Biology subjects

Sim, M. J. W.

Publications and source records attributed to Sim, M. J. W..

7 recordsLinked to original sources

bioRxiv2026

Using peptide-exchange systems to interrogate peptide-specific KIR binding to HLA Class -I

The killer-cell immunoglobulin-like receptors (KIR) are a family of activating and inhibitory HLA class I (HLA-I) binding receptors expressed on natural killer (NK) cells and subsets of T cells. The KIR detect HLA-I molecules in a peptide-dependent manner, with some KIR displaying exquisite peptide-specificity. Studying peptide recognition by KIR often uses TAP-deficient cell lines expressing single HLA-I alleles, which are heterogenous and time consuming to generate. Here, we established an alternative approach using peptide-exchange technologies hitherto developed for studying T cell recognition of HLA-I. We tested two methods; dipeptide-mediated peptide exchange and open-HLA-I, HLA-I molecules consisting of heavy chain-{beta}2m disulphide bonded dimers. We combined peptide-exchange technologies with SpyTag-SpyCatcher chemistry to allow rapid detection of KIR binding via HLA-I displayed on plates or cells. We demonstrated the fidelity of this system with peptides of known KIR specificity bound to HLA-C*05:01. We then screened a peptide library to identify novel strong KIR2DS4 binding peptides presented by HLA-C*04:01. Peptide-exchanged HLA-C was functionally competent, promoting activation of KIR2DS4+ NK cells and inhibiting activation of KIR2DL1+ NK cells. Together, we show that peptide-exchangeable HLA-I molecules are ligands for KIR, presenting a flexible, efficient system for examining the peptide-sequence dependent recognition of HLA-I by KIR.

immunology↗

bioRxiv2025

Atom-level mechanism of tapasin-independent peptide editing by Major Histocompatibility Complex class I molecules

Peptide binding to major histocompatibility complex class I molecules (MHC-I) and their presentation to cytotoxic immune cells is a keystone of the adaptive immune system. The selection of MHC-I bound peptides is facilitated by the chaperone tapasin, which allows MHC-I to iteratively sample peptides until they are loaded with optimal binding peptides, known as peptide editing. However, some MHC-I allotypes can select high affinity binding peptides independently of tapasin, and the molecular mechanism(s) for such peptide editing are unknown. Here, we used enhanced sampling molecular dynamics simulations of peptide-deficient MHC-I to investigate tapasin-independent peptide editing. Our simulations revealed transient disruption of hydrogen bonds between MHC-I and the peptide backbone could allow for peptide editing, a process we term "active displacement". Destabilisation of interactions with the peptide backbone, necessitates sequence-specific sidechain interactions to maintain peptide binding. Our active displacement model predicts surface expression levels for multiple MHC-I allotypes and accounts for the presentation of an immunogenic mutant KRAS-G12D neoepitope by HLA-C*08:02, but not by closely related HLA-C*05:01. Together our data provide a molecular mechanism for tapasin-independent MHC-I peptide editing, influencing the surface immunopeptidome and anti-tumour immunity. Significance StatementMajor histocompatibility complex class I molecules (MHC-I) bind and present peptides to specialised killer cells of the immune system. These immune cells can unleash their cytotoxic effector functions if they recognise the peptide-MHC-I complex. Which peptides are presented by MHC-I is therefore highly important. Peptide selection is usually assisted by the tapasin protein, although some MHC-I molecules can select peptides independently of tapasin, but it is not known how this occurs. Here, we provide an atomistic description of the tapasin-independent peptide selection mechanism. Our mechanism applies to multiple MHC-I allotypes and illustrates how an immunogenic peptide is presented by one MHC-I molecule, but not by another closely related molecule. This new insight provides a rational basis for therapeutic treatments.

immunology↗

bioRxiv2024

Identification and Structural Characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3

Mutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that can be targeted in adoptive T cell therapy in metastatic diseases. To expand mutant KRAS specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen (7VVVGAVGVGK16) using a vaccination approach with transgenic mice expressing the common HLA-I allotype, HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not Wt KRAS peptides. To investigate the molecular basis for neoantigen recognition by This TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3{beta} and CDR1 {beta} formed a hydrophobic pocket to interact with p6 Val of the G12V but not Wt KRAS peptide. To improve the tumor sensitivity of This TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding to HLA-A3 (G12V), but did not sufficiently improve T cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations. [203]

immunology↗

bioRxiv2023

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

Genetic studies associate killer-cell immunoglobulin-like receptors (KIR) and their HLA class I ligands with a variety of human diseases. The basis for these associations, and the relative contribution of inhibitory and activating KIR to NK cell responses are unclear. As KIR binding to HLA-I is peptide-dependent, we performed systematic screens totaling over 3,500 specific interactions to determine the specificity of five KIR for peptides presented by four HLA-C ligands. Inhibitory KIR2DL1 was largely peptide sequence agnostic, binding approximately 60% of hundreds of HLA-peptide complexes tested. Inhibitory KIR2DL2, KIR2DL3, and activating KIR2DS1 and KIR2DS4 bound only 10%, down to 1% of HLA-peptide complexes tested, respectively. Activating KIR2DS1, previously described as weak, had high binding affinity for HLA-C with high peptide sequence specificity. Our data revealed MHC-restricted peptide recognition by germ-line encoded NK receptors and imply that NK cell responses can be shaped by HLA-I bound immunopeptidomes in the context of disease or infection.

immunology↗

bioRxiv2021

T cells discriminate between groups C1 and C2 HLA-C

Dimorphic residues 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 groups C1 and C2 HLA-C, due to effects on peptide presentation and TCR affinity. Structural and functional experiments combined with immunopeptidomics analysis revealed that C1-HLA-C favors smaller amino acids at the peptide C-terminus minus-1 position (p{Omega}-1), and that larger p{Omega}-1 residues diminished TCR recognition of C1-HLA-C. After controlling for peptide presentation, TCRs exhibited weaker affinities for C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism impacts peptide presentation and HLA-C restricted T cell responses, with implications in multiple disease contexts including adoptive T cell therapy targeting KRAS-G12D-induced cancers.

immunology↗

bioRxiv2019

HLA-C-restricted presentation of a conserved bacterial epitope to an innate NK cell receptor

The killer-cell Ig-like receptor (KIR) family, expressed mainly in natural killer (NK) cells, includes an activation receptor of unknown function, KIR2DS4. Here we show that KIR2DS4 is restricted by HLA-C*05:01 with a strong preference for tryptophan at position 8 of 9-mer peptides. Self peptides with Trp8 eluted from HLA-C*05:01 are rare and only one out of 12 bound KIR2DS4. An HLA-C*05:01-peptide complex that bound KIR2DS4 was sufficient for strong activation of primary KIR2DS4+ NK cells, independently of coactivation by other receptors and of prior NK cell licensing. A highly conserved sequence in bacterial recombinase A, which is essential for DNA repair and survival, includes an epitope that bound to HLA-C*05:01 and activated KIR2DS4+ NK cells. Thus, in addition to their established role in defense against viruses and cancer, NK cells may have also evolved to detect and respond to hundreds of bacterial species through recognition of a conserved RecA epitope.

immunology↗

bioRxiv2016

Canonical and cross-reactive binding of NK cell inhibitory receptors to HLA-C allotypes is dictated by peptides bound to HLA-C

BackgroundHuman natural killer (NK) cell activity is regulated by a family of killer-cell Ig-like receptors (KIR) that bind human leucocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys80) and KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn80). However, this model does not capture allelic diversity in HLA-C or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes.\n\nResultsThe impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides, or predicted HIV Gag peptides, by HLA-C can promote KIR cross-reactive binding.\n\nConclusionsKIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, which provides an explanation for why KIR2DL3-C1 interactions appear weaker than KIR2DL1-C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide selectivity of KIR-HLA-C interactions with relevance to NK cell biology and human disease associations. This selective peptide sequence-driven binding of KIR provides a potential mechanism for pathogen as well as self-peptide to modulate NK cell activation through altering levels of inhibition.

immunology↗