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）已成功开发了用于 以患者为中心的癌症治疗策略的优先级和评估。通过此费用延长我们 试图完成与原始演员的目的有关的剩余工作 大流行。特别是，我们将： 评估胰腺导管中致癌前体细胞种群的肿瘤补充潜力 腺癌（PDA）：在PDA中，我们已经推断并实验证实了三个存在 转录不同的细胞状态。从这些研究中提出的最关键的假设，如 RNA速度研究是，与另外两个不同的致癌前体（OP）种群不同 所有PDA的主要组成部分，以前未被发现 - 代表关键肿瘤维持 通过补充形态学和谱系亚群来补充储层。为了确认这一假设， 就我们对这种肿瘤的理解而言，这将是范式转移，我们正在计划基于条形码 我们已经证明包含OP和形态学细胞的细胞系中的谱系跟踪测定法 （KP4）或OP和谱系细胞（CAPAN1）。 增强癌症稳态蛋白数据库（CHOPD）的结构信息注释：其中之一 关键的铸造可交付成果，Chopd是一个全面的，功能和结构注释的清单 主要调节剂（MR）蛋白质，通过系统地剖析样品的肿瘤检查点 公开可用的存储库。该章已在Neo4J数据库中作为图形数据库实现 系统并已通过PrePPI得出的标准癌症标志部分注释。我们现在 建议将铸造结构信息资源的完整曲目纳入此数据库，以创建 CHOPD版本，其中包含从已开发的工具中得出的广泛注释 演员项目1和3的上下文。 完全开发了一个高度可扩展的单细胞DNA和RNA测序的平台：其中之一 Cast Project 2的主要技术目标是开发简单单一的可扩展技术 细胞DNA和RNA-seq。如前所述，我们已经开发了一种新型的不对称微孔阵列 技术简单地包裹的技术与数千个单个细胞与正好的两个珠子 - 一个 携带寡核苷酸直接对基因组DNA进行直接条形码，另一种用于mRNA捕获和条形码。 我们已经证明了该设备设备同时捕获mRNA和溶液阶段 从单个细胞中捕获GDNA。在这里，我们建议完成DNA条形码的开发 珠子并优化我们的片库构造的性能，以进行全面展示 技术。 从基准数据集中的SCRNA-SEQ配置文件中推断复制号更改：我们开发了 毕加索（从SCRNA-SEQ观察中拷贝数变化的系统发育推断）推断副本 单细胞RNA测序数据的数字变化。毕加索被证明超过了最先进 在模拟数据上，诸如honeybadger之类的艺术方法，在该数据中，真理答案是已知的。我们进一步 在铸造胰腺癌数据集上证明了准确性。基于这些初步数据，我们建议 系统地将毕加索应用于多种癌症类型的公开可用的scrna-seq数据集，重点 在人类肿瘤网络上。