Analysis of novel in vivo derived Plasmodium falciparum transcriptional profiles

描述（由申请人提供）：感染疟疾寄生虫恶性疟原虫会导致儿童出现各种不同的临床症状，从轻微的流感样症状到昏迷和死亡。尽管具有巨大的医学意义，但这种多样性的遗传和分子基础在很大程度上仍然未知。我们推测，寄生在人类宿主体内的寄生虫需要适应这种特殊的环境，这种环境在温度、底物和免疫反应方面都有变化。为了描述寄生虫的生物学特征，我们对感染患者新鲜血液样本中的寄生虫进行了全基因组分析。通过这种方法，我们已经确定了寄生虫在人类宿主体内的三种生物状态。其中一种体内状态与实验室生长的转录谱高度相关，现在我们已经确定了两种新的状态。这些状态的生物学基础可以通过与酵母（Saccharomyces cerevisiae）中大量表达数据的比较来解释。这三种状态在体内非常相似：(1)基于糖酵解代谢的主动生长“体外样状态”；（ii）伴有氧化磷酸化的饥饿反应；（三）环境应激反应。这些结果揭示了疟疾寄生虫体内生物学中以前未知的生理多样性，特别是无性期寄生虫中功能性线粒体的证据，并指出了体内和体外研究，以确定这种变异如何影响疾病表现和治疗。这项工作强调了与人类样本一起工作以探索临床相关寄生虫生物学的重要性。通过进一步的临床研究，我们建议：1)确定与这些新的生物状态相关的宿主因子；2)确定在严重疾病中特异性发现的寄生虫生物学；3)使用体外模型在受控条件下测试寄生虫的环境反应。我们正在开发一种全新的模型来研究这种寄生虫中宿主与病原体的相互作用。临床研究为体外模型提供信息，反过来，该模型的结果可以在临床研究中进行前瞻性测试。此外，我们还培养了临床疟疾、计算生物学和分子生物学领域的领导团队，将他们的技能结合起来，进一步加深我们对疾病的理解。长期目标是确定可以靶向的寄生虫生物学，以减少恶性疟原虫的个人和全球健康负担。公共卫生相关性：恶性疟原虫在人类中引起感染，从无症状到高度严重的疾病，往往导致死亡。为什么有些病人有严重的疾病，而另一些病人则完全健康，这仍然知之甚少，这可能与人类体内寄生虫的特殊生物学有关。通过使用基因组学，我们已经确定了寄生在人类体内的全新寄生虫生物学，这个项目将确定这种新的生物学是否与疾病结果的差异有关。这项研究汇集了计算生物学和疟疾流行病学方面的专家，以开发寄生虫生物学的临床相关模型，为疾病干预提供信息，以减少疟疾感染对个人和全球健康的影响。

DESCRIPTION (provided by applicant): Infection with the malaria parasite Plasmodium falciparum leads to widely different clinical conditions in children - ranging from mild flu-like symptoms to coma and death. Despite the immense medical implications, the genetic and molecular basis of this diversity remains largely unknown. We hypothesize that parasites residing in the human host have needed to adapt to this specialized environment that varies in temperature, substrate and immune response. To characterize parasite biology we have utilized whole genome analysis of the parasite from fresh blood samples of infected patients. With this approach we have identified three biologic states of the parasite when it resides in the human host. One of these in vivo states correlates highly to the laboratory grown transcriptional profile, and now we have identified two novel states. The biological basis of these states can be interpreted by comparison with an extensive compendium of expression data in the yeast, Saccharomyces cerevisiae. The three states in vivo closely resemble (i) active growth based on glycolytic metabolism "the in vitro like state"; (ii) a starvation response accompanied by oxidative phosphorylation; and (iii) an environmental stress response. The results reveal a previously unknown physiological diversity in the in vivo biology of the malaria parasite, in particular, evidence for functional mitochondria in the asexual stage parasite, and point to in vivo and in vitro studies to determine how this variation may impact disease manifestations and treatment. This work highlights the importance of working with human samples to explore clinically relevant parasite biology. Through further clinical studies we propose to 1) identify the host factors that are associated with these novel biologic states 2) identify parasite biology that is specifically found in severe disease 3) test environmental responses of the parasite under controlled conditions using the in vitro model. We are developing a completely novel model for the host pathogen interaction in this parasite. The clinical studies inform the in vitro model and conversely, results of this model can then be tested prospectively in the clinical studies. Furthermore we have developed team of leaders in clinical malaria, computational biology and molecular biology to combine their skills to further our understanding of disease. The long term goal is to identify parasite biology that can be targeted to reduce individual and global health burden of Plasmodium falciparum. PUBLIC HEALTH RELEVANCE: Plasmodium falciparum causes infections in humans which range from asymptomatic to highly severe illness often leading to death. Why some patients have severe disease and others are completely well remains poorly understood, and this may be related to specialized parasite biology that occurs in humans. Through the use of genomics, we have identified completely new parasite biology when it resides in humans and this project will determine if this novel biology is related to differences in disease outcomes. This study brings together experts in computational biology and malaria epidemiology to develop clinically relevant models of parasite biology to inform disease interventions to reduce the impact of malaria infection on individual and global health.