Natural Killer Cell Interactions with Classical and Non-Classical Human Leukocyte Antigen Class I in HIV-1 Infection

Upregulation of the NKG2D Ligand ULBP2 by JC Polyomavirus Infection Promotes Immune Recognition by Natural Killer Cells

BACKGROUND

JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML), a potentially fatal complication of severe immune suppression with no effective treatment. Natural killer (NK) cells play critical roles in defense against viral infections; however, NK-cell response to JCPyV infection remains unexplored.

METHODS

NK- and T-cell responses against the JCPyV VP1 were compared using intracellular cytokine staining upon stimulation with peptide pools. A novel flow cytometry-based assay was developed to determine NK-cell killing efficiency of JCPyV-infected astrocyte-derived SVG-A cells. Blocking antibodies were used to evaluate the contribution of NK-cell receptors in immune recognition of JCPyV-infected cells.

RESULTS

In about 40% of healthy donors, we detected robust CD107a upregulation and IFN-γ production by NK cells, extending beyond T-cell responses. Next, using the NK-cell-mediated killing assay, we showed that coculture of NK cells and JCPyV-infected SVG-A cells leads to a 60% reduction in infection, on average. JCPyV-infected cells had enhanced expression of ULBP2-a ligand for the activating NK-cell receptor NKG2D, and addition of NKG2D blocking antibodies decreased NK-cell degranulation.

CONCLUSIONS

NKG2D-mediated activation of NK cells plays a key role in controlling JCPyV replication and may be a promising immunotherapeutic target to boost NK-cell anti-JCPyV activity.

Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health

Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.

NK Cells, Monocytes and Macrophages in HIV-1 Control: Impact of Innate Immune Responses

Rapid and synchronized responses of innate immune cells are an integral part of managing viral spread in acute virus infections. In human immunodeficiency virus type 1 (HIV-1) infection, increased immune control has been associated with the expression of certain natural killer (NK) cell receptors. Further, immune activation of monocytes/macrophages and the presence of specific cytokines was linked to low levels of HIV-1 replication. In addition to the intrinsic antiviral capabilities of NK cells and monocytes/macrophages, interaction between these cell types has been shown to substantially enhance NK cell function in the context of viral infections. This review discusses the involvement of NK cells and monocytes/macrophages in the effective control of HIV-1 and highlights aspects of innate immune crosstalk in viral infections that may be of relevance to HIV-1 infection.

Immunomodulatory Potential of Non-Classical HLA-G in Infections including COVID-19 and Parasitic Diseases

Human Leukocyte Antigen-G (HLA-G), a polymorphic non-classical HLA (HLA-Ib) with immune-regulatory properties in cancers and infectious diseases, presents both membrane-bound and soluble (sHLA-G) isoforms. Polymorphism has implications in host responses to pathogen infections and in pathogenesis. Differential expression patterns of HLA-G/sHLA-G or its polymorphism seem to be related to different pathological conditions, potentially acting as a disease progression biomarker. Pathogen antigens might be involved in the regulation of both membrane-bound and sHLA-G levels and impact immune responses during co-infections. The upregulation of HLA-G in viral and bacterial infections induce tolerance to infection. Recently, sHLA-G was found useful to identify the prognosis of Coronavirus disease 2019 (COVID-19) among patients and it was observed that the high levels of sHLA-G are associated with worse prognosis. The use of pathogens, such as Plasmodium falciparum, as immune modulators for other infections could be extended for the modulation of membrane-bound HLA-G in COVID-19-infected tissues. Overall, such information might open new avenues concerning the effect of some pathogens such as parasites in decreasing the expression level of HLA-G to restrict pathogenesis in some infections or to influence the immune responses after vaccination among others.

KIR3DS1 directs NK cell-mediated protection against human adenovirus infections

[Figure: see text].

Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians

Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.

