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

我们已经开始测试HLA变异与多种癌症类型对免疫检查点抑制剂（ICI）反应的公开数据之间的关联。最近的研究表明，HLA I类的纯合性与检查点阻断免疫治疗的不良反应有关，这与我们早期关于纯合性对HIV疾病进展的有害影响的发现相似。纯合性理论上限制了呈献给CTL的肽库，与具有更多样化的I类基因型的人相比，导致整体免疫反应较弱。为了更彻底地研究HLA I类变异对免疫治疗的影响，我们使用了先前一项研究的公开数据，该研究包括1535名晚期癌症患者，他们接受了靶向CTLA4和/或PD1、PDL1的药物治疗。我们观察到HLA A03与联合癌细胞类型对检查点阻断免疫治疗的不良反应之间存在关联，并且HLA A0301纯合性比任何其他HLA a等位基因的纯合性具有更强的影响。如果排除黑色素瘤和非小细胞肺癌患者，效果更为明显，这表明HLA效应可能在一定程度上具有癌症类型特异性。我们将尝试在一个独立的队列中验证这些发现，并确定哪些癌症导致了这种效果。我们打算更严格地继续进行这一研究，以帮助预测哪些患者或多或少可能对检查点阻断免疫疗法有反应。我们已经开始与美国国立卫生研究院临床中心的临床医生合作，获得他们ICI治疗试验的材料，以便我们能够更详细地研究这些效果。我们将获得NCI试验的DNA以及匹配的临床和遗传数据，这些数据在公共数据库中是不可用的。hiv - 1可以通过病毒蛋白Vpu下调感染细胞上的HLA - C，这种下调的幅度在原发hiv - 1变体之间差异很大。选择压力导致病毒在某些个体中下调HLA - C，但在其他个体中保留表面HLA - C的原因尚不清楚。为了更好地理解靶向HLA - C的病毒免疫逃避，我们研究了一系列原发hiv - 1病毒对HLA - C的下调。从19个接受有效抗逆转录病毒治疗的个体中分离出128株具有复制能力的病毒，结果表明，有相当一部分个体携带强烈下调HLA C的潜伏病毒库病毒。未经治疗的感染在感染的前6个月没有显示HLA C下调的变化，但在慢性感染中可以检测到病毒准种之间的差异。从195例未接受治疗的慢性感染患者血浆中克隆的Vpu分子表明，HLA C的下调适应宿主HLA基因型。HLA - C等位基因的下调压力不同，HLA - C表达水平高的个体更倾向于病毒对HLA - C的下调。对原代和突变分子的研究发现，Vpu的跨膜区有5个残基，HLA - C的跨膜结构域有4个残基，这些残基决定了Vpu和HLA之间的相互作用。观察到的vpu介导的下调对宿主基因型的适应性表明，HLA - C等位基因介导被病毒下调破坏的CTL反应的可能性不同，并且在没有这些反应的情况下，HLA - C表达的保存更有利。发现潜伏库病毒可以下调HLA - C，可能会对某些个体的hiv治愈治疗方法产生影响。人类3号染色体上的趋化因子受体基因簇编码HIV的主要共受体CCR5。多个全基因组研究已经确定了人类免疫缺陷病毒（HIV）感染的结果与编码HIV共受体CCR5的基因及其周围的多态性之间的关联，但这些关联中最强的rs1015164AG的功能基础尚不清楚。我们发现rs1015164标志着激活转录因子1结合位点的变异，该位点控制反义长链非编码RNA (lncRNA) CCR5AS的表达。CCR5AS表达的敲低或增强导致CD4 T细胞上CCR5表达的相应变化。CCR5AS干扰RNA结合蛋白Raly与CCR5 3'非翻译区之间的相互作用，保护CCR5信使RNA免受Raly介导的降解。体外通过抑制CCR5AS降低CCR5表达可减少CCR5嗜性HIV对CD4 T细胞的感染。这些数据代表了对全基因组疾病关联的功能重要性的罕见确定，其中lncRNA的表达影响HIV感染和疾病进展。

We have begun to test for associations between HLA variation and publicly available data on responses to immune checkpoint inhibitors (ICI) across a number of cancer types. It was recently demonstrated that homozygosity at HLA class I associates with poor response to checkpoint blockade immunotherapy, which parallels our earlier findings on a deleterious effect of homozygosity on HIV disease progression. Homozygosity theoretically limits the peptide repertoire presented to CTL, resulting in overall weaker immune responses compared to that in people with more diverse class I genotypes. We have used publicly available data from a previous study, which includes 1535 advanced cancer patients treated with drugs targeting CTLA4 and or PD1, PDL1, in order to investigate more thoroughly the influence of HLA class I variation on immunotherapy. We observed an association between HLA A03 and poor response to checkpoint blockade immunotherapy among combined cancer cell types, and HLA A0301 homozygosity has a stronger effect than homozygosity for any other HLA A allele. The effect was more pronounced if patients with melanoma and non-small cell lung cancer were excluded, suggesting that HLA effects are likely to be cancer type specific to some extent. We will attempt to validate these findings in an independent cohort and determine which cancers are driving the effect. This line of research, which we intend to continue more rigorously, could help predict which patients are more or less likely to respond to checkpoint blockade immunotherapy. We have begun to work with clinicians in the NIH Clinical Center