Effects of genetic polymorphism in MHC, KIR, and related loci on human disease

MHC、KIR及相关位点遗传多态性对人类疾病的影响

• 批准号: 9556364
• 负责人: Mary N. Carrington
• 金额: $ 117.27万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9556364
• 关键词: Acquired Immunodeficiency Syndrome; Affect; Affinity; Agreement; Alleles; Amino Acids; Antibody Formation; Antibody Response; Antigens; Antiviral Agents; Autoimmune Diseases; Autologous; B-Cell Development; Bacterial Polysaccharides; Binding; Biological; Biological Assay; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; Cell Line; Cell surface; Cells; Characteristics; Chronic small plaque psoriasis; Coculture Techniques; Collaborations; Communicable Diseases; Complex; Confidence Intervals; Data; Dendritic Cells; Development; Disease; Disease Progression; Down-Regulation; Employment; Extracellular Domain; GEM gene; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genotype; Goals; HIV; HIV-1; HLA Class I Genes; HLA-B Antigens; HLA-Bw4; HLA-C Antigens; Haplotypes; Heterogeneity; Immune; Immune Evasion; Immune Response Genes; Immune System Diseases; Immune System and Related Disorders; Immune response; Immunogenetics; Immunoglobulin Genes; Immunologic Surveillance; In Vitro; Individual; Infection; Inflammatory; Inflammatory Response; Institutes; Interferon Type II; Isoleucine; KIR3DS1; Laboratories; Leukocytes; Ligand Binding; Ligands; Link; Linkage Disequilibrium; Logistic Regressions; MICA protein; Major Histocompatibility Complex; Malignant Neoplasms; Mediating; Messenger RNA; Molecular Conformation; NK Cell Activation; NK cell receptor NKB1; Natural Killer Cells; Odds Ratio; Outcome; Outcome Measure; Pathogenesis; Pathologic; Patients; Peptides; Positioning Attribute; Predisposition; Production; Proteins; Psoriatic Arthritis; Recurrence; Reporter; Resistance; Risk; Role; Spouses; Stress; Surface; TNF gene; TYRP1 gene; Testing; Transplantation; Ursidae Family; Valine; Variant; Viremia; Virus Diseases; base; cohort; conformer; cytokine; cytotoxic; cytotoxicity; disorder risk; genome sequencing; genome wide association study; genome-wide; human disease; immunoregulation; insight; interest; macrophage; pathogen; pleiotropism; protective effect; protein B; receptor; receptor binding; response; tumor; whole genome

KIR3DS1 was the first KIR to be associated with the outcome of a viral infection, namely, delayed HIV disease progression in patients with certain HLA B alleles. Since then, it has been extensively linked to other viral infections, autoimmune disorders, cancer development/clearance, and transplantation outcomes. Consequently, it has become one of the most studied KIRs. KIR3DS1 is an activating receptor that stimulates cytotoxicity and IFN-gamma production in NK cells. It is encoded in the KIR3DL1/KIR3DS1 gene locus, a unique KIR locus because it encodes for functionally divergent alleles. Remarkably, while sharing 95% homology in their extracellular domain, KIR3DS1 and its inhibitory counterpart KIR3DL1 have different ligand binding profiles. KIR3DL1 has conclusively been shown to bind HLA A and B proteins with a Bw4 motif. However, attempts to identify a KIR3DS1 ligand by various