The Role of HLA and KIR Immunogenetics in BK Virus Infection after Kidney Transplantation

BK virus (BKV) is a polyomavirus with high seroprevalence in the general population with an unremarkable clinical presentation in healthy people, but a potential for causing serious complications in immunosuppressed transplanted patients. Reactivation or primary infection in kidney allograft recipients may lead to allograft dysfunction and subsequent loss. Currently, there is no widely accepted specific treatment for BKV infection and reduction of immunosuppressive therapy is the mainstay therapy. Given this and the sequential appearance of viruria-viremia-nephropathy, screening and early detection are of utmost importance. There are numerous risk factors associated with BKV infection including genetic factors, among them human leukocyte antigens (HLA) and killer cell immunoglobulin-like receptors (KIR) alleles have been shown to be the strongest so far. Identification of patients at risk for BKV infection would be useful in prevention or early action to reduce morbidity and progression to frank nephropathy. Assessment of risk involving HLA ligands and KIR genotyping of recipients in the pre-transplant or early post-transplant period might be useful in clinical practice. This review summarizes current knowledge of the association between HLA, KIR and BKV infection and potential future directions of research, which might lead to optimal utilization of these genetic markers.

HIV-1 induced changes in HLA-C*03 : 04-presented peptide repertoires lead to reduced engagement of inhibitory natural killer cell receptors

OBJECTIVE

Viral infections influence intracellular peptide repertoires available for presentation by HLA-I. Alterations in HLA-I/peptide complexes can modulate binding of killer immunoglobuline-like receptors (KIRs) and thereby the function of natural killer (NK) cells. Although multiple studies have provided evidence that HLA-I/KIR interactions play a role in HIV-1 disease progression, the consequence of HIV-1 infection for HLA-I/KIR interactions remain largely unknown.

DESIGN

We determined changes in HLA-I presented peptides resulting from HIV-1-infection of primary human CD4 T cells and assessed the impact of changes in peptide repertoires on HLA-I/KIR interactions.

METHODS

Liquid chromatography-coupled tandem mass spectrometry to identify HLA-I presented peptides, cell-based in-vitro assays to evaluate functional consequences of alterations in immunopeptidome and atomistic molecular dynamics simulations to confirm experimental data.

RESULTS

A total of 583 peptides exclusively presented on HIV-1-infected cells were identified, of which only 0.2% represented HIV-1 derived peptides. Focusing on HLA-C*03 : 04/KIR2DL3 interactions, we observed that HLA-C*03 : 04-presented peptides derived from noninfected CD4 T cells mediated stronger binding of inhibitory KIR2DL3 than peptides derived from HIV-1-infected cells. Furthermore, the most abundant peptide presented by HLA-C*03 : 04 on noninfected CD4 T cells (VIYPARISL) mediated the strongest KIR2DL3-binding, while the most abundant peptide presented on HIV-1-infected cells (YAIQATETL) did not mediate KIR2DL3-binding. Molecular dynamics simulations of HLA-C*03 : 04/KIR2DL3 interactions in the context of these two peptides revealed that VIYPARISL significantly enhanced the HLA-C*03 : 04/peptide contact area to KIR2DL3 compared with YAIQATETL.

CONCLUSION

These data demonstrate that HIV-1 infection-induced changes in HLA-I-presented peptides can reduce engagement of inhibitory KIRs, providing a mechanism for enhanced activation of NK cells by virus-infected cells.

HLA-G Polymorphisms Associated with HIV Infection and Preeclampsia in South Africans of African Ancestry

OBJECTIVES

HLA-G, part of the major histocompatibility complex (MHC), is associated with the risk of developing preeclampsia (PE). In this study, we determined the contribution of specific HLA-G polymorphisms on the risk of developing preeclampsia in HIV-infected and uninfected South Africans of African ancestry.

METHODS

One hundred and ninety-three women of African ancestry were enrolled (74 HIV-uninfected normotensive, 60 HIV-infected normotensive, 34 HIV-uninfected, and 25 HIV-infected preeclamptics). Sanger sequencing of the untranslated region was performed to genotype six SNPs, i.e., 14 bp Ins/Del of rs66554220, rs1710, rs1063320, rs1610696, rs9380142, and rs1707).

