Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding

Walters, Lucy; Harlos, K.; Brackenridge, Simon; Rozbeský, Daniel; Barrett, Jordan R.; Jain, Vitul; Walter, T S; O’Callaghan, C A; Borrow, Persephone; Toebes, Mireille; Hansen, Scott G.; Sacha, Jonah B.; Abdulhaqq, Shaheed; Greene, Justin M.; Früh, Klaus; Marshall, Emily E.; Picker, Louis J.; Jones, E Y; McMichael, Andrew J.; Gillespie, Geraldine M.

doi:10.1038/s41467-018-05459-z

Cited by 60 publications

(124 citation statements)

References 70 publications

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“…Regardless of the peptide source, it is tempting to speculate that alterations in the HLA-E ligandome surveyed by the NKG2C receptor contribute differentially to the accumulation, differentiation and effector functions of adaptive NKG2C+ NK cells during infection. Whether HIV-1 peptides could further exploit the HLA-E/NKG2 axis as recently suggested (39) requires further evaluation.…”

Section: Discussionmentioning

confidence: 99%

Subordinate effect of −21M HLA-B dimorphism on NK cell repertoire diversity and function in HIV-1 infected individuals of African origin

Cubero

Ogbe

Cohen

et al. 2019

Preprint

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Natural Killer (NK) cells play an important role in antiviral defence and their potent effector function identifies them as key candidates for immunotherapeutic interventions in chronic viral infections. Their remarkable functional agility is achieved by virtue of a wide array of germline encoded inhibitory and activating receptors ensuring a self-tolerant and tunable repertoire. NK cell diversity is generated by a combination of factors including genetic determinants and infections/environmental factors, which together shape the NK cell pool and functional potential. Recently a genetic polymorphism at position −21 of HLA-B, which influences the supply of HLA-E binding peptides and availability of HLA-E for recognition by the inhibitory NK cell receptor NKG2A, was shown to have a marked influence on NK cell functionality in healthy human cytomegalovirus (HCMV) seronegative Caucasian individuals. In this study, −21 methionine (M)-expressing alleles supplying HLA-E binding peptides were largely poor ligands for inhibitory killer immunoglobulin-like receptors (KIRs), and a bias to NKG2A-mediated education of functionally-potent NK cells was observed. Here, we investigated the effect of this polymorphism on the phenotype and functional capacity of NK cells in a cohort of African individuals with human immunodeficiency virus type 1 (HIV-1)/HCMV co-infection. A similarly profound influence of dimorphism at position −21 of HLA-B on NK cells was not evident in these subjects. They predominantly expressed African specific HLA-B and −C alleles that contribute a distinct supply of NKG2A and KIR ligands, and these genetic differences were compounded by the marked effect of HIV/HCMV coinfection on NK cell differentiation. Together, these factors resulted in a lack of correlation of the HLA-B −21 polymorphism with surface abundance of HLA-E and loss of the NK cell functional advantage in subjects with −21M HLA-B alleles. Instead our data suggest that during HIV/HCMV co-infection exposure of NK cells to an environment that displays altered HLA-E ligands drives adaptive NKG2C+ NK cell expansions influencing effector responses. Increased efforts to understand how NK cells are functionally calibrated to self-HLA during chronic viral infections will pave the way to developing targeted therapeutic interventions to overcome the current barriers to enhancing immune-based antiviral control.

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Section: Discussionmentioning

confidence: 99%

Subordinate effect of −21M HLA-B dimorphism on NK cell repertoire diversity and function in HIV-1 infected individuals of African origin

Cubero

Ogbe

Cohen

et al. 2019

Preprint

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“…Trained immunity differs from innate memory, as the heightened response is not specific to the original pathogen, although is stronger compared to antigennaive innate cells [62] and occurs as a result of histone methylation at the H3K4me1 locus of innate immune cells, inducing a lasting enhanced level of NK cell activation and cytokine production [56,63,71]. [72][73][74], and recently in CMV-vectored vaccines against simian immunodeficiency virus (SIV) [5].…”

Section: Nk Cells and Trained Immunitymentioning

confidence: 99%

“…Unusually, for any known pathogen, there is a large population of CD8 + T cells restricted by HLA-E induced by infection [76], possibly enhanced by the up-regulation of HLA-E on the surface of Mtb-infected phagosomes [65,70]. Multiple peptides within the Mtb genome can be presented (including peptides from p49 and Mtb44 proteins, Table 2) [61,72,74]. Their varying amino acid length implies that HLA-E has higher peptide binding plasticity than solely the VL9 peptide [75].…”

Section: Mycobacterium Tuberculosismentioning

confidence: 99%

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HLA-E: exploiting pathogen-host interactions for vaccine development

