A network-based method for predicting gene interactions in artemisinin resistance

 描述（由申请人提供）：疟疾寄生虫，恶性疟原虫，继续以惊人的速度杀死人们。要解决对青蒿素（ART）联合疗法新出现的耐药性这一艰巨挑战，将需要全套传统和创新的新工具。最近一项令人兴奋的发现指出了13号染色体基因中的突变，该基因编码kelch螺旋桨结构域作为新出现的ART耐药（ART-R）的标记，但对其功能或相互作用的伴侣一无所知。将基因组规模信息的基本知识转化为理解ART-R机制的重要一步是阐明生物系统组成部分之间的相互作用。了解这些成分可以指导适当的干预措施，以延长这种关键药物的使用。我们概述了一种新的方法，该方法对全基因组数据的两个主要限制是鲁棒的：假阳性和不完整的信息。我们验证了我们的方法与黄金标准的知识，pfcrt是氯喹（CQ）耐药的主要决定因素，并证明其实用性解剖ART-R。在构建了全面的参考转录网络之后，我们生成了2个新的和独立的查询列表：i）在CQR和CQS寄生虫之间“重新连接”的基因，即在它们的共表达关系中显著分歧的基因，和ii）被piggyBac（pB）插入中断的表现出改变的药物敏感性的基因。对于这些信息丰富的输入基因集合中的每一个，我们使用参考网络来找到在这些基因中的许多基因之间完成短路径连接的节点。本申请的直接目标是将这种方法应用于紧急和棘手的新兴ART-R问题，通过扩展参考网络并使用来自泰国-缅甸边境的一组特殊临床分离株确定顶部重新连接基因（Aim 1），并通过筛选128个pB突变体和转染系的ART易感性和转录应答谱的变化（Aim 2）。这些信息将用于独立验证候选基因和预测功能相互作用（目标3）。

 DESCRIPTION (provided by applicant): The malaria parasite, Plasmodium falciparum, continues to kill people at an alarming rate. Solving the difficult challenge of emerging resistance to artemisinin (ART)-based combination therapies will take the full set of traditional and innovative new tools. An exciting recent discovery pinpointed mutations in a chromosome 13 gene that encodes a kelch propeller domain as a marker for emerging ART-resistance (ART-R), however nothing is known about its function or its interacting partners. An important step in converting primary knowledge of genome-scale information to understanding the mechanisms of ART-R is the elucidation of the interactions among the component parts of the biological system. Knowledge of these components can guide appropriate interventions to prolong this crucial drug. We outline a novel approach that is robust to 2 main limitations of genome-wide data: false positives and incomplete information. We validate our approach with the gold standard knowledge that pfcrt is the primary determinant of chloroquine (CQ) resistance and demonstrate its utility for dissecting ART-R. After constructing a comprehensive reference transcriptional network, we generated 2 novel and independent query lists: i) genes that are 'rewired', i.e. diverge dramatically in their co- expression relationships, between CQR and CQS parasites and ii) genes interrupted by piggyBac (pB) insertions that exhibit altered drug susceptibility. For each of these richly informative input gene sets, we used the reference network to find nodes that complete a short path connection among many of these genes. The immediate goal of this application is to apply this approach to the urgent and vexing problem of emerging ART- R, by expanding the reference network and determining the top rewired genes using an extraordinary panel of clinical isolates from the Thailand-Myanmar border (Aim 1) and by screening 128 pB mutants and transfected lines for shifts in ART susceptibility and transcriptional response profiles (Aim 2). This information will be used to independently validate candidate genes and predict functional interactions (Aim 3).