HLA Micropolymorphisms Strongly Affect Peptide–MHC Multimer–Based Monitoring of Antigen-Specific CD8+ T Cell Responses

Abstract

Peptide–MHC (pMHC) multimers have become one of the most widely used tools to measure Ag-specific T cell responses in humans. With the aim of understanding the requirements for pMHC-based personalized immunomonitoring, in which individuals expressing subtypes of the commonly studied HLA alleles are encountered, we assessed how the ability to detect Ag-specific T cells for a given peptide is affected by micropolymorphic differences between HLA subtypes. First, analysis of a set of 10 HLA-A*02:01–restricted T cell clones demonstrated that staining with pMHC multimers of seven distinct subtypes of the HLA-A*02 allele group was highly variable and not predicted by sequence homology. Second, to analyze the effect of minor sequence variation in a clinical setting, we screened tumor-infiltrating lymphocytes of an HLA-A*02:06 melanoma patient with either subtype-matched or HLA-A*02:01 multimers loaded with 145 different melanoma-associated Ags. This revealed that of the four HLA-A*02:06–restricted melanoma-associated T cell responses observed in this patient, two responses were underestimated and one was overlooked when using subtype-mismatched pMHC multimer collections. To our knowledge, these data provide the first demonstration of the strong effect of minor sequence variation on pMHC-based personalized immunomonitoring, and they provide tools to prevent this issue for common variants within the HLA-A*02 allele group.

The Immunodominant Influenza A Virus M158–66Cytotoxic T Lymphocyte Epitope Exhibits Degenerate Class I Major Histocompatibility Complex Restriction in Humans

“…Indeed, the HLA-A*02-restricted GILGFVFTL-specific CTLs that could not be detected previously by HLA-A*02:01 tetramers were readily quantified with HLA-A*02:06 tetramers. This agrees with the observation that minor sequence variations between HLA-A*02:01, -A*02:06, and -A*02:07 can profoundly affect antigen-specific CD8 T cell detection with MHC multimers (31). HLA-A*02:01 differs from HLA-A*02:06 at F9Y and also from HLA-A*02:07 at Y99C.…”

“…2D). We have shown recently that HLA-A*02:01-restricted GILGFVFTL T cell clones could bind only to HLA-A*02:01, -A*02:71, and -A*02:77 tetramers, whereas other HLA-A2 subtype tetramers, including HLA-A*02:06 tetramers, could not be recognized by the T cells (31). Therefore, it can be concluded that small differences among HLA-A*02 products can lead to functionally different antigen presentations, highlighting the fine specificity of these CTLs.…”

Design and validation of conditional ligands for HLA‐B*08:01, HLA‐B*15:01, HLA‐B*35:01, and HLA‐B*44:05

“…These data indicate a very limited overlap between the T‐cell recognition presented by HLA‐B*15:01 and HLA‐B*15:02 and point to the importance of detailed tissue typing and use of matching HLA molecules when T‐cell immunity is measured via staining with MHC Class I multimers. A similar difference among HLA‐A*02:06 and HLA‐A*02:01 subtypes was recently described although the HLA‐A*02:06 heavy chain differs only by a single amino acid from that of HLA‐A*02:01 . The HLA‐B*15:01 and −B*15:02 heavy chains, on the contrary, differ at five amino acid positions, including three functional residues expected to participate in the T‐cell receptor binding .…”

Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2–Restricted T Cell Epitopes

“…Other PBMC samples were obtained from healthy individuals or from patients with stage IV melanoma in accordance with local guidelines, and following informed consent. Ag specific CD8 + T cell clones were generated as described elsewhere (37).…”