Genome-wide sieve analysis and immunological validation to identify targets of protective efficacy in field trials of a whole-organism malaria vaccine

摘要 PfSPZ疫苗是一种针对恶性疟的辐射减毒全生物疫苗，其基础是 PF NF54菌株一直显示出持久的、高(85%)的保护效力，对同源 控制人类疟疾感染(CHMI)后的寄生虫株。这一结果代表着 与每年夺去40万人生命的疾病作斗争。在目前的剂量下，PfSPZ疫苗已经 被证明对自然获得的疟疾感染具有显著但仍不完全的保护效果，如 以及对异源菌株CHMI的抑制作用。最快速、最了解情况的途径来扩大 这种疫苗依赖于对寄生虫蛋白的了解，免疫系统可以针对这些寄生虫蛋白 PfSPZ疫苗免疫后的保护性反应。在这里，我们建议使用寄生虫， PfSPZ疫苗三个最大效力现场试验的样本和临床结果， 鉴定和验证疫苗诱导保护性免疫反应的寄生虫蛋白靶标。 我们将从来自对照和接种者的约400例PF感染中生成全基因组序列(WGS)数据 在单独供资的情况下，在肯尼亚、东非和中非的加蓬进行了三次实地药效试验 非洲。在目标1中，我们将从最近收集的EAST菌株中开发新的PF基因组参考组件 和西非，以提高在这些基因中发现的序列变体(SNPs和Indels)的质量和数量 临床样本。在AIM 2中，我们将使用这400个样本中的全基因组基因型呼叫进行比较 为了识别PfSPZ疫苗诱导的寄生虫抗原，接种者与对照组的感染情况 保护性免疫(“靶基因座”)，假设在这些靶基因座中，等位基因频率分布 在现场药效试验中，疫苗与对照药物在疟疾感染方面会有所不同，包括频率较低 NF54-样等位基因在接种者中的分布高于对照组。我们将使用来自控制和疫苗部门的类似样本 一项新的PfSPZ疫苗现场试验将于2018年在赤道几内亚开始，以验证这些结果。最后，在AIM中 3、我们将对PfSPZ疫苗诱导保护的PF靶标进行高通量免疫学验证 这将决定等位基因特异性效应是否真的是一种影响整体 基于生物体的疫苗。这些结果将被用来为选择更多的恶性疟原虫菌株提供依据。 用它来设计具有更广泛效力的多价疫苗，并有望减少疾病 增加负担，改善根除疟疾的前景。通过定义免疫反应的靶点 疟疾寄生虫，这项研究也可能扩大我们对宿主免疫反应的理解。 针对寄生虫病的生物疫苗，并加快这一领域的未来发展。

Abstract PfSPZ Vaccine, a radiation-attenuated, whole-organism vaccine against P. falciparum (Pf) malaria, based on the Pf NF54 strain, has consistently shown durable, high (>85%) protective efficacy against a homologous parasite strain after controlled human malaria infection (CHMI). This result represents a major milestone in the fight against a disease that kills >400,000 people annually. At current dosages, PfSPZ Vaccine has been shown to have significant but still incomplete protective efficacy against naturally acquired malaria infection, as well as against CHMI with a heterologous strain. The most expedited, informed path to broaden the efficacy of this vaccine relies on the knowledge of the parasite proteins against which the immune system mounts a protective response following immunization with PfSPZ Vaccine. Here, we propose to use parasites, specimen samples and clinical outcomes from the three largest efficacy field trials of PfSPZ Vaccine, to identify and validate parasite protein targets of the vaccine-induced protective immune response. We will generate whole genome sequence (WGS) data from ~400 Pf infections from controls and vaccinees in three field efficacy trials conducted, under separate funding, in Kenya, East Africa, and in Gabon, Central Africa. In AIM 1 we will develop new Pf genome reference assemblies from recently collected strains for East and West Africa, to increase the quality and quantity of sequence variants (SNPs and indels) identified in these clinical samples. In AIM 2, we will use the genome-wide genotype calls in these 400 samples to compare infections in vaccinees vs. controls, in order to identify parasite antigens targeted by PfSPZ Vaccine-induced protective immunity (“target loci”), under the assumption that, in these target loci, allele frequency distributions will differ in malaria infections in the vaccine vs. control arms of field efficacy trials, including a lower frequency of NF54-like alleles in vaccinees than in controls. We will use similar samples from control and vaccine arms of a new PfSPZ Vaccine field trial, to start in Equatorial Guinea in 2018, to validate these results. Finally, in AIM 3, we will conduct a high-throughput immunologic validation of Pf targets of PfSPZ Vaccine-induced protection that will determine whether or not allele-specific efficacy is indeed a phenomenon that impacts whole organism-based vaccines. These results will be used to inform the choice of additional P. falciparum strains with which to design multivalent vaccines with broader efficacy, and hopefully lead to a decrease in disease burden and improve the prospects of malaria eradication. By defining the targets of the immune response to a malaria parasite, this research may also expand our understanding of host immune responses to whole- organism vaccines against parasitic diseases, and accelerate future developments in this field.