Center for Advanced Multi-Omic Characterization of Cancer

项目摘要 PNNL蛋白质组表征中心（PCC）的总体目标是全面表征 由美国国家癌症研究所（NCI）提供的人类肿瘤样品，并整合多组学 测量，以支持改善对表征癌症的分子变化的理解， 所以在临床结果的背景下。PNNL参与了NCI的临床蛋白质组学肿瘤分析 联盟（CPTAC）作为一个PCC在过去的十年里，与全面的蛋白质组学的责任， 高级别浆液性卵巢癌、结肠癌和子宫内膜癌以及胶质母细胞瘤的表征。计划 PNNL PCC将在这些成就的基础上，扩大和推进CPTAC的全面使命， 将人类癌症的蛋白质基因组学特征转化为其他癌症类型，达到或超过CPTAC 对样本通量、覆盖率、样本大小和数据质量的关键期望或要求。种利用 先进的分析平台，PNNL计划将乙酰组和泛素组的分析添加到 前瞻性收集人类肿瘤的磷酸化蛋白质组，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学和 脂质组分析，以及选择的数据驱动的空间或单细胞蛋白质组学分析。这将提供 关于潜在代谢脆弱性和肿瘤异质性的其他重要见解，以及 微环境的贡献。这种多组学分析策略也将应用于临床前样品， 例如细胞系、类器官和患者来源的异种移植物。我们还将开发针对性的质谱 使用来自CPTAC联盟，特别是蛋白基因组数据分析中心的输入的分析 （PGDAC），优先考虑进一步探索独立的重要机制蛋白质组学变化的目标， 队列。在整个工作中，我们的测量将受益于进一步的性能提高（例如， 灵敏度和吞吐量）的基础上完善，验证和实施的发展，从PNNL和 其他CPTAC中心。 PNNL PCC将通过蛋白质组学和分子生物学技术识别有前景的癌症特征和信号网络。 对选定的2-3种癌症类型的人体生物样本和相关临床前样本进行代谢组学分析 由CPTAC，使用最先进的液相色谱-串联质谱仪器，高度 多重同量异位素质量标签标记（TMT 16-plex），和整合的样品工作流程，以及额外的 先进的代谢组学、空间和单细胞蛋白质组学平面图，每年处理300个样品。 我们也将探讨在人体标本和模型系统中重要的蛋白质组学变化的机制 使用尖端的靶向蛋白质组学平台，分析验证和高度多重靶向测定， 以及符合CPTAC Tier 2检测指南的工作流程。200个高度特异性，多重靶向 将开发蛋白质组学分析方法，并用于每年300个样本的测量。PNNL PCC 将实现癌症的无偏见和有针对性的多组学表征， 提高深度，吞吐量和质量的公正和有针对性的数据所产生的实施 并部署相关的新技术，如纳米级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密切合作， 整合和生物信息学分析，以及翻译应用。

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.