T Cells Discriminate Between Groups C1 And C2 HLA-C - ELife

The classical class I human leukocyte antigens (HLA-I; HLA-A, HLA-B, and HLA-C) are the most polymorphic genes across human populations and are associated with a myriad of human diseases (Dendrou et al., 2018; Robinson et al., 2017). HLA-I molecules present short peptides on the cell surface of nucleated cells where they form ligands for receptors of the immune system including T cell receptors (TCRs) and natural killer (NK) cell receptors. HLA-I-bound peptides are collectively known as the immunopeptidome, which defines the subset of the proteome bound as peptides to a particular HLA-I allotype (Istrail et al., 2004). Immunopeptidomes can be highly diverse, consisting of hundreds to thousands of different sequences as they are shaped by polymorphic amino acid residues that form pockets (A to F) in the HLA-I peptide-binding groove (PBG) (Di Marco et al., 2017; Madden, 1995; Sarkizova et al., 2020). These pockets restrict the peptide repertoire to those peptides with certain amino acid side chains at particular positions, which form anchor residues that define allotype-specific motifs (Di Marco et al., 2017; Falk et al., 1991; Sarkizova et al., 2020). The ‘anchor’ residues are often position 2 (p2) or p3 (B and C pockets) and the C-terminus (pΩ; F pocket), while residues outside the anchors can vary extensively allowing immunopeptidome diversification (Di Marco et al., 2017; Falk et al., 1991; Madden, 1995; Sarkizova et al., 2020). HLA-I allotypes with similar PBGs bind similar peptides, but subtle amino acid differences can modify the side-chain orientation impacting interactions with TCRs and NK cell receptors (Illing et al., 2018; Illing et al., 2012; Saunders et al., 2020; Stewart-Jones et al., 2012; Tynan et al., 2005). Understanding how HLA-I polymorphism impacts the immunopeptidome and interactions with immunoreceptors is critical for constructing molecular mechanisms that underpin disease risk associated with specific HLA-I alleles (Dendrou et al., 2018).

HLA-C is thought to play a lesser role in T cell responses compared to that of HLA-A and HLA-B due to its lower cell surface expression level (Apps et al., 2015; McCutcheon et al., 1995). However, HLA-C-restricted T cells are implicated in several disease settings. In HIV infection, HLA-C allotypes with a high expression were associated with increased T cell responses and slower progression to AIDS, while higher HLA-C expression was also linked with susceptibility to Crohn’s disease (Apps et al., 2013). In psoriasis, the strongest genetic association is with HLA-C*06:02, thought to be mediated by HLA-C*06:02-restricted T cells (Chen and Tsai, 2018; Lande et al., 2014). Furthermore, recent efforts to define the specificities of tumor-infiltrating lymphocytes (TIL) readily identified HLA-C-restricted T cells (Levin et al., 2021; Lu et al., 2014; Murata et al., 2020; Tran et al., 2015; Tran et al., 2016). Most notably, multiple HLA-C*08:02-restricted TCRs specific for the oncogenic hotspot mutation KRAS-G12D were identified in several cancer patients (Tran et al., 2015; Tran et al., 2016). Adoptive transfer of expanded KRAS-G12D-specific TILs successfully treated a patient with metastatic colorectal cancer, leading to complete regression of all but one metastatic lesion (Tran et al., 2016). The remaining lesion lost HLA-C*08:02 from its genome demonstrating conclusively that HLA-C-restricted T cells can mediate effective antitumor responses (Tran et al., 2016). Despite the clinical relevance of HLA-C-restricted T cells, few studies have examined TCR-HLA-C interactions with a molecular and structural focus. Indeed, our recent study on HLA-C*08:02-restricted KRAS-G12D-specific TCRs was the first to present crystal structures of any TCR in complex with HLA-C (Sim et al., 2020).

HLA-C is the most recently evolved classical HLA-I gene, present in only humans and other apes, and has several unique features (Adams and Parham, 2001). HLA-C, not HLA-A or HLA-B, is expressed on fetal extravillous trophoblast cells, making it the most polymorphic molecule expressed at the maternal–fetal interface (King et al., 2000). In addition, all HLA-C allotypes serve as ligands for the killer-cell immunoglobulin-like receptors (KIR), whereas only a subset of HLA-A and HLA-B allotypes bind KIRs (Hilton and Parham, 2017; Moesta et al., 2008). The KIR are a family of activating and inhibitory receptors expressed primarily on NK cells (Hilton and Parham, 2017; Saunders et al., 2015). HLA-C allotypes form two groups, C1 and C2, based on two dimorphic amino acid residues at positions 77 and 80 (Biassoni et al., 1995; Parham et al., 2012). C1 HLA-C allotypes carry Ser77 and Asn80 and are ligands for the inhibitory receptors KIR2DL2/3. The inhibitory receptor KIR2DL1 binds C2 HLA-C allotypes, which carry Asn77 and Lys80. The KIR discriminate C1 and C2 HLA-C largely via position 44 in the KIR (Winter and Long, 1997) and direct interactions with HLA-C position 80 (Boyington et al., 2000; Boyington and Sun, 2002; Fan et al., 2001). Genetic association studies link C1/C2 status and the presence or absence of specific KIR-HLA combinations with risk of multiple human diseases, including cancer, infectious diseases, autoimmunity, and disorders of pregnancy (Hiby et al., 2004; Khakoo et al., 2004; Kulkarni et al., 2008; Littera et al., 2016; Parham and Moffett, 2013; Rajagopalan and Long, 2005; Venstrom et al., 2012). Whether the C1/C2 dimorphism impacts HLA-C interactions with other immunoreceptors is unknown.

Given the clinical relevance of HLA-C-restricted T cells and that all HLA-C allotypes are either C1 or C2, it is important to ask whether this dimorphism impacts T cell recognition. It was hitherto assumed that the C1/C2 dimorphism would not directly affect T cell recognition as it lies outside the general TCR footprint. To answer this question, we studied two HLA-C*08:02 (C1)-restricted TCRs specific for different KRAS-G12D neoantigens. TCR9a is specific for G12D-9mer (GADGVGKSA), while TCR10 is specific for G12D-10mer (GADGVGKSAL) (Sim et al., 2020; Tran et al., 2016). TCR9a and TCR10 do not share TCR V genes and recognize their peptide antigens in different ways (Sim et al., 2020; Tran et al., 2016). We compared TCR9a and TCR10 recognition of HLA-C*08:02 (C1) with that of HLA-C*05:01, a C2 allotype that is identical in sequence to HLA-C*08:02 apart from the C1/C2 defining residues at positions 77 and 80 (Sim et al., 2017). In a previous study, we showed that 28 different ‘self’ peptides eluted from HLA-C*05:01 bound to both HLA-C*05:01 (C2) and HLA-C*08:02 (C1), suggesting a minimal impact of the C1/C2 dimorphism on peptide binding to HLA-C (Sim et al., 2017). Here, we found that T cells discriminate between C1 and C2 HLA-C due to differences in peptide binding to HLA-C and in peptide presentation to TCR, which revealed unsuspected features of the C1/C2 dimorphism governing interactions of HLA-C with immunoreceptors. Further, our data suggest that HLA-C*05:01-positive individuals may be eligible for immunotherapies targeting KRAS-G12D-10mer.