RESULTS

For rs66554220, we have the following results: (a) based on pregnancy type-the Ins/Ins and Del/Ins genotype frequency was higher in preeclampsia (PE) compared to normotensive pregnancies (Ins/Ins vs. Del/Ins, P = 0.02∗: OR (95%CI) = 13.44 (0.7222-249.9); Del/Del vs. Del/Ins, P = 0.03∗: OR (95%CI) = 2.95 (1.10-7.920)); (b) based on HIV status-the Ins/Ins showed both genotypic and allelic association with HIV infection. HIV-infected PE has higher Ins/Ins genotypic and allelic frequencies compared to HIV-uninfected PE (Ins/Ins vs. Del/Ins, P = 0.005∗∗: OR (95%CI) = 21.32 (1.71-4.17); Ins, P = 0.005∗∗; OR (95%IC) = 21.32 (1.71-4.17)). For rs1707, we have the following results: (a) based on pregnancy type-there were CT genotypic frequencies in PE, more especially LOPE compared to normotensive pregnancies (TT vs. CT, P = 0.0092∗∗: OR (95%CI) = 5.(1.39 - 25.64)), and no allelic association was noted; (b) based on HIV status-CT was higher in HIV-infected LOPE compared to uninfected LOPE (TT vs. TC, P = 0.0006∗∗∗: OR (95%CI) = 40.00 (2.89 - 555.1)). For rs1710 and rs1063320, no significant differences in the genotype and allele frequencies were noted based on pregnancy type and HIV status. For rs9380142, we have the following results: (a) based on pregnancy type-no significant differences were noted between normotensive compared to PE pregnancies; (b) based on HIV status-AA genotypes occurred more in the HIV-infected PE group (AA vs. GG, P = 0.02∗: OR (95%CI) = 13.97 (0.73 - 269.4)), while A allelic frequency occurred more in HIV-infected PE, especially LOPE compared to uninfected groups (A vs. G, P = 0.0003∗∗∗: OR (95%CI) = 10.72 (2.380 - 48.32); P = 0.02∗: OR (95%CI) = 9.00 (1.07 - 75.74)). For rs1610696, we have the following results: (a) based on pregnancy type-genotypic and allelic frequencies of CC were higher in PE compared to normotensive pregnancies (CC vs. GG, P = 0.0003∗∗∗: OR (95%CI) = 31.87 (1.861 - 545.9); C, P = 0.0001∗∗∗: OR (95%IC) = 21.91 (2.84 - 169.0)); (b) based on HIV status-GG frequencies were higher in the HIV-infected PE more especially LOPE groups (GG vs. GC, P = 0.02∗: OR (95%CI) = 16.87 (0.81 - 352.1); GG vs. CC, P = 0.0001∗∗∗: OR (95%CI) = 159.5 (13.10 - 1942)).

CONCLUSION

Selected HLA-G 14 bp polymorphisms (Ins/Ins) and genotypic and allelic differences in rs9380142, rs1610696, and rs1707 are associated with the pathogenesis of preeclampsia in HIV-infected South African women of African ancestry. More genetic studies evaluating the association between preeclampsia and HIV infection are needed to improve diagnosis and antenatal care.

Timing of Antiretroviral Therapy Initiation Determines Rectal Natural Killer Cell Populations

Despite antiretroviral therapy (ART), innate and adaptive immunologic damage persists in the periphery and gut. T memory stem cells (Tscm) and natural killer (NK) cells are pivotal for host defense. Tscm are memory cells capable of antigen response and self-renewal, and circulating and gut NK cell populations may facilitate HIV control. The impact of early ART on circulating and gut Tscm and NK cells is unknown. We enrolled participants who initiated ART during acute versus chronic HIV-1 infection versus no ART in chronic infection. We performed flow cytometry to identify NK and Tscm cells in the blood and rectum and polymerase chain reaction to quantify the HIV-1 reservoir in both sites. We used the Mann-Whitney U-test and Spearman correlation coefficients for analysis. Participants who started ART in acute infection had lower rectal CD56^brightCD16^dim cell frequencies than participants who started ART in chronic HIV-1 infection and lower CD56^bright and CD56^brightCD16^- cell frequencies than participants with chronic infection without ART. Higher circulating NK cell, CD56^-CD16^bright, CD56^dim, and CD56^dimCD16^bright frequencies correlated with higher HIV-1 DNA levels in rectal CD4⁺ T cells, whereas higher circulating CD4⁺ T cell counts correlated with higher rectal NK, CD56^brightCD16^dim, and CD56^dimCD16^bright frequencies. Peripheral CD56^brightCD16^- cells were inversely associated with rectal CD56^-CD16^bright cells. Rectal CD8⁺ Tscm frequencies were higher in participants without ART than participants with chronic infection on ART. Timing of ART initiation determines rectal NK cell populations, and ART may influence rectal Tscm populations. Whether the gut reservoir contributes to NK cell activation requires further study.