to gain access to materials in their trials of ICI therapy so that we can study these effects in much greater detail. We will have access to DNA from the NCI trials along with matched clinical and genetic data, the likes of which are not available in public databases. HIV1 can downregulate HLA C on infected cells, using the viral protein Vpu, and the magnitude of this downregulation varies widely between primary HIV1 variants. The selection pressures that result in viral downregulation of HLA C in some individuals, but preservation of surface HLA C in others are not clear. To better understand viral immune evasion targeting HLA C, we have characterized HLA C downregulation by a range of primary HIV1 viruses. 128 replication competent viral isolates from 19 individuals with effective anti-retroviral therapy, show that a substantial minority of individuals harbor latent reservoir virus which strongly downregulates HLA C. Untreated infections display no change in HLA C downregulation during the first 6 months of infection, but variation between viral quasispecies can be detected in chronic infection. Vpu molecules cloned from plasma of 195 treatment naive individuals in chronic infection demonstrate that downregulation of HLA C adapts to host HLA genotype. HLA C alleles differ in the pressure they exert for downregulation, and individuals with higher levels of HLA C expression favor greater viral downregulation of HLA C. Studies of primary and mutant molecules identify 5 residues in the transmembrane region of Vpu, and 4 residues in the transmembrane domain of HLA C, which determine interactions between Vpu and HLA. The observed adaptation of Vpu-mediated downregulation to host genotype indicates that HLA C alleles differ in likelihood of mediating a CTL response that is subverted by viral downregulation, and that preservation of HLA C expression is favored in the absence of these responses. Finding that latent reservoir viruses can downregulate HLA C could have implications for HIV1 cure therapy approaches in some individuals. The chemokine receptor gene cluster on human chromosome 3 encodes the primary co-receptor for HIV, CCR5. Multiple genomewide studies have identified associations between outcome of human immunodeficiency virus (HIV) infection and polymorphisms in and around the gene encoding the HIV coreceptor CCR5, but the functional basis for the strongest of these associations, rs1015164AG, is unknown. We found that rs1015164 marks variation in an activating transcription factor 1 binding site that controls expression of the antisense long noncoding RNA (lncRNA) CCR5AS. Knockdown or enhancement of CCR5AS expression resulted in a corresponding change in CCR5 expression on CD4 T cells. CCR5AS interfered with interactions between the RNA-binding protein Raly and the CCR5 3'untranslated region, protecting CCR5 messenger RNA from Raly mediated degradation. Reduction in CCR5 expression through inhibition of CCR5AS diminished infection of CD4 T cells with CCR5 tropic HIV in vitro. These data represent a rare determination of the functional importance of a genomewide disease association where expression of a lncRNA affects HIV infection and disease progression.