Biology subjects

Brackenridge, S.

Publications and source records attributed to Brackenridge, S..

6 recordsLinked to original sources

bioRxiv2024

A high affinity monoclonal antibody against HLA-E-VL9 enhances natural killer cell anti-tumor killing

A major natural killer (NK) cell and CD8+ T cell checkpoint is mediated by the inhibitory receptor NKG2A/CD94 and its ligand, HLA-E complexed with 9 amino acid HLA-Ia leader sequence-derived peptides termed VL9 (HLA-E-VL9). Here, we used structure-based design and high throughput library screening to generate antibodies that block NKG2A/CD94 interactions, resulting in direct NK and CD8+ T cell cytotoxicity, and trigger NK cell antibody-dependent cellular cytotoxicity (ADCC). Anti-HLA-E-VL9 antibodies limited HLA-E-VL9+ tumor growth in mice, demonstrating checkpoint inhibition activity in vivo. HLA-E-VL9 was found to be expressed on HIV-infected cells, and its engagement by HLA-E-VL9 antibodies eliminated infected cells by NK-mediated ADCC. HLA-E-VL9 antibodies also enhanced the killing of HIV-infected cells by NKG2A/CD94+ CD8+ T cells targeting a novel HLA-E binding HIV Rev-derived epitope. Therefore, anti-HLA-E-VL9 antibodies represent a novel approach to eliminate pathogenic target cells by enhancing NK and CD8+ T cell function and promoting ADCC.

immunology↗

bioRxiv2022

REGULATION OF THE CELL SURFACE EXPRESSION OF CLASSICAL AND NON-CLASSICAL MHC PROTEINS BY THE HUMAN CYTOMEGALOVIRUS UL40 AND RHESUS CYTOMEGALOVIRUS RH67 PROTEINS

The signal sequences of the human cytomegalovirus (CMV) UL40 protein, and its rhesus CMV counterpart, Rh67, contain a peptide (VMAPRT[L/V][F/I/L/V]L, VL9) that can be presented by Major Histocompatibility Complex (MHC) antigen E. The CMV VL9 peptides replace VL9 peptides derived from classical MHC (Ia) signal sequences, which are lost when CMV disrupts MHC Ia expression, as well as antigen processing and presentation. This allows infected cells to maintain surface expression of MHC-E and escape killing by NK cells expressing the inhibitory NKG2A/CD94 receptor. We demonstrate that processing of the Rh67 VL9 peptide mirrors that of UL40, despite the lack of sequence conservation elsewhere in the two proteins. As previously shown for UL40, up-regulation of MHC-E expression by Rh67 only requires its signal sequence, with sequences upstream of VL9 critical for conferring independence from TAP, the Transporter Associated with Antigen Processing. Additionally, we show that processing of both VL9 peptides depends on cleavage of the signal sequences by the host protease Signal Peptide Peptidase. Notably, our results also reveal that the mature UL40 and Rh67 proteins contribute to CMV immune evasion by down-regulating surface expression of MHC Ia. Unexpectedly, while the Rh67 VL9 peptide is resistant to the effects of the Rh67 protein, the UL40 protein is able to counteract up-regulation of MHC-E expression mediated by its own VL9 peptide. This suggests differences in the mechanisms by which the two VL9 peptides up-regulate MHC-E, which may have implications for translating a RhCMV-vectored SIV vaccine to HIV-1 using HCMV as a vector. IMPORTANCECell surface MHC-E expression, which requires a peptide (VMAPRT[L/V][F/I/L/V]L, "VL9") from the signal sequences of other MHC class I proteins, prevents cells from being killed by CD94/NKG2A-expressing Natural Killer cells. In cells infected with human CMV, the endogenous VL9 peptide is replaced by one from the signal sequence of the HCMV UL40 protein. We show that processing of the VL9 peptide of Rh67, the rhesus CMV equivalent of UL40, mirrors that of UL40, despite a lack of sequence homology between the two proteins. Of note, we also show that the mature UL40 and Rh67 proteins, which have no previously described function, contribute to CMV immune evasion by reducing classical MHC class I surface expression. Importantly, the mature UL40 protein, but not the mature Rh67 protein, can decrease the up-regulation of MHC-E mediated by its signal sequence VL9 peptide, which may have implications for HCMV as a vaccine vector.