Natural Killer Cells Offer Differential Protection From Leukemia in Chinese Southern Han

Interactions of human natural killer (NK) cell inhibitory receptors with polymorphic HLA-A, -B and -C molecules educate NK cells for immune surveillance against tumor cells. The KIR A haplotype encodes a distinctive set of HLA-specific NK cell inhibiting receptors having strong influence on immunity. We observed higher frequency of KIR A homozygosity among 745 healthy Chinese Southern Han than 836 adult patients representing three types of leukemia: ALL (OR = 0.68, 95% CI = 0.52-0.89, p = 0.004), AML (OR = 0.76, 95% CI = 0.59-0.98, p = 0.034), and CML (OR = 0.72 95% CI = 0.51-1.0, ns). We observed the same trend for NHL (OR = 0.47 95% CI = 0.26-0.88 p = 0.017). For ALL, the protective effect of the KIR AA genotype was greater in the presence of KIR ligands C1 (Pc = 0.01) and Bw4 (Pc = 0.001), which are tightly linked in East Asians. By contrast, the C2 ligand strengthened protection from CML (Pc = 0.004). NK cells isolated from KIR AA individuals were significantly more cytotoxic toward leukemic cells than those from other KIR genotypes (p < 0.0001). These data suggest KIR allotypes encoded by East Asian KIR A haplotypes are strongly inhibitory, arming NK cells to respond to leukemogenic cells having altered HLA expression. Thus, the study of populations with distinct KIR and HLA distributions enlightens understanding of immune mechanisms that significantly impact leukemia pathogenesis.

The Emerging Roles of Human Leukocyte Antigen-F in Immune Modulation and Viral Infection

Human leukocyte antigens (HLAs) play various critical roles in both innate and adaptive immunity through processes such as presenting antigens to T cells and serving as ligands for receptors expressed on natural killer (NK) cells. Among the HLA class I family, the clinical significance and biological function of HLA-F have been the least investigated and have remained elusive for a long period of time. Previous studies have revealed that HLA-F expression might be involved in various physiological and pathological processes, such as pregnancy, viral infection, cancer, transplantation, and autoimmune diseases. However, recent data have shown that, akin to other HLA family members, HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. These important findings pave new avenues for investigations regarding the functions of HLA-F as an important immune regulatory molecule. In the present review, we summarize the studies on the role of HLA-F in immune modulation, with a special emphasis placed on the roles of HLA-F and KIR3DS1 interactions in viral infection.

Characterization of three new HLA Class I Alleles in Chinese individuals, HLA-B*46:68,-B*46:71,-B*46:72

Three new HLA class I alleles were described in the Chinese population. HLA-B*46:68,-B*46:71,-B*46:72 alleles differ from HLA-B*46:01:01 by a single nucleotide substitution at position 485C>T, 484A>G, 299T>A respectively.

Defining the role of NK cells during dengue virus infection

In recent years, our understanding of the complex number of signals that need to be integrated between a diverse number of receptors present on natural killer (NK) cells and ligands present on target cells has improved. Here, we review the progress made in identifying interactions between dengue viral peptides presented on HLA Class 1 molecules with inhibitory and activating killer-like immunoglobulin receptors on NK cells, direct interactions of viral proteins with NK cell receptors, the involvement of dengue virus-specific antibodies in mediating antibody-dependent cell-mediated cytotoxicity and the role of soluble factors in modulating NK cell responses. We discuss findings of NK cell activation early after natural dengue infection, and point to the role that NK cells may play in regulating both innate and adaptive immune responses, in the context of our new appreciation of interactions of dengue virus with specific NK cell receptors. With a number of flavivirus vaccine candidates in clinical trials, how NK cells respond to attenuated dengue virus and subunit protein vaccine candidates and shape adaptive immunity will need to be considered.