Spatial Metabolomics for Human Kidneys

项目概要/摘要 急性肾损伤（阿基）和慢性肾脏疾病（CKD）是总体发病率的主要贡献者， 美国患者的死亡率。拟议研究的总体目标是建立无针对性和 对来自正常和患病肾脏的组织进行靶向空间代谢组学分析以评估细胞代谢 与健康功能、急性损伤、慢性病症和恢复相关的代谢状态。我们会委聘 超高分辨力成像质谱法（例如，MALDI-FTICR-IMS）补充了新的 生物信息学（例如，METASPACE），用于代谢物注释和大数据查询策略， 与正常肾脏相比，患病肾脏的代谢变化。我们的组织询问站点将 由转化肾脏病学和成像质量领导力组成的多学科协调计划 UCSD的光谱分析，太平洋西北国家大学的多组学分析杰出设施 实验室（PNNL）和生物信息学的质谱成像和三维重建设在 欧洲分子生物学实验室（EMBL）。每个阶段的三个具体目标（即，UG 3和UH 3）是 提出了特别是，我们将建立一个非靶向和靶向的空间代谢组学平台， 肾脏询问和开发用于数据询问、3-D重建 分子解释和公开分享。在UH 3阶段，非目标平台和目标平台将 扩大规模，以提高代谢物覆盖率，并开发特定肾脏疾病的关键代谢途径 阿基、CKD和疾病亚组的个体的肾脏中的区室。此外，生物信息学 该平台还将扩大规模，以建立基于代谢物的肾脏3D（下一代技术）图谱 正常和患病肾脏的结构。将实施网络服务SM-Kidney作为在线平台 让所有的数据集和结果都可以公开共享。我们将与中央政府合作， Hub（CH）整合我们的服务，以形成分子肾脏图谱。强大的合作 在来自UCSD、PNNL、EMBL和其他大学、研究所和行业合作伙伴的关键人员中， 我们的多学科团队将在UG 3和UH 3阶段达到关键的里程碑。里程碑包括 1)开发一个全面的非靶向数据库的代谢物注释在正常人 肾隔室，2）针对所选代谢物类别的靶向空间代谢组学分析，以及 途径，3）符合组织采购、初始处理和后续处理严格QC标准的方法和SOP 以及4）为在线服务SM-Kidney提供图形用户界面， 评估与肾脏疾病和发病机制相关的空间代谢谱。所有的方案，样本， 正常、阿基和CKD样本的数据和代谢物图谱将在KPMP中共享。

Project Summary / Abstract Acute kidney injury (AKI) and chronic kidney disease (CKD) are major contributors to overall morbidity and mortality in patients in the US. The overall objective of the proposed study is to establish untargeted and targeted spatial metabolomics analysis of tissues from normal and diseased kidneys to assess cellular metabolic states associated with healthy function, acute injury, chronic condition, and recovery. We will employ ultra-high resolving power imaging mass spectrometry (e.g., MALDI-FTICR-IMS) complemented with novel bioinformatics (e.g., METASPACE) for metabolite annotation and big data interrogation strategies to identify alterations of metabolism in diseased kidneys compared with normal ones. Our Tissue Interrogation Site will be a multi-disciplinary coordinated program composed of leadership in translational nephrology and imaging mass spectrometry at UCSD, outstanding facilities for multi-omics analysis at Pacific Northwest National Laboratories (PNNL), and bioinformatics for mass spectrometry imaging and 3-D reconstruction housed at European Molecular Biology Laboratories (EMBL). Three specific aims in each phase (i.e., UG3 and UH3) are proposed. In particular, we will establish an untargeted and targeted spatial metabolomics platforms for human kidney interrogation and develop an open bioinformatics platform for data interrogation, 3-D reconstruction, molecular interpretation and public sharing. In the UH3 phase, the untargeted and targeted platforms will be scaled up to improve metabolite coverage and develop key metabolic pathways for specific renal compartments in kidneys from individuals with AKI, CKD, and disease subgroups. Moreover, the bioinformatics platform will also be scaled up to establish 3D (a next-generation technology) metabolite-based maps of kidney structure in normal and diseased kidneys. A web-service SM-Kidney will be implemented as the online platform to have all the datasets and the results publicly sharable. We will contribute and collaborate with the Central Hub (CH) to integrate our service for the formation of a molecular kidney atlas. With strong collaborations among the key personnel from UCSD, PNNL, EMBL, and other universities, institutes, and industry partners, our multidisciplinary team will reach key milestones during both the UG3 and UH3 phases. Milestones include 1) the development of a comprehensive untargeted database of metabolite annotations in the normal human renal compartments, 2) targeted spatial metabolomics analysis for selected classes of metabolites and pathways, 3) methods and SOPs that meet rigorous QC standards for tissue procurement, initial processing and IMS with optical imaging and 4) providing the online service SM-Kidney with a graphical user interface to evalaute spatial metabolic profiles associated with kidney disease and pathogenesis. All protocols, samples, data, and metabolite atlas of normal, AKI, and CKD samples will be shared across the KPMP.