤ θ ≤ 25°) ( 34 ). Rare complexes showing limited TCRαβ contacts with peptide or unconventional orientations have been reported ( 26 , 30 , 35 – 37 ). Variation of diagonal and tilting angles, and of register and extent of peptide contacts suggests that, while systematically zeroing in on MHC, TCRαβ binding site exploits many opportunities for subtle or overt adjustments aimed to augment specificity for the peptide and ligand affinity.…”