groups have repeatedly failed. The goal of this study was to identify ligands of KIR3DS1 and thus uncover the mechanistic basis for its influence in various human diseases. To this end, in collaboration with Dr. Marcus Altfeld at the Ragon Institute, we employed soluble receptor binding assays and cell-based functional assays to comprehensively screen HLA class I proteins in two biologically relevant conformation states: as HLA class I complexes, which are folded heavy chains bound to B2 microglobulin (B2m) and peptide, and as HLA class I open conformers (OCs), which are HLA class I heavy chains without bound B2m or peptide. We identified that HLA F OCs are high-affinity ligands of KIR3DS1, and also lower affinity ligands of the inhibitory receptors KIR3DL1 and KIR3DL2. We also demonstrated that this interaction is of functional relevance using reporter cell lines, primary KIR3DS1+ NK cells, and primary CD4+ T cells, providing an explanation for the widespread influence of KIR3DS1 in human disease. This newly identified KIR3DS1+HLA-F axis has many similarities to the well-known stress-induced NKG2D-MIC-A/B axis, even in the context of HIV-1 infection. Although it is less well-studied, HLA-F bears unique and distinguishing characteristics that separates it from all other HLA class I genes. In agreement with previous studies, our data show that HLA-F OCs are expressed on the surface of activated CD4+ T cells. Additionally, HIV-1 infection of CD4+ T cells increased transcription of HLA-F but reduced KIR3DS1 ligand expression, particularly in late-infected cells, which might suggest the employment of an immune-evasion strategy, potentially through the downregulation of HLA F by HIV1 accessory proteins, similar to what has been described for HIV1 Nef for HLA A and HLA B and NKG2D ligands including MIC A. KIR3DS1/HLA F interactions between NK cells and pathologically altered target cells would incur the well-known innate function of NK cells to recognize and eliminate target cells expressing "stressed self" ligands. This is supported by our in vitro co-culture assay, which showed that NK cells singly expressing KIR3DS1 are more effective at suppressing HIV1 replication in autologous CD4+ T cells as compared to KIR3DS1 negative NK cells. In addition, our data show that KIR3DS1/HLA-F interactions elicit NK cell production of antiviral and pro-inflammatory cytokines such as IFNgamma, TNF, and MIP1Beta, which would have pleiotropic effects on immune responses. Furthermore, KIR3DS1/HLA F interactions between NK cells and activated CD4+ T cells would also suggest a means of NK cell-mediated adaptive immune regulation. Thus, KIR3DS1 recognition of HLA F OCs expressed on activated immune cells and/or infected target cells provides a mechanistic link between KIR3DS1 and HIV1 disease progression, and will also have relevance for the pathogenesis of other infectious diseases, autoimmune disorders, and tumor immune-surveillance. HLA-B*57 is well known to associate with control of HIV, an observation that has largely been attributed to enhanced CD8+ T cell responses to infected cells. There is, however, extensive heterogeneity in control of