Determination of the Interactome between Haemophilus ducreyi and the Human Host.

在我们对传染病的理解中，一个主要的空白是缺乏分子间相互作用的信息 感染病原体和人类宿主之间的网络，这对于细菌来说还没有完成。 人类感染。本申请的目的是在转录水平上定义相互作用基因组， 使用RNA在实验感染的人类志愿者中的主要皮肤病原体杜克雷嗜血杆菌（HD） 测序（RNA-seq）和代谢组学。HD导致软下疳，这是一种生殖器溃疡（GU）疾病， 艾滋病毒的传播，是一个主要的原因皮肤溃疡（CU）的儿童在雅司病流行的国家。 用抗生素根除HD相关CU的努力由于环境水库而失败。研究 HD生物学，我们开发了一个模型，其中HD GU菌株35000 HP及其衍生物接种 植入成年志愿者上臂的皮肤中。全基因组测序显示，大多数CU菌株是 与35000 HP几乎相同，表明我们的模型与GU和CU高度相关。在模型中， 天然软下疳，HD存在于脓肿中，周围被多形核白细胞包围， 通过逃避吞噬作用而保持在细胞外。在我们新的初步数据中，我们显示 HD和宿主之间存在相互作用网络，宿主和细菌的差异转录物 表达与感染部位相对于受伤部位的代谢组学变化相关。HD主要上调 参与适应厌氧生活和吸收利用金属离子的基因的表达， 替代碳源，如抗坏血酸，符合“营养毒性”的想法。我们的新 代谢组学数据显示抗坏血酸途径在损伤中上调。因此，我们假设， 宿主调节其基因转录以吞噬和限制营养物到HD，HD调节其 基因转录来抵消这些宿主防御，宿主基因表达与 在感染部位的代谢谱，以及细菌基因参与适应 由宿主反应产生的代谢生态位将是毒力所必需的。我们的具体目标是：（1） 定义代谢组和感染组织中HD与人类宿主之间的相互作用组， 将宿主转录反应与病变中的代谢变化相关联; 2）鉴定负责的细胞 使用单细胞RNA-seq进行宿主转录反应; 3）确定HD基因是否 参与利用宿主生态位的基因是人类毒力所必需的， 这些基因有助于毒性。这项研究的重要性在于，我们将首先确定一个 在细菌人类感染位点的相互作用体，定义了负责转录的宿主细胞。 反应，将宿主反应与病变中的代谢组学变化相关联，并研究HD如何利用这些变化。 代谢物。我们将提供新的见解之间的相互作用模型细胞外细菌和 揭示了控制HD相关CU新策略。

A major gap in our understanding of infectious diseases is the lack of information about molecular interaction networks between an infecting pathogen and the human host, which has yet to be accomplished for a bacterial infection in humans. The purpose of this application is to define an interactome on a transcript level for the primary skin pathogen, Haemophilus ducreyi (HD), in experimentally infected human volunteers using RNA sequencing (RNA-seq) and metabolomics. HD causes chancroid, a genital ulcer (GU) disease that facilitates HIV transmission and is as a major cause of cutaneous ulcers (CU) in children in yaws-endemic countries. Efforts to eradicate HD-associated CU with antibiotics failed due to environmental reservoirs. To study the biology of HD, we developed a model in which the HD GU strain 35000HP and its derivatives are inoculated into the skin of the upper arm of adult volunteers. Whole genome sequencing shows that most CU strains are nearly identical to 35000HP, indicating that our model is highly relevant to GU and CU. In the model and in natural chancroid, HD resides in an abscess where it is surrounded by polymorphonuclear leukocytes and macrophages and remains extracellular by evading phagocytosis. In our new preliminary data, we show that an interaction network exists between HD and the host and that differential host and bacterial transcript expression correlates with metabolomic changes at infected vs. wounded sites. HD primarily upregulates the expression of genes involved in adapting to anaerobiosis and uptake and utilization of metal ions and alternative carbon sources, such as ascorbic acid, consistent with the idea of “nutritional virulence.” Our new metabolomics data show that ascorbic acid pathways are upregulated in lesions. Thus, we hypothesize that the host regulates its gene transcription to phagocytize and limit nutrients to HD, that HD regulates its gene transcription to counteract these host defenses, that host gene expression correlates with metabolomic profiles at infected sites, and that bacterial genes that are involved in adaptation to the metabolic niche created by the host response will be required for virulence. Our specific aims are 1) to define the metabolome and the interactome between HD and the human host in infected tissue and to correlate the host transcriptional response to metabolic changes in lesions; 2) to identify the cells responsible for the host transcriptional response using single cell RNA-seq; 3) to determine whether the HD genes involved in exploitation of the host niche are required for virulence in humans and the mechanism(s) by which these genes contribute to virulence. The importance of this study is that we will be the first to determine an interactome at a site of a bacterial human infection, define the host cells responsible for the transcriptional response, correlate the host response to metabolomic changes in lesions, and study how HD exploits these metabolites. We will provide new insights into the interaction between a model extracellular bacterium and the human host and unmask novel strategies to control HD-associated CU.