Consequences of immune escape on viral fitness

免疫逃逸对病毒适应性的影响

• 批准号: 7854611
• 负责人: ERIC J ARTS
• 金额: $ 38.78万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-15 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7854611
• 关键词: Acute; Affect; Alleles; Appearance; Autologous; Capsid; Cells; Cloning; Code; Cytotoxic T-Lymphocytes; Data; Disease Progression; Drug resistance; Employee Strikes; Epitopes; Financial compensation; Gagging; Gene Targeting; Genes; Genome; Grant; HIV-1; HIV-1 drug resistance; Human; Immune; Individual; Infection; Laboratories; Lymphocyte antigen; Membrane Proteins; Methods; Mutation; Pathway interactions; Peptide Hydrolases; Pilot Projects; Plastics; Population; Proteins; RNA-Directed DNA Polymerase; Recruitment Activity; Structure; Variant; Vertebral column; Viral; Virus; Yeasts; base; cost; env Genes; fitness; in vivo; interest; novel; pressure; protective effect; response

Background/Rationale: Human lymphocyte antigen (HLA)-restricted cytotoxic T lymphocytes (CTL) target HIVinfected cells expressing cognate HlV-1 epitopes. Numerous studies have examined the dynamics of CTL response and escape mutations following acute infection and disease progression. CTL escape mutations are typically associated with a fitness "cost", inferred by the reversion of these mutations in absence of CTL selection pressure. It is important to note that multiple factors may contribute to in vivo fitness but fitness "cost" is typically defined as a decrease in replicative capacity within target cells. Thus, this "cost" is often ascribed to (DTL escape mutafions due to their absence in the CTL-suscepfible or "wild type" sequence but few studies have actually empirically examined replicative fitness of HIV-1 escape variants. During the current grant period we accessed the costs of CTL escape mutations on replicative fitness of the infecting HIV-1 isolate. In general, we observed that in a subject's HIV-1 population, CTL escape mutations impart different fitness costs. CTL escape mutations in Gag emerged later in infection and were associated with higher fitness costs than the CTL escape mutations selected in Env (go to article)^. These pilot studies involved HlV-1 sequence and IFN-y ELISpot analyses to first identify 19 escape and compensatory mutafions that emerged in two epitopes encoded by gag and five in env during infection of SEAPIP subject 1362 (PIC1362)^¿. Each of the 19 mutafions was then individually introduced into the autologous HlV-1 gag and env genes from the founder virus. Fitness analyses were performed using direct competitions between the chimeric viruses, which harbored the subject gag or env genes with or without the CTL escape mutafions. This is the most comprehensive analysis to date that examined the interplay between CTL response, selection of escape variants, and the associated fitness costs. The findings were quite striking in that 8/9 CTL escape mutations in env were either neutral or resulted in a fitness increase, rather than any loss in replicative capacity^. Based on our inifial findings, we have structured this renewal proposal to first compare the cost of CTL escape mutafions in more conserved versus more heterogeneous HIV-1 coding regions throughout the genome (AIM 1). We propose that low genefic diversity and limited functional plasficity within HlV-1 coding regions will slow the appearance of CTL escape mutafions due to higher fitness costs. Even in the same epitope under the same HLA-restriction, divergent HIV-1 isolates often take distinct evolutionary pathways towards different CTL escape mutations. Thus, In AIM 2, we will explore how specific CTL escape mutations in an HLA A3, A25, B27, and B57-restricted p24 epitopes affect replicative fitness of a virus derived from the autologous capsid (CA) p24 sequence, heterologous p24 sequence (but from a subject sharing the same restricfing HLA allele), and of a laboratory strain. Again, preliminary data would suggest a minimal fitness impact in the autologous versus heterologous background and emphasize the need to study these CTL escape mutations in the native context. Given the protective effects of B57 and B27 HLA alleles, we will also assessed whether CTL escape mutations confer higher fitness costs in unique B57- or B27-specific epitopes. Our preliminary studies on drug resistant and CTL escape mutafions suggest that the enfire HIV-1 genome evolves to compensate for any fitness loss. For this reason, fitness costs are often over-emphasized when analyzed in a heterologous HIV-1 background. In AIM 3, we examine how a loss in replicative fitness conferred by CTL escape mutations will be compensated by mutations within the targeted gene and throughout the genome. Specifically, we have found that the HIV-1 env gene and the efficiency of host cell entry is dominant over all other HIV-1 genes and replicafion steps in determining fitness^. In fact, we found that many drug resistant HIV-1 isolates maintain high replicative fitness by increasing the efficiency of host cell entry to compensate for a loss in protease (PR) or reverse transcriptase (RT) activity. The same scenario may exist with CTL escape mutafions.

