Pharmaco Response Signatures and Disease Mechanism

描述（由申请人提供）：HMS LINCS中心的总体目标是在单细胞和细胞群体水平上描述细胞对摄动原反应的基本原理，并通过基于网络的浏览、查询和编程接口使反应数据常规可用。这将涉及开发和测试新的测量方法、计算算法和不同人类细胞类型暴露于单独和组合扰动的响应特征。我们将强调系统收集目前在现有公共数据库中无法获得的数据，包括活细胞和固定细胞成像，信号蛋白的生化数据和多因子药物反应表型。关注各种转化细胞和原代细胞，包括来自健康和患病供体的细胞，以及临床级小分子（激酶抑制剂和表观基因组药物）将增加我们工作的转化影响。拟议的LINCS中心代表了在LINCS试点阶段U54授予下运行约3.5年的项目的延续。我们将扩大本中心的范围和复杂性，投入大量精力来(i)提高数据分析和可视化的质量，特别是关于摄动原多药的复杂性；（ii）使用已被证明可以产生可靠和信息丰富的数据的方法加速摄动原反应特征的释放，特别强调原代和非转化细胞；（iii）开发和应用新的测量方法。特别是用于分析细胞群的质谱法和用于分析单个细胞的活细胞成像。这项工作将涉及九个相互补充但又相互独立的目标。在数据生成中，Aim 1将在单细胞水平上对摄动原反应进行系统分析。目标2将使用一套互补成像、质谱和基于脑珠的检测方法收集有关摄动原反应的多重蛋白质和mRNA数据。目的3将LINCS方法应用于非转化免疫细胞和诱导多能干细胞，并探索签名是否可以指导详细的药物化学活动。在数据分析中，Aim 4将使用统计建模、网络推理和机器学习方法构建摄动响应签名。目标5将开发新的方法来理解和分析单细胞中多种表型的药物相互作用。目的6将开发一种新的压缩传感框架来分析激酶抑制剂的多药理学。Aim 7将增强HMS LINCS网站和数据库的查询、浏览和探索功能，以及与UCSC基因组浏览器的集成。在社区互动和外展方面，目标8将实施多样化的培训和外展活动，包括与LINCS和非LINCS研究小组合作。在管理方面，Aim 9将确保中心的有效管理，持续访问LINCS项目中产生的工具和数据，并遵守计划目标。

DESCRIPTION (provided by applicant): The overall goal of the HMS LINCS Center is to delineate the fundamental principles of cellular response to perturbagens at the level of single-cells and cell populations and to make response data routinely available via web-based browse, query and programmatic interfaces. This will involve the development and testing of new measurement methods, computational algorithms, and response signatures for diverse human cell types exposed to perturbations individually and in combination. We will emphasize the systematic collection of data not currently available in existing public databases including live and fixed-cell imaging, biochemical data on signaling proteins and multi-factorial drug-response phenotypes. A focus on diverse transformed and primary cells, including those derived from healthy and diseased donors, and on clinical grade small molecules (kinase inhibitors and epigenome drugs) will increase the translational impact of our work. The proposed LINCS Center represents a continuation of a program in operation for ~3.5 years under a LINCS pilot phase U54 award. We will expand the scope and sophistication of our Center, devoting significant effort to (i) improving the quality of data analysis and visualization, particularly wih respect to the complexities of perturbagen polypharmacy (ii) accelerating the release of perturbagen-response signatures using methods that have been demonstrated to yield reliable and informative data, with a particular emphasis on primary and non-transformed cells (iii) developing and applying new measurement methods, particularly mass spectrometry for analysis of cell populations and live-cell imaging for analysis of single cells. The work will involve nine complementary but independent aims. In Data Generation, Aim 1 will perform systematic analysis of perturbagen responses at a single-cell level. Aim 2 will collect multiplex protein and mRNA data on perturbagen response using a set of complementary imaging, mass spectrometry and bead-based assays. Aim 3 will apply LINCS methods to non-transformed immune cells and induced pluripotent stem cells, and explore if signatures can guide a detailed medicinal chemistry campaign. In Data Analysis, Aim 4 will construct perturbagen-response signatures using statistical modeling, network inference and machine learning methods. Aim 5 will develop new approaches to understanding and analyzing drug interactions on multiple phenotypes in single cells. Aim 6 will develop a novel compressed sensing framework for analyzing the poly-pharmacology of kinase inhibitors. Aim 7 will enhance the query, browse and explore functions of the HMS LINCS website and database and its integration with the UCSC Genome Browser. In Community Interaction and Outreach, Aim 8 will implement diverse training and outreach activities, including collaboration with LINCS and non-LINCS research groups. In Administration, Aim 9 will ensure effective management of the Center, sustained access to tools and data produced within the LINCS Project, and compliance with program goals.