Structural and Functional Biology-based analysis of non-oncogene cancer dependencies

基于结构和功能生物学的非癌基因癌症依赖性分析

• 批准号: 10401148
• 负责人: ANDREA CALIFANO
• 金额: $ 50万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-12 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10401148
• 关键词: Atlases; Bar Codes; Benchmarking; Biological Assay; Biology; COVID-19 pandemic; Cancer Center; Cell Line; Cell Lineage; Cells; Collection; Combined Modality Therapy; DNA; DNA sequencing; Data; Data Set; Database Management Systems; Databases; Dependence; Development; Devices; Equipment and supply inventories; Evaluation; Fostering; Genetic Transcription; Genomic DNA; Graph; Homeostasis; Human; Individual; Joints; Libraries; Maintenance; Malignant Neoplasms; Malignant neoplasm of pancreas; Messenger RNA; Methodology; Methods; Oligonucleotides; Oncogenic; Pancreatic Ductal Adenocarcinoma; Patients; Performance; Phase; Phylogenetic Analysis; Population; Protein Databases; Proteins; RNA; Reporting; Residual state; Resources; Sampling; Solid; Structure; System; Systems Biology; Technology; Therapeutic; Work; base; cancer type; cost; innovation; novel; precursor cell; proteostasis; public repository; single-cell RNA sequencing; tool; transcriptome sequencing; tumor

The Columbia Center for Cancer Systems Therapeutics (CaST) has successfully developed methodologies for the patient-centric prioritization and evaluation of cancer therapeutic strategies. Through this cost extension we seek to complete residual work related to the original CaST aims that was delayed due to the COVID-19 pandemic. Specifically, we will: Assess the tumor replenishing potential of the oncogenic precursor cell population in pancreatic ductal adenocarcinoma (PDA): In PDA we have inferred and experimentally validated the existence of three transcriptionally distinct cell states. The most critical hypothesis emerging from these studies, as supported by RNA velocity studies, is that the oncogenic precursor (OP) population – which unlike the other two, represents a dominant component of all PDAs and was previously undetected – represents the key tumor maintenance reservoir by replenishing both the morphogenic and the lineage sub-populations. To confirm this hypothesis, which would be paradigm shifting in terms of our understanding of this tumor, we are planning barcode-based lineage tracing assays in cell lines that we have already shown to comprise either OP and morphogenic cells (KP4) or OP and lineage cells (CAPAN1). Enhance the structure-informed annotation of the Cancer Homeostasis Proteins Database (CHoPD): One of the key CaST deliverables, the CHoPD is a comprehensive, functionally and structurally annotated inventory of master regulator (MR) proteins, compiled by systematically dissecting tumor checkpoints across samples from publicly available repositories. The CHoPD has been implemented as a graph database in the Neo4j database system and has been partially annotated with the standard cancer hallmarks as derived from PrePPI. We now propose to incorporate the full repertoire of CaST structure-informed resources into this database, so as to create a version of CHoPD that will contain extensive annotation derived from tools that have been developed in the context of CaST Projects 1 and 3. Complete development of a highly scalable platform for joint single-cell DNA and RNA sequencing: One of the major technical objectives of CaST Project 2 is the development of scalable technology for simultaneous single cell DNA- and RNA-seq. As previously reported, we have developed a novel asymmetric microwell array technology for simultaneous co-encapsulation of thousands of individual cells with exactly two beads – one harboring oligonucleotides for direct barcoding of genomic DNA and the other for mRNA capture and barcoding. We have demonstrated that this device facilitates simultaneous solid-phase capture of mRNA and solution-phase capture of gDNA from individual cells. Here we propose to complete the development of our DNA barcoding beads and optimize the performance of our on-chip library construction for a full-scale demonstration of the technology. Infer copy number alterations from scRNA-Seq profiles in a collection of benchmark datasets: We developed PICASSO (Phylogenetic Inference from Copy number Alterations in Scrna-Seq Observations) to infer copy number changes from single-cell RNA sequencing data. PICASSO was demonstrated to outperform state-of- the-art methods, such as HoneyBadger, on simulated data, where ground truth answers are known. We further demonstrated accuracy on a CaST pancreatic cancer dataset. Based on these preliminary data, we propose to systematically apply PICASSO to publicly available scRNA-seq datasets across multiple cancer types, focusing on the Human Tumor Atlas Network.

哥伦比亚癌症系统治疗中心 (CaST) 已成功开发出以下方法： 通过这种成本扩展，我们对癌症治疗策略进行了以患者为中心的优先排序和评估。 寻求完成与最初的 CaST 目标相关的剩余工作，这些工作因 COVID-19 而被推迟 具体来说，我们将： 评估胰腺导管中致癌前体细胞群的肿瘤补充潜力 腺癌 (PDA)：在 PDA 中，我们推断并通过实验验证了三种腺癌的存在 这些研究中出现的最关键的假设是转录上不同的细胞状态，并得到了支持。 RNA 速度研究的重点是致癌前体 (OP) 群体——与其他两个不同，它代表 所有 PDA 的主要组成部分，之前未被检测到 - 代表肿瘤维持的关键 通过补充形态和谱系亚群来证实这一假设。 就我们对这种肿瘤的理解而言，这将是范式转变，我们正在计划基于条形码的 我们已经证明包含 OP 和形态发生细胞的细胞系中的谱系追踪分析 (KP4) 或 OP 和谱系细胞 (CAPAN1)。 增强癌症稳态蛋白数据库 (CHoPD) 的结构知情注释：其中之一 关键的 CaST 可交付成果，CHoPD 是一个全面的、在功能和结构上都带有注释的清单 主调节蛋白（MR），通过系统地剖析来自不同样本的肿瘤检查点来编译 CHoPD 已作为 Neo4j 数据库中的图形数据库实现。 系统，并已部分注释来自 PrePPI We now 的标准癌症标志。 建议将 CaST 结构信息资源的全部内容纳入该数据库，以便创建 CHoPD 的一个版本，将包含从已开发的工具中派生的大量注释 CaST 项目 1 和 3 的背景。 完整开发用于联合单细胞 DNA 和 RNA 测序的高度可扩展的平台：其中之一 CaST项目2的主要技术目标是开发可扩展的同步单 正如之前报道的，我们开发了一种新型的不对称微孔阵列。 用恰好两个珠子同时共封装数千个单个细胞的技术 - 一个 包含用于直接对基因组 DNA 进行条形码编码的寡核苷酸，另一个用于 mRNA 捕获和条形码。 我们已经证明该装置有助于同时固相捕获 mRNA 和溶液相 从单个细胞中捕获 gDNA，我们建议完成 DNA 条形码的开发。 珠子并优化我们的片上库构建的性能，以进行全面的演示 技术。 从一组基准数据集中的 scRNA-Seq 配置文件推断拷贝数变化：我们开发了 PICASSO（Scrna-Seq 观察中的拷贝数改变的系统发育推断）推断拷贝 单细胞 RNA 测序数据的数量变化被证明优于现状。 我们进一步使用最先进的方法，例如 HoneyBadger，对模拟数据进行分析，其中真实答案是已知的。 根据这些初步数据，我们建议在 CaST 胰腺癌数据集上证明准确性。 系统地将 PICASSO 应用于多种癌症类型的公开 scRNA-seq 数据集，重点关注 在人类肿瘤图谱网络上。