immunology↗

bioRxiv2022

Mapping the epitopes of the Human Leukocyte Antigen E antibodies 3D12 and 4D12

The commonly used commercially available antibodies 3D12 and 4D12 recognise the human leukocyte antigen E (HLA-E) protein. 3D12 is known to exhibit minimal cross-reactivity with classical HLA-Ia allotypes and we confirm that this is also the case for 4D12. These antibodies bind different epitopes on HLA-E, and differ in their ability to recognise alleles of the major histocompatibility complex E (MHC-E) proteins of rhesus and cynomolgus macaques. Using hybrids of different MHC-E alleles, we have mapped the regions that are critical for the binding of these two antibodies. 3D12 recognises a region on the alpha 3 domain that is unique to HLA-E, on the opposite side to that bound by {beta}2-microglobulin, while 4D12 recognises the start of the alpha 2 domain, adjacent to the C terminus of the presented peptide. Knowledge of the binding sites of these two antibodies will facilitate selection of the best antibody for a given application, and inform interpretation of the resulting data.

immunology↗

bioRxiv2021

HLA binding of self-peptides is biased towards proteins with specific molecular functions

Human leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.

bioinformatics↗

bioRxiv2020

IgM Natural Antibodies Bind HLA-E-Leader Peptide Complexes and Modulate NK Cell Cytotoxicity

HLA-E is a non-classical class Ib molecule that has limited polymorphism and binds HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we isolated a murine IgM antibody 3H4, that specifically recognized HLA-E-VL9 bound complexes and enhanced killing of HLA-E-VL9-expressing cells by an NKG2A+ NK cell line. Structural analysis revealed how 3H4 prevents CD94/NKG2A docking on HLA-E-VL9 by binding with an overlapping footprint. Upon in vitro maturation, an affinity-optimized 3H4 IgG showed enhanced NK killing of HLA-E-VL9-expressing cells. Remarkably, HLA-E-VL9-specific IgM autoantibodies with similar specificity and functions to 3H4 were subsequently isolated from naive B cells of cytomegalovirus (CMV)-negative, healthy male human donors. Thus, a repertoire of germline low affinity HLA-E-VL9-reactive antibodies are present in both naive human and murine B cell repertoires. These antibodies can enhance NK cell cytotoxicity and therefore have potential for therapeutic modulation of NK cell function.

immunology↗

bioRxiv2020

HLA-E restricted, HIV-1 suppressing, Gag specific CD8+ T cells offer universal vaccine opportunities

Human leukocyte antigen-E (HLA-E) normally presents a HLA class Ia signal peptide to the NKG2A/C-CD94 regulatory receptors on natural killer (NK) cells and T cell subsets. Rhesus macaques immunized with a cytomegalovirus vectored simian immunodeficiency virus (SIV) vaccine, generated Mamu-E (HLA-E homolog) restricted T cell responses that mediated post-challenge SIV replication arrest in >50% of animals. However, human immunodeficiency virus type 1 (HIV-1) specific HLA-E restricted T cells have not been observed in HIV-1-infected individuals. Here we primed HLA-E restricted HIV-1 specific CD8+ T cells in vitro. These T cell clones, and allogeneic CD8+ T cells transduced with their T cell receptors, suppressed HIV-1 replication in CD4+ T cells in vitro. Vaccine induction of efficacious HLA-E restricted HIV-1 specific T cells should therefore be possible. One Sentence SummaryCD8+ T cells that recognize a Gag peptide presented by HLA-E suppress HIV-1 replication in vitro.

immunology↗