Sharpe

Bowyer

Brackenridge

et al. 2019

Clinical and Experimental Immunology

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Summary Viruses, when used as vectors for vaccine antigen delivery, can induce strong cellular and humoral responses against target epitopes. Recent work by Hansen et al. describes the use of a cytomegalovirus‐vectored vaccine, which is able to generate a stable effector‐memory T cell population at the sites of vaccination in rhesus macaques. This vaccine, targeted towards multiple epitopes in simian immunodeficiency virus (SIV), did not induce classical CD8+ T cells. However, non‐canonical CD8+ T cell induction occurred via major histocompatibility complex (MHC) class II and MHC‐E. The MHC‐E‐restricted T cells could recognize broad epitopes across the SIV peptides, and conferred protection against viral challenge to 55% of vaccinated macaques. The human homologue, human leucocyte antigen (HLA)‐E, is now being targeted as a new avenue for vaccine development. In humans, HLA‐E is an unusually oligomorphic class Ib MHC molecule, in comparison to highly polymorphic MHC class Ia. Whereas MHC class Ia presents peptides derived from pathogens to T cells, HLA‐E classically binds defined leader peptides from class Ia MHC peptides and down‐regulates NK cell cytolytic activity when presented on the cell surface. HLA‐E can also restrict non‐canonical CD8+ T cells during natural infection with various pathogens, although the extent to which they are involved in pathogen control is mostly unknown. In this review, an overview is provided of HLA‐E and its ability to interact with NK cells and non‐canonical T cells. Also discussed are the unforeseen beneficial effects of vaccination, including trained immunity of NK cells from bacille Calmette–Guérin (BCG) vaccination, and the broad restriction of non‐canonical CD8+ T cells by cytomegalovirus (CMV)‐vectored vaccines in pre‐clinical trials.

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“…However, these Mamu-E-restricted epitopes are sequence-diverse, contain non-canonical anchor residues and lack a common motif 17 . Notably, despite a considerable degree of sequence divergence between the human and rhesus MHC-E homologues, heavy chain-derived residues forming the B, D, C, E and F pockets of the binding groove exhibit strong sequence conservation 20 . Given this stringent sequence conservation between pocketforming residues, it is likely these homologues share a largely overlapping peptide binding repertoire.…”

Section: Introductionmentioning

confidence: 99%

Detailed and atypical HLA-E peptide binding motifs revealed by a novel peptide exchange binding assay

Walters

McMichael

Gillespie

2020

Preprint

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Diverse SIV epitopes that bind the rhesus homologue of HLA-E, Mamu-E, have recently been identified in SIV-vaccine studies using a recombinant Rhesus cytomegalovirus (RhCMV 68-1) vector, where unprecedented protection against SIV challenge was achieved. Additionally, several Mycobacterial peptides identified both algorithmically and following elution from infected cells, are presented to CD8 + T cells by HLA-E in humans. Yet, a comparative and comprehensive analysis of relative HLA-E peptide binding strength via a reliable, high throughput in vitro assay is currently lacking. To address this we developed and optimised a novel, highly sensitive peptide exchange ELISA-based assay that relatively quantitates peptide binding to HLA-E. Using this approach we screened multiple peptides, including peptide panels derived from HIV, SIV and Mtb predicted to bind HLA-E. Our results indicate that although HLA-E preferentially accommodates canonical MHC class I leader peptides, many noncanonical, sequence diverse, pathogen-derived peptides also bind HLA-E, albeit generally with lower relative binding strength. Additionally, our screens demonstrate that the majority of peptides tested, including some key Mtb and SIV epitopes which have been shown to elicit strong Mamu-E-restricted T cell responses, either bind HLA-E extremely weakly or give signals that are indistinguishable from the negative, peptide-free controls.Given the identification of a large number of non-VL9 pathogen-and self-derived HLA-E-binding peptides, we recognised the need to develop an assay to reliably and comparatively assess the HLA-E peptidome. We therefore designed and optimised a new in vitro peptide exchange ELISA-based assay to validate and relatively quantitate peptide binding to HLA-E. Although we previously validated HLA-E peptide binding 17 using a micro-refolding ELISA-based assay, originally developed to determine peptide binding affinity to classical MHC class I molecules 7 22 , this assay suffered from variability between biological repeats, so that very large numbers of replicate assays were required to achieve statistically robust results. The variability was likely caused by assay-to-assay fluctuations in protein refolding in addition to unusually high background signals, due to partial HLA-E-b2M refolding in the absence of added peptide 20 . To improve the system we adopted a new UV peptide exchange ELISAbased assay 23 . In this assay, HLA-E heavy chain and β2M are pre-refolded with a UV-labile HLA-E binding peptide based on the VL9 sequence in which the solvent exposed Arg at position 5 of VL9 was replaced with a photo-cleavable, unnatural 2-nitrophenylamino acid residue 20 23 . Such conditional peptide ligand technology was originally developed for HLA-A*02:01 23 and subsequently adapted to facilitate peptide exchange in HLA-A*1, -A*3, -A*11, -B*7 and -B*57 molecules 24 25 . Specifically, the nitrophenyl moiety within the substituted beta amino acid is sensitive to UV illumination at >350nm. This results in peptide cleavage and successiv...

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Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding

Cited by 60 publications

References 70 publications

Subordinate effect of −21M HLA-B dimorphism on NK cell repertoire diversity and function in HIV-1 infected individuals of African origin

Subordinate effect of −21M HLA-B dimorphism on NK cell repertoire diversity and function in HIV-1 infected individuals of African origin

HLA-E: exploiting pathogen-host interactions for vaccine development

Detailed and atypical HLA-E peptide binding motifs revealed by a novel peptide exchange binding assay

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