背景/原理：人类淋巴细胞抗原(HLA)限制性细胞毒性T淋巴细胞(CTL)靶向HIV感染 表达HLV-1同源表位的细胞。许多研究已经检验了CTL反应的动力学 以及急性感染和疾病进展后的逃逸突变。CTL逃逸突变是 通常与适合度“成本”相关，在没有CTL选择的情况下，通过这些突变的逆转来推断 压力。重要的是要注意到，多种因素可能有助于体内健康，但健身“成本”是 通常被定义为目标细胞内复制能力的下降。因此，这种“成本”常常被归因于 (DTL逃逸突变是因为它们不存在于CTL敏感或“野生型”序列中，但很少有研究 实际上对HIV-1逃逸变种的复制适合性进行了经验检验。 在当前的授权期内，我们获得了CTL逃逸突变的成本对 感染HIV-1分离株。总的来说，我们观察到在受试者的HIV-1群体中，CTL逃逸突变 提供不同的健身费用。GAG中的CTL逃逸突变在感染后出现，并 与Env中选择的CTL逃逸突变相比，适应成本更高(转至文章)^。这些 初步研究包括HLV-1序列和干扰素-γELISpot分析，以首次确定19个逃逸和代偿 SEAPIP感染过程中GAG编码的两个表位和环境中的五个表位出现的突变 1362(PIC1362)^。然后将19个突变片段分别引入到自体HLV-1 Gag中 以及方正病毒的env基因。健康分析是使用直接竞争的方式进行的 带有或不带有CTL基因的嵌合病毒能够逃脱突变。这 是迄今为止最全面的分析，考察了CTL反应、选择 逃逸变种，以及相关的健身成本。这些发现是相当惊人的，因为8/9的CTL逃逸突变 在环境中要么是中性的，要么是导致适合度增加，而不是复制能力的任何损失。 根据我们的初步发现，我们构建了这份更新建议，以首先比较CTL逃脱的成本 基因组中更保守的HIV-1编码区与更多异质性的编码区的突变(AIM 1)。我们认为HLV-1编码区的低基因多样性和有限的功能可塑性将放缓 CTL逃逸突变的出现是由于较高的健身成本。即使在相同的抗原表位下，不同的HIV-1分离株通常也会对不同的CTL逃逸突变采取不同的进化途径。因此，在AIM 2中，我们将探索HLAA3、A25、B27和B57限制性p24表位中特定的CTL逃逸突变如何影响源自自体衣壳(CA)p24序列、异源p24序列(但来自具有相同限制性等位基因的受试者)的病毒和实验室毒株的复制适合性。同样，初步数据将表明，在自体和异源背景下，适合性影响最小，并强调在自然背景下研究这些CTL逃逸突变的必要性。考虑到B57和B27等位基因的保护作用，我们还将评估CTL逃逸突变是否会在独特的B57或B27特异性表位上带来更高的适合度成本。 我们对耐药突变和CTL逃逸突变的初步研究表明，Enfire HIV-1基因组的进化是为了弥补任何适应性损失。出于这个原因，当在异源HIV-1背景下进行分析时，健康成本往往被过分强调。在AIM 3中，我们研究了CTL逃逸突变导致的复制适合性损失如何被靶基因内和整个基因组中的突变所补偿。 具体地说，我们发现HIV-1的env基因和宿主细胞的进入效率是占主导地位的 比所有其他HIV-1基因和复制步骤更能确定健康状况。事实上，我们发现许多耐药的HIV-1分离株通过提高宿主细胞进入的效率来补偿蛋白酶(PR)或逆转录酶(RT)活性的丧失，从而保持高复制适合性。CTL逃逸突变也可能存在同样的情况。