Malaria parasite and vector genomics: transmission, pathology, and therapeutics

在真核寄生虫引起的任何疾病中，疟疾对全球健康造成的负担最大， 每年造成约60万人死亡最近在控制疟疾方面取得了进展， 但是疟疾寄生虫和按蚊的媒介倾向于进化出抗药性 杀虫剂意味着需要工具来保持现有治疗和控制的功效， 措施，并在基础研究投资是必要的，以保持发展管道储备， 新的候选药物、疫苗和杀虫剂。我们建议通过以下方式推进这些努力： 基因组技术的创新应用，解决疟疾传播领域的关键问题， 发病机理和治疗方法。我们的项目是专门设计来利用资源和专业知识 在基因组测序中心之外并不常见， 调查员在外地。我们将采用16S测序、全基因组鸟枪测序和GWAS， 测试蚊子先天免疫基因在塑造蚊子微生物组中发挥作用的假设 社区，已被证明影响矢量能力（目标1）。我们将尽最大努力 敏感的单细胞转录组学分析，以弥合导致P的线索中的关键知识差距。 恶性疟原虫进行性分化，这对于传播至关重要（目标2）。我们将 创造前所未有的质量从头组装，以探索迄今为止未表征的基因组 疟原虫亚端粒的“暗物质”，其中重要的抗原基因家族介导发病机制 生存和发展（目标3）。最后，我们将采用杂交选择来富集疟原虫DNA并进行测序 从泰国西北部的一个地区，一个关键的10年纵向收集的临床疟疾样本， 其中最近出现了对当前一线药物疗法（青蒿素）的耐药性（目标4）。我们 假设与抗性相关等位基因频率的变化在纵向上是可检测的， 选择屏幕。我们提出的工作不仅将把疟疾基因组学的前沿推向大胆的新领域， 这不仅是一个区域性问题，而且产生了适用于广泛疾病的经验和分析方法。

Malaria exerts the largest burden on global health of any disease caused by a eukaryotic parasite, and is responsible for approximately 600,000 deaths a year. Recent gains have been made in controlling malaria, but the proclivity for malaria parasites and their Anopheline mosquito vectors to evolve resistance to drugs and insecticides means that tools are needed to preserve the efficacy of existing therapeutics and control measures, and that investment in basic research is necessary to keep development pipelines stocked with new candidate drugs, vaccines, and insecticides. We propose to advance these efforts by coupling innovative applications of genomic technologies with key questions in the fields of malaria transmission, pathogenesis, and therapeutics. Our projects were specifically designed to leverage resources and expertise not commonly found outside of genome sequencing centers, and involve collaborations with leading investigators in the field. We will employ 16S sequencing, whole genome shotgun sequencing, and GWAS to test a hypothesis that mosquito innate immune genes play a role in shaping mosquito microbiome communities, which have been demonstrated to affect vectorial capacity (Aim 1). We will employ extremely sensitive single-cell transcriptomic profiling to bridge a key knowledge gap in the cues that cause P. falciparum parasites to commit to sexual differentiation, which is essential for transmission (Aim 2). We will create de novo assemblies of unprecedented quality to explore the heretofore uncharacterized genomic dark matter' of Plasmodium subtelomeres, where important antigenic gene families mediating pathogenesis reside and evolve (Aim 3). Finally, we will employ hybrid selection to enrich and sequence Plasmodium DNA from a critical 10 year longitudinal collection of clinical malaria samples from northwestern Thailand, a region where resistance to the current first line drug therapy (artemesinin) has recently arisen (Aim 4). We hypothesize that changes in allele frequency associated with resistance will be detectable in a longitudinal selection screen. The work we propose will not only push the frontier of malaria genomics into bold new territories, but generate empirical and analytical approaches applicable to a broad range of diseases.