Multi-omic network-directed proteoform discovery, dissection and functional validation to prioritize novel AD therapeutic targets

在阿尔茨海默病加速药物伙伴关系(AMP-AD)的第一阶段，我们 完成了从分子网络构建和确认开始的一系列新的靶标验证， 进展到识别网络中的驱动基因，并结束于目标基因验证，通过这两个 目标器官的体外微扰和蛋白质组学测量。在这里，我们描述了那些经过验证的 更详细的基因，并部署结合了来自单个细胞的数据的第三代网络图 从500个大脑中提取，以产生细胞类型特定版本的我们的网络。此外，在这一发现中 阶段，我们将使用对蛋白质翻译后修饰的评估来确定通常 掩盖在组织水平的大脑RNA和通用蛋白水平，这是迄今为止可用的。新的 网络还将整合最新的AMP-AD数据，涵盖基因组、转录组、表观基因组、蛋白质组、 以及来自不同成员组的代谢组数据集。由此产生的新目标，以及那些 在第一个资助周期中得到验证，将进行进一步的解剖，以了解哪种蛋白质亚型或 修饰与疾病最相关。我们继续进行微扰实验， 在丰富的体外多细胞培养环境中对基因进行优先排序并确定关键的蛋白质结构域 在选定的候选人中。最后，我们扩展了我们的研究资源共享中心，以促进 分发我们项目中的样本和数据。

In the first period of the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD), we completed an arc of novel target validation that began with molecular network construction and confirmation, progressed to identifying driver genes within the network, and ended with target gene validation, through both in vitro perturbation and proteomic measurement in the target organ. Here, we characterize those validated genes in greater detail and deploy a third-generation network map that incorporates data from single cells extracted from 500 brains to produce a cell-type specific version of our networks. Further, in the discovery phase, we will use an assessment of protein post-translational modifications to identify targets that are typically masked in the tissue-level brain RNA and generic protein levels that have been available to date. The new network will also integrate the latest AMP-AD data, spanning genomic, transcriptomic, epigenomic, proteomic, and metabolomic data sets from the various member groups. The resulting new targets, along with those validated in the first funding cycle, will undergo further dissection to understand which protein isoform or modification is most relevant to disease. We go on to perform perturbation experiments for each of the prioritized genes in an enriched in vitro multicellular culture context and to identify critical protein domains within selected candidates. Finally, we expand our Research Resource Sharing Hub that facilitates the distribution of samples and data from our project.