Project 2 - Host-virus networks regulating flu replication and host responses ex vivo

项目2：调节流感复制和体外宿主反应的宿主-病毒网络。 苏米特·昌达，项目负责人；梅根·肖，联合调查员；伊万·马拉齐，内万·克罗根，联合调查员， 联合调查员。 在这项提议中，我们假设多条不连续的分子通路决定流感疾病。 严重性，并且这些途径引发可通过基于网络的识别的生物标记签名 系统级测量的建模。在项目2中，我们建议使用前沿的OMICS方法 确定与临床疾病结局相关的体外分子特征。说明和说明 对控制结果相关生物标志物签名的因素的表征提供了潜在的 新的抗病毒疗法的开发。在目标1中，我们将使用系统生物学的方法来阐明 与临床流感严重程度相关的网络签名。在这里，我们将分析对主机的更改 转录组、蛋白质组和代谢组，用不同致病性的病毒对感染作出反应，如 以及与临床结果相关的额外宿主扰动。相关的体外分子特征 疾病严重程度将与项目1中产生的体内和临床数据进行整合和建模。 我们建议使用遗传工具来识别与结果相关的分子签名中的关键节点 宿主反应途径和病毒复制的调节者(“驱动基因”)。目标1和目标2都将依赖于 反复实验和建模的范例，将体外特征与临床表型联系起来，以及 确定宿主蛋白和控制它们的途径。在目标3中，那些被发现调节通路的基因 与疾病结果(驱动基因)相关的特征将进一步描述。我们建议 采用基于CRISPR的转录、表观遗传、蛋白质组和代谢图谱分析，以提供 洞察这些因素在调节与疾病结果相关的反应中的作用(CRISPR-Economics)。 将进行更多的分子、细胞、生化和体内研究，以进一步确定这些 决定疾病结果的节点，作为潜在的治疗目标。

PROJECT 2: Host-virus networks regulating flu replication and host responses ex vivo. Sumit Chanda, Project Leader; Megan Shaw, Co-Investigator; Ivan Marazzi, Co-Investigator, Nevan Krogan , Co-Investigator. In this proposal, we hypothesize that multiple, discrete molecular pathways determine influenza disease severity, and that these pathways elicit biomarker signatures that can be identified through network-based modeling of system-level measurements. In Project 2, we propose to utilize leading edge OMICS approaches to identify ex vivo molecular signatures that correlate with clinical disease outcomes. The elucidation and characterization of factors that govern outcome-related biomarker signatures offer the potential for the development of novel antiviral therapies. In Aim 1, we will use a systems biology approach to elucidate network signatures associated with clinical influenza severity. Here, we will profile changes to the host transcriptome, proteome and metabolome, in response to infection using viruses of different pathogenicity, as well as additional host perturbations linked to clinical outcome. Ex vivo molecular signatures correlated with disease severity will be integrated and modeled with in vivo and clinical data generated in Project 1. In Aim 2, we propose to use genetic tools to identify nodes within outcome-related molecular signatures that are critical regulators of host response pathways and viral replication (`driver genes'). Both Aims 1 and 2 will rely on a paradigm of reiterative experimentation and modeling to link ex vivo signatures to clinical phenotypes, and identify the host proteins and pathways that govern them. In Aim 3, those genes found to regulate pathways and signatures associated with disease outcome (driver genes) will be further characterized. We propose to employ CRISPR-based analysis of transcriptional, epigenetic, proteomic, and metabolic profiles to provide insight into the role of these factors in regulating responses linked to disease outcomes (CRISPR-OMICs). Additional molecular, cellular, biochemical and in vivo studies will be conducted to further characterize those nodes that determine disease outcomes as potential therapeutic targets.