HIV among B*57+ individuals, where many progress as rapidly to AIDS as B*57 negative subjects, indicating that there are other factors contributing to B*57 protection. We sought to identify genetic modifiers of B*57 using whole genome sequencing (WGS) of 100 HIV controllers and 100 non-controllers, all carrying one or two copies of HLA-B*57. A polymorphism (rs643347A/G) located in the KIR3DL1 gene that encodes an isoleucine to valine substitution at amino acid 47 (I47V) was the only variant to reach genome wide significance, with valine conferring protection. An independent B*57+ cohort in which KIR3DL1 was typed confirmed the protective effect of KIR3DL1 47V. The protective effect replicated across multiple alternative outcome measures, including longitudinal values for both mean viremia and CD4+ Tcell counts. Positions 2, 47, and 54, which are in near perfect linkage disequilibrium (LD) with one another, associated most strongly with HIV control relative to all other KIR3DL1 amino acid variants. Moreover, the effect was confined specifically to B*57:01, with no effect seen for the closely related B*57:03. These data implicate KIR3DL1 in modifying the effect of B*57:01 in control of HIV and provide insight into the factors that underlie the differential control of HIV across B*57+ subjects. We are now performing functional analyses in order to define the underlying mechanism(s) that explain the genetic data. Patients with common variable immune deficiency (CVID) display hypogammaglobulinemia, blunted antibody responses to bacterial polysaccharides, and recurrent sinopulmonary infections. Major histocompatibility complex (MHC) haplotypes associated with some autoimmune disorders are linked to CVID. However, inheritance of these haplotypes is insufficient for CVID development. We postulated a role for other immunogenetic factors that might interact with the MHC such as KIR. We tested whether KIR/HLA genotypes influence the risk of CVID in patients from the Southeastern USA. We genotyped KIR and HLA, and performed an ImmunoChip Assay on 175 affected individuals and on 72 spousal controls without evidence of immune dysfunction. We used logistic regression to estimate odds ratios and corresponding confidence intervals (CI). KIR genes associated with disease risk included activating KIR2DS1 (OR=1.45; P=0.03) and KIR3DS1 (OR = 1.54; P=0.01) and inhibitory KIR2DL5 (OR=1.43; P=0.04), (Figure 1). All three genes are found on KIR "B" haplotypes in linkage disequilibrium (6). KIR2DL5 has previously been shown to confer susceptibility to the autoimmune disease psoriasis vulgaris (PV), and KIR2DS1 is associated with both PV and psoriatic arthritis (PsA). Analysis of KIR/HLA receptor-ligand combinations on disease risk indicated an increased risk with the compound genotype KIR3DS1+HLA-Bw4. KIR2DL1+HLA-C group 2 was protective (OR=0.58, P=0.002), while homozygosity for KIR2DL3+HLA-C group 1 was associated with increased CHI risk (OR=1.88, P=0.002). Overall, the data suggest that CVID risk increases in patients where NK cell activation can be facilitated. The mechanism by which KIR alleles could influence the development of CVID is