Center for Advanced Multi-Omic Characterization of Cancer

项目总结 PNNL蛋白质组鉴定中心(PCC)的总体目标是全面鉴定 人类肿瘤样本由美国国家癌症研究所(NCI)提供，并整合了多个基因组 支持对表征癌症的分子变化的更好理解的测量，以及 因此，在临床结果的背景下。PNNL参与了NCI的临床蛋白质组肿瘤分析 联盟(CPTAC)在过去十年中担任PCC，负责综合蛋白质组学 高级别浆液性卵巢癌、结肠癌、子宫内膜癌和胶质母细胞瘤的特征。计划中的 PNNL PCC将在这些成就的基础上，延长和推进CPTAC的全面发展使命 符合或超过CPTAC的其他癌症类型的人类癌症的蛋白质基因组特征 对样本吞吐量、覆盖范围、样本大小和数据质量的关键期望或要求。利用一种 先进的分析平台，PNNL计划将乙酰组和泛素组的分析添加到 未来收集的人类肿瘤的磷蛋白质组，以更好地阐明关键的生化过程 与蛋白质-蛋白质相互作用、蛋白质降解和信号转导有关。我们还将补充 核心蛋白质组和翻译后修饰(PTM)-组分析与全球代谢组和 脂体分析，以及精选数据驱动的空间或单细胞蛋白质组学分析。这将提供 对潜在的代谢易损性和肿瘤异质性以及 微环境的贡献。这一多组学分析策略也将应用于临床前样本， 例如细胞系、有机化合物和患者来源的异种移植。我们还将开发定向质谱学 使用CPTAC联盟，特别是蛋白质组数据分析中心的投入进行分析 (PGDAC)，为进一步探索重要的机械性蛋白质组变化确定优先目标 队列(S)。在整个工作中，我们的测量将受益于性能的进一步提高(例如， 敏感度和吞吐量)基于精炼、验证和实施来自PNNL和 其他CPTAC中心。 PNNL PCC将通过蛋白质组学和信号网络识别有希望的癌症信号和信号网络 选择2-3种癌症类型的人生物样本和相关临床前样本的代谢组学分析 由CPTAC使用最先进的液相色谱-串联质谱仪，高度 多路等压质量标记(TMT 16-plex)、集成的样本工作流程以及其他 先进的代谢组、空间和单细胞蛋白质组计划，每年可生产300个样品。 我们还将探索在人类标本和模型系统中具有机械重要性的蛋白质组变化。 使用尖端的靶向蛋白质组平台，经过分析验证的高度多元化的靶向分析， 以及符合CPTAC Tier 2化验指南的工作流程。两百个高度具体、多路传输的目标 蛋白质组学分析将被开发并用于每年300个样本的测量。PNNL PCC 将实现对癌症的无偏见和有针对性的多组学表征 提高通过实施以下方法生成的无偏见数据和目标数据的深度、吞吐量和质量 部署相关新技术，如纳米PTM、代谢组学分析和单细胞 蛋白质组学分析。 PNNL PCC将与CPTAC网络中的其他PCC、PGDAC和PTRC在数据方面进行密切合作 整合和生物信息学分析，以及翻译应用程序。

PROJECT SUMMARY The overall objective of the PNNL Proteome Characterization Center (PCC) is to comprehensively characterize human tumor samples provided by the National Cancer Institute (NCI), and to integrate the multi-omic measurements to support improved understanding of the molecular changes that characterize cancer, and do so in the context of clinical outcome. PNNL has participated in the NCI’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) as a PCC for the past ten years, with responsibility for comprehensive proteogenomic characterization of high-grade serous ovarian, colon, and endometrial cancers, and glioblastoma. The planned PNNL PCC will build on those achievements to extend and advance the CPTAC mission of comprehensive proteogenomic characterization of human cancers to additional cancer types, meeting or exceeding CPTAC key expectations or requirements for sample throughput, coverage, sample size, and data quality. Utilizing an advanced analytical platform, PNNL plans to add analysis of both acetylome and ubiquitinome to the phosphoproteome of prospectively collected human tumors, to betters illuminate key biochemical processes related to protein-protein interactions, protein degradation, and signal transduction. We will also complement the core proteome and post-translational modification (PTM)-ome analysis with global metabolome and lipidome analysis, as well as selected data driven spatial or single-cell proteomics analysis. This will provide additional critical insights on potential metabolic vulnerabilities and tumor heterogeneity as well as microenvironment contributions. This multi-omic analysis strategy will also be applied to preclinical samples, such as cell lines, organoids and patient-derived xenografts. We will also develop targeted mass spectrometric assays using input from the CPTAC consortium, and particularly the Proteogenomic Data Analysis Centers (PGDACs), to prioritize targets for further exploring important mechanistic proteomic changes in independent cohort(s). Throughout this work our measurements will benefit from further performance increases (e.g., sensitivity and throughput) based on refining, validating and implementing developments from both PNNL and the other CPTAC Centers. The PNNL PCC will identify promising cancer signatures and signaling networks through proteomic and metabolomic analysis of human biospecimens and relevant preclinical samples for 2-3 cancer types selected by the CPTAC, using state-of-the-art liquid chromatography-tandem mass spectrometry instrumentation, highly multiplexed isobaric mass-tag labeling (TMT 16-plex), and integrated sample workflows, as well as additional advanced metabolomic, spatial and single-cell proteomic planforms, at a throughput of 300 samples per year. We will also explore mechanistically important proteomic changes in human specimens and model systems using cutting-edge targeted proteomic platforms, analytically validated and highly multiplexed targeted assays, and workflows meeting the CPTAC Tier 2 assay guidelines. Two hundred highly specific, multiplexed targeted proteomics assays will be developed and used for measurements in 300 samples each year. The PNNL PCC will accomplish both unbiased and targeted multi-omic characterization of cancers in conjunction with improving the depth, throughput and quality of both unbiased and targeted data generated by implementing and deploying relevant new technologies, such as nanoscale PTM, metabolomic analysis, and single-cell proteomics analysis. The PNNL PCC will work closely with the other PCCs, PGDACs and PTRCs in the CPTAC network on data integration and bioinformatics analysis, as well as translational applications.