T cells discriminate between groups C1 and C2 HLA-C

Abstract

Dimorphic amino acids at positions 77 and 80 delineate HLA-C allotypes into two groups, C1 and C2, which associate with disease through interactions with C1 and C2-specific natural killer cell receptors. How the C1/C2 dimorphism affects T cell recognition is unknown. Using HLA-C allotypes that differ only by the C1/C2-defining residues, we found that KRAS-G12D neoantigen-specific T cell receptors (TCR) discriminated between C1 and C2 presenting the same KRAS-G12D peptides. Structural and functional experiments, and immunopeptidomics analysis revealed that Ser77 in C1 and Asn77 in C2 influence amino acid preference near the peptide C-terminus (pW), including the pW-1 position, in which C1 favors small and C2 prefers large residues. This resulted in weaker TCR affinity for KRAS-G12D-bound C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism on its own impacts peptide presentation and HLA-C restricted T cell responses, with implications in disease, including adoptive T cell therapy targeting KRAS-G12D-induced cancers.

Innate receptors with high specificity for HLA class I–peptide complexes

“…5F). Ser77 is associated with the presentation of peptides with smaller residues at p8, as compared to Asn77 42 , and smaller p8 residues are favored by 2DL2/3 and 2DS1, which could explain the correlation between peptides favored by 2DS1 and 2DL2 (Fig. 5B).…”

“…To directly compare the specificities of 2DL1, 2DL2, and 2DL3 for the same peptides, we used pairs of HLA-C allotypes that differ only by the C1/C2 dimorphism (positions 77 and 80). The same peptides bind to the C1/C2 pair HLA-C*08:02 and HLA-C*05:01, provided they contain canonical anchor residues 14, 42 . Here, we have also used the C1/C2 pair HLA-C*16:01 and HLA-C*16:02.…”

“…721.221 cells (221) cells expressing HLA-C*05:01 and TAP inhibitor ICP47 (221-C*05-ICP47) and TAP1 deficient 221 cells expressing HLA-C*08:02 (221-C*08-TAP-KO) were previously described 14, 42 . ICP47 was expressed with GFP via an internal ribosomal entry sequence (IRES).…”

“…ICP47 was expressed with GFP via an internal ribosomal entry sequence (IRES). TAP1 deficient 221-C*08:02 cells were generated by expression of HLA-C*08:02 in 221-Cas9 cells followed by transduction with two gRNA targeting TAP1 (Genscript) 42 . BWNG KIR2DS1 reporter cells were a kind gift from Prof. Erik Dissen (University of Oslo, Norway) and have been previously described 7, 79 .…”

“…For peptide libraries, working dilutions of peptide ( 2 previously described 14,42 . ICP47 was expressed with GFP via an internal ribosomal entry sequence (IRES).…”