Proteogenomic Characterization of Tumor Tissues and Preclinical Models with High Precision

摘要 在CPTAC2和CPTAC3的最后10年里，JHU蛋白质组鉴定中心(JHU/PCC) 反复展示了卓越的技术创新和强大的数据生成能力 CPTAC的核心使命是加速理解分子基础，这对CPTAC的成功发挥了关键作用 通过大规模蛋白质组和基因组分析技术对不同癌症的应用 类型。作为目前的3个CPTAC3PCCs之一，我们建立了稳健和标准化的蛋白质组分析 协议和技术，并将它们应用于7个人类癌症队列和另外200名患者衍生的 患者衍生模型库中的异种移植物。与蛋白质组数据分析中心一起 (PGDAC)，我们发表了关于四种癌症类型的综合蛋白质基因组研究的文章。对于我们的CPTAC4 PCC应用程序，我们PCC的首要目标是使用 敏感、定量和标准化的技术。我们将利用我们已建立的中心 基础设施和利用我们在临床癌症蛋白质组发现方面的成功来表征 与癌症基因组改变相关的蛋白质、蛋白质修饰和蛋白质复合体 来自更多的人类肿瘤类型和临床前模型。我们将确定固有的独特功能 到蛋白质，如包括乙酰化和泛素化的翻译后修饰，以及蛋白质- 除了糖基化和磷酸化以外的蛋白质相互作用已经包括在我们目前的PCC中。 我们提出了一个三步策略来表征定义的基因组学表征的样本集，使用 CPTAC3期间验证的技术平台：(1)从两个临床标本中发现目标蛋白 以及使用串联质量标签和数据依赖获取质量的定量蛋白质组学的临床前模型 光谱分析；(2)使用与数据无关的正交采集质谱学验证结果；以及 (3)使用经分析验证的高吞吐量CPTAC第2层目标来确认已验证的目标 多反应监测质谱仪(MRM-MS)分析。我们进一步建议进行试验性研究，以 技术进步。虽然这一PCC应用集中在临床的蛋白质组学特征上 样本和临床前模型，我们相信对蛋白质基因组数据的理解和专业知识 分析和翻译将对PCC和整个CPTAC网络的成功至关重要。我们有 组建了一支优秀的调查团队，他们具有互补的专业知识和多年的 CPTAC计划(CPTAC2和CPTAC3)，以及与来自以下国家的调查人员/PI成功合作的证据 CPTAC PGDAC和蛋白质组翻译研究中心(PTRC)我们相信我们的PCC 为成功表征生物和临床样本提供最佳机会 并确定癌症靶点，以推进精准癌症医学。

Summary During the last 10 years of both CPTAC2 and CPTAC3, the JHU Proteome Characterization Center (JHU/PCC) has repeatedly demonstrated superior technological innovation and robust data generation that have played critical roles in the success of CPTAC's core mission of accelerating the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis technologies to different cancer types. As one of the 3 current CPTAC3 PCCs, we established robust and standardized proteomic analysis protocols and technologies and applied them to 7 human cancer cohorts and an additional 200 patient-derived xenografts from the Patient-Derived Models Repository. Together with the Proteogenomic Data Analysis Centers (PGDACs), we published articles on integrated proteogenomic studies in four cancer types. For our CPTAC4 PCC application, the overarching goal of our PCC is to generate accurate and reproducible data using sensitive, quantitative, and standardized technologies. We will leverage our established Center's infrastructure and capitalize on our success in clinical cancer proteogenomic discoveries to characterize proteins, protein modifications, and protein complexes associated with genomic alterations of cancer from additional human tumor types and pre-clinical models. We will identify unique features that are inherent to proteins such as post-translational modifications covering acetylation and ubiquitination, as well as protein- protein interactions in addition to glycosylation and phosphorylation that have been included in our current PCC. We propose a three-step strategy to characterize defined sets of genomics-characterized samples using technology platforms validated during CPTAC3: (1) Discovery of target proteins from both clinical specimens and preclinical models using quantitative proteomics by tandem mass tags and data dependent acquisition mass spectrometry; (2) Verification of findings using orthogonal data-independent acquisition mass spectrometry; and (3) Confirmation of the verified targets using high-throughput, CPTAC Tier 2 analytically-validated targeted Multiple Reaction Monitoring Mass Spectrometry (MRM-MS) assays. We further propose pilot studies for technology improvement. While this PCC application is focused on the proteomic characterization of clinical specimens and preclinical models, we believe that the understanding of and the expertise in proteogenomic data analysis and translation will be critical for the success of the PCC and the overall CPTAC network. We have assembled a team of outstanding investigators with complementary expertise and years of experience in the CPTAC program (CPTAC2 and CPTAC3), and evidence of successful collaborations with investigators/PIs from the CPTAC PGDACs and Proteogenomic Translational Research Centers (PTRCs). We believe that our PCC offers the best opportunity for the successful characterization of biological and clinical specimens to discover and confirm cancer targets to advance precision cancer medicine.