unknown. Upon activation, NK cells become cytotoxic, produce inflammatory cytokines and interact with dendritic cells and macrophages. It is possible that enhanced NK activation could be advantageous for patients exposed to infection, but detrimental in a disease such as CVID where enhancement of an inflammatory response to an antigen, either environmental or pathogen derived, could set up a regulatory cascade that results in a variable block in B cell development and antibody production.

KIR3DS1是第一个与病毒感染结果相关的KIR，即在具有某些HLA B等位基因的患者中延迟HIV疾病进展。从那时起，它被广泛地与其他病毒感染、自身免疫性疾病、癌症发展/清除和移植结果联系在一起。因此，它已成为研究最多的kir之一。KIR3DS1是一种激活受体，刺激NK细胞的细胞毒性和ifn - γ的产生。它编码于KIR3DL1/KIR3DS1基因座，这是一个独特的KIR基因座，因为它编码功能分化的等位基因。值得注意的是，尽管KIR3DS1和其抑制对应体KIR3DL1在细胞外结构域具有95%的同源性，但它们具有不同的配体结合谱。KIR3DL1已被证实结合HLA A和B蛋白与Bw4基序。然而，各种小组试图鉴定KIR3DS1配体的尝试一再失败。本研究的目的是鉴定KIR3DS1的配体，从而揭示其影响各种人类疾病的机制基础。为此，我们与拉根研究所的Marcus Altfeld博士合作，采用可溶性受体结合试验和基于细胞的功能试验，全面筛选两种生物相关构象状态的HLA I类蛋白：HLA I类复合物，是折叠的重链结合B2微球蛋白（B2m）和肽，以及HLA I类开放构象（OCs），是没有结合B2m或肽的HLA I类重链。我们发现HLA F oc是KIR3DS1的高亲和力配体，也是抑制受体KIR3DL1和KIR3DL2的低亲和力配体。我们还通过报告细胞系、原代KIR3DS1+ NK细胞和原代CD4+ T细胞证明了这种相互作用具有功能相关性，为KIR3DS1在人类疾病中的广泛影响提供了解释。这个新发现的KIR3DS1+HLA-F轴与众所周知的应激诱导的NKG2D-MIC-A/B轴有许多相似之处，即使在HIV-1感染的背景下也是如此。尽管对它的研究较少，但HLA- f具有将其与所有其他HLA I类基因区分开来的独特特征。与之前的研究一致，我们的数据显示HLA-F oc在活化的CD4+ T细胞表面表达。此外，HIV-1感染CD4+ T细胞增加了HLA-F的转录，但降低了KIR3DS1配体的表达，特别是在晚期感染细胞中，这可能表明采用了免疫逃避策略，可能通过HIV-1辅助蛋白下调HLA-F。与hiv - 1 Nef对HLA A、HLA B和NKG2D配体（包括MIC A）的作用类似，NK细胞和病理改变的靶细胞之间的KIR3DS1/HLA F相互作用会导致NK细胞识别和消除表达“应激自我”配体的靶细胞的众所周知的先天功能。我们的体外共培养实验支持了这一点，结果表明，与KIR3DS1阴性的NK细胞相比，单独表达KIR3DS1的NK细胞在抑制自体CD4+ T细胞中的hiv复制方面更有效。此外，我们的数据显示，KIR3DS1/HLA-F相互作用可诱导NK细胞产生抗病毒和促炎细胞因子，如IFNgamma、TNF和MIP1Beta，这将对免疫反应产生多效性影响。此外，NK细胞与活化的CD4+ T细胞之间的KIR3DS1/HLA F相互作用也提示NK细胞介导的适应性免疫调节手段。因此，KIR3DS1对活化免疫细胞和/或感染靶细胞上表达的HLA F OCs的识别提供了KIR3DS1与HIV1疾病进展之间的机制联系，也将与其他感染性疾病、自身免疫性疾病和肿瘤免疫监测的发病机制相关。众所周知，HLA-B*57与HIV的控制有关，这一观察结果在很大程度上归因于CD8+ T细胞对感染细胞的反应增强。然而，在B*57阳性个体的艾滋病毒控制方面存在广泛的异质性，其中许多人与B*57阴性受试者一样迅速发展为艾滋病，这表明还有其他因素有助于B*57保护。研究人员对100名HIV控制者和100名非控制者进行了全基因组测序（WGS），以确定B*57的遗传修饰因子，这些控制者都携带一个或两个HLA-B*57拷贝。KIR3DL1基因中的多态性（rs643347A/G）编码氨基酸47 （I47V）的异亮氨酸到缬氨酸的替代，这是唯一具有全基因组意义的变异，缬氨酸具有保护作用。KIR3DL1分型的独立B*57+队列证实了KIR3DL1 47V的保护作用。保护作用在多个可选结果测量中得到复制，包括平均病毒血症和CD4+ t细胞计数的纵向值。位置2、47和54彼此之间处于接近完美的连锁不平衡（LD），相对于所有其他KIR3DL1氨基酸变体，它们与HIV控制的相关性最强。此外，这种影响仅限于B*57:01，而对密切相关的B*57:03没有影响。这些数据暗示KIR3DL1在改变B*57:01在HIV控制中的作用，并提供了在B*57+受试者中导致HIV控制差异的因素。我们现在正在进行功能分析，以确定解释遗传数据的潜在机制。常见可变免疫缺陷（CVID）患者表现为低丙种球蛋白血症，对细菌多糖的抗体反应迟钝，以及复发性肺感染。与一些自身免疫性疾病相关的主要组织相容性复合体（MHC）单倍型与CVID有关。然而，这些单倍型的遗传对于CVID的发展是不够的。我们假设了其他可能与MHC相互作用的免疫遗传因子（如KIR）的作用。我们测试了KIR/HLA基因型是否影响美国东南部患者CVID的风险。我们对175名受影响的个体和72名无免疫功能障碍的配偶对照进行了免疫芯片分析，对KIR和HLA进行了基因分型。我们使用逻辑回归来估计比值比和相应的置信区间（CI）。与疾病风险相关的KIR基因包括激活KIR2DS1 （OR=1.45； P=0.03）和KIR3DS1 （OR= 1.54； P=0.01）和抑制KIR2DL5 (OR=1.43； P=0.04),（图1）。这三个基因都存在于连锁不平衡的KIR“B”单倍型中(6)。KIR2DL5先前已被证明与自身免疫性疾病寻常性银屑病（PV）易感性相关，KIR2DS1与PV和银屑病关节炎（PsA）相关。KIR/HLA受体-配体组合对疾病风险的分析表明，复合基因型KIR3DS1+HLA- bw4的风险增加。KIR2DL1+HLA-C组2具有保护作用（OR=0.58， P=0.002），而KIR2DL3+HLA-C组1的纯合性与CHI风险增加相关（OR=1.88， P=0.002）。总的来说，数据表明，在NK细胞激活可以促进的患者中，CVID风险增加。KIR等位基因影响CVID发展的机制尚不清楚。激活后，NK细胞具有细胞毒性，产生炎性细胞因子，并与树突状细胞和巨噬细胞相互作用。增强NK活化可能对暴露于感染的患者是有利的，但对CVID等疾病是有害的，其中对抗原（环境或病原体来源）的炎症反应增强可能建立一个调节级联，导致B细胞发育和抗体产生的可变阻断。