The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer

Abstract

MHC class I downregulation represents a significant challenge for successful T cell–based immunotherapy. T cell epitopes associated with impaired peptide processing (TEIPP) constitute a novel category of immunogenic Ags that are selectively presented on transporter associated with Ag processing–deficient cells. The TEIPP neoepitopes are CD8 T cell targets, derived from nonmutated self-proteins that might be exploited to prevent immune escape. In this study, the crystal structure of H-2Db in complex with the first identified TEIPP Ag (MCLRMTAVM) derived from the Trh4 protein has been determined to 2.25 Å resolution. In contrast to prototypic H-2Db peptides, Trh4 takes a noncanonical peptide-binding pattern with extensive sulfur–π interactions that contribute to the overall complex stability. Importantly, the noncanonical methionine at peptide position 5 acts as a main anchor, altering only the conformation of the H-2Db residues Y156 and H155 and thereby forming a unique MHC/peptide conformer that is essential for recognition by TEIPP-specific T cells. Substitution of peptide residues p2C and p5M to the conservative α-aminobutyric acid and norleucine, respectively, significantly reduced complex stability, without altering peptide conformation or T cell recognition. In contrast, substitution of p5M to a conventional asparagine abolished recognition by the H-2Db/Trh4-specific T cell clone LnB5. We anticipate that the H-2Db/Trh4 complex represents the first example, to our knowledge, of a broader repertoire of alternative MHC class I binders.

Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin

“…MHC-I | tapasin | peptide editing | TAPBPR P eptide presentation by major histocompatibility class I (MHC-I) molecules is essential for recognition of intracellular pathogens and malignancies (1)(2)(3)(4)(5)(6). Following their transfer by the transporter associated with antigen processing (TAP) into the endoplasmic reticulum (ER), peptides are selectively loaded on MHC-I with the help of the peptide loading complex (PLC) multiprotein machinery, which consists of tapasin, ERp57, and calreticulin (7).…”

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability

“…We have also recently determined the crystal structure of H-2D b in complex with the first prototypic TEIPP peptide Trh4 (12). The structure revealed that the peptide takes a noncanonical peptidebinding pattern forming extensive sulfur-p interactions that contribute to the overall complex stability.…”

“…Indeed, in contrast to all previously reported crystal structures of H-2D b epitopes, the TEIPP peptide Trh4 (MCLRMTAVM), derived from the commonly expressed cellular protein Trh4 (10,13), does not contain an asparagine at position 5 and comprises an unusually large number of sulfur-containing residues at positions 1, 2, 5, and 9. The crystal structure of H-2D b /Trh4 combined with site-directed mutagenesis analysis on peptide binding capacity revealed that Trh4 makes primary use of peptide residues p2C, p5M, and p9M for binding, interacting with specific aromatic residues in H-2D b (12). Indeed, the removal of sulfur atoms through the conservative substitutions of p2C or p5M to a-aminobutyric acid and norleucine, respectively, severely reduced the overall stability of the H-2D b complexes, indicating the importance of SH-p and van der Waals interactions for the stability of the MHC/peptide complex.…”

Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health

“…In addition to somatic mutation-derived neoantigens, nonmutated endogenous proteins, called T-cell epitope associated with impaired peptide process neoantigens, can also act as immunogenic epitopes (van der Burg et al, 2016). A new study provided more unique structural mechanisms of the first identified T-cell epitope associated with impaired peptide process antigens derived from Trh4 proteins using crystallographic investigation, highlighting a significant advance in the search for novel immunotherapeutic targets (Hafstrand et al, 2016).…”