Genomic Determinants of Intrinsic Antiviral Host Defenses

描述（由申请人提供）：个体对HIV-1感染的易感性差异很大，疾病进展率不仅取决于病毒特性，还取决于宿主因素。该建议的中心假设是APOBEC3 （A3）限制因子家族的广泛多样化有助于HIV-1在体内复制的高度变异性。越来越多的证据表明，基因组变异——从单核苷酸多态性（snp）到大的结构变异——会影响宿主抗病毒防御的效力。事实上，我们有证据表明，自然发生的snp调节A3F和A3H的抗病毒活性。此外，我们已经确定了A3位点附近和内部的三个区域，这些区域显示了在HapMap人群中拷贝数的变化（基于450个西非、亚洲和欧洲血统个体的数据）。这些拷贝数变异（CNV）与A3B、A3E和A3F外显子重叠，并可能与APOBEC基因座的上游调控序列重叠。初步数据表明，来自HIV-1感染的长期非进展者（LTNP）的APOBEC位点在A3拷贝数变异中富集，表明A3拷贝数变异具有保护作用。相反，我们已经证明，A3-CNV2拷贝丢失（A3B基因完全缺失）的纯合子细胞在体外更容易感染HIV-1。总的来说，我们的初步数据有力地支持A3区域具有结构多态性的观点，并且由此产生的A3变异对HIV-1复制具有关键影响。在具体目标1 （CNV发现和定位）中，我们将使用尖端技术以非常高的分辨率询问A3基因家族集群，以捕获嵌入该位点的广泛CNV。为此，我们将使用来自不同种族（18个不同群体）或表型选择（LTNP）群体的样本。在特定目标2（基因表达）中，我们将确定A3- cnv基因型特有的mRNA表达模式，并鉴定与重排A3位点相关的蛋白质变异。我们还将比较ltnp和治疗进展者淋巴细胞和树突状细胞中A3基因组变异的转录调控。在特定目标3（基因功能）中，将使用来自已知A3基因型个体的淋巴细胞以及表达代表自然循环A3基因组变体的基因产物的模型细胞系，测试A3- cnvs和snp对病毒限制的影响。这些实验将整合A3区域的基因组变异数据，了解A3脱氨酶的调控和抗病毒功能。这项对A3基因组结构高变异性的功能后果的全面调查将有助于确定新的生物标志物，以便在未来逆转录病毒感染的流行病学研究中进行检测。此外，了解内在防御因子的功能多样性有可能创造新的治疗策略，旨在长期抑制艾滋病毒/艾滋病疾病。

DESCRIPTION (provided by applicant): Susceptibility to HIV-1 infection varies greatly between individuals, with disease progression rates determined not only by viral properties but also host factors. The central hypothesis of this proposal is that the extensive diversification of the APOBEC3 (A3) family of restriction factors contributes to the high degree of variability in HIV-1 replication in vivo. There is growing evidence that genomic variation - ranging from single nucleotide polymorphisms (SNPs) to large structural variants - influences the efficacy of host antiviral defenses. Indeed, we have evidence that naturally occurring SNPs modulate the antiviral activity of A3F and A3H. Moreover, we have identified three regions near and within the A3 locus itself that show copy number variations among HapMap populations (based on data from 450 individuals of West-African, Asian and European ancestry). These copy number variants (CNV) overlap with A3B, A3E and A3F exons and possibly upstream regulatory sequences of the APOBEC locus. Preliminary data indicate that the APOBEC loci from HIV-1 infected long-term non-progressors (LTNP) are enriched for A3 copy number variants, suggesting a protective role of A3 copy number variation. Conversely, we have shown that cells homozygous for A3-CNV2 copy loss (complete deletion of the A3B gene) are more susceptible to HIV-1 infection in vitro. Collectively, our preliminary data strongly support the notion that A3 regions are structurally polymorphic and that the resulting A3 variants exert a key impact on HIV-1 replication. In specific aim 1 (CNV discovery and mapping), we will interrogate the A3 gene family cluster at very high resolution using cutting edge technologies to capture the wide range of CNVs embedded in this locus. For this purpose, we will use samples from ethnically diverse (18 different groups) or phenotypically selected (LTNP) populations. In specific aim 2 (gene expression), we will determine the mRNA expression pattern specific for A3-CNV genotypes and identify protein variants associated with the panel of rearranged A3 loci. We will also compare the transcriptional regulation of A3 genomic variants in lymphocytes and dendritic cells of LTNPs and treated progressors. In specific aim 3 (gene function), the impact of A3-CNVs and SNPs on viral restriction will be tested, using lymphocytes from individuals with known A3 genotypes, as well as model cell-lines expressing gene products representing naturally circulating A3 genomic variants. These experiments will integrate genomic variation data of the A3 region with an understanding of the regulation and antiviral functions of A3 deaminases. This comprehensive investigation into the functional consequences of the high variability in A3 genomic architecture should help identify new biomarkers to be tested in future epidemiological studies of retroviral infections. In addition, understanding the functional diversity of intrinsic defense factors has the potential to create novel treatment strategies aimed at a long- lasting suppression of HIV/AIDS disease. PUBLIC HEALTH RELEVANCE: Susceptibility to HIV-1 infection and AIDS disease progression varies greatly among individuals. The goal of this proposal is to determine the degree of structural genomic variation within the APOBEC 3 locus, and to assess how variability of these intrinsic resistance genes impacts on HIV-1 replication.