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）已经成功开发了用于治疗癌症的方法。 以患者为中心的癌症治疗策略的优先级排序和评估。通过这一成本扩展， 寻求完成因COVID-19而延迟的与原始CastT目标相关的剩余工作 流行病具体而言，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，我们已经推断并实验验证了三种 转录不同的细胞状态。从这些研究中出现的最关键的假设，如支持， RNA速度研究，是致癌前体（OP）人口-这与其他两个，代表 所有PDA的主要成分，以前未被检测到-代表了肿瘤维持的关键 通过补充形态发生亚群和谱系亚群来补充水库。为了证实这一假设， 这将是我们对这种肿瘤的理解的范式转变，我们计划基于条形码， 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测定 (KP4)或OP和谱系细胞（CAPAN 1）。 增强癌症稳态蛋白质数据库（CHoPD）的结构信息注释： 关键的CAST可交付成果，CHoPD是一个全面的，功能和结构注释的库存， 主调节因子（MR）蛋白，通过系统地解剖来自 公开可用的存储库。CHoPD已在Neo4j数据库中作为图形数据库实现 系统，并已部分注释了标准的癌症标志来自PrePPI。我们现在 我建议将全部的CAST结构信息资源库纳入这个数据库，以便创建 CHoPD的一个版本，将包含从已在 项目1和项目3。 完成单细胞DNA和RNA联合测序的高度可扩展平台的开发： CastProject 2的主要技术目标是开发可扩展的技术， 细胞DNA和RNA-seq.如前所述，我们开发了一种新型的非对称微孔阵列， 同时共封装数千个单个细胞的技术，正好有两个珠-一个 一个具有用于基因组DNA的直接条形码化的寡核苷酸，另一个具有用于mRNA捕获和条形码化的寡核苷酸。 我们已经证明，这种装置有利于同时固相捕获mRNA和液相 从单个细胞中捕获gDNA。在这里，我们建议完成我们的DNA条形码的发展， 珠，并优化我们的芯片上的库建设的全面展示的性能， 技术. 从一系列基准数据集中的scRNA-Seq图谱推断拷贝数变化：我们开发了 PICASSO（从Scrna-Seq观察中的拷贝数变化推断系统发育） 单细胞RNA测序数据的数量变化。PICASSO被证明优于国家， 最先进的方法，如HoneyBadger，对模拟数据，其中地面真实答案是已知的。我们进一步 在Castpancreatic cancer dataset上证明了准确性。根据这些初步数据，我们建议 系统地将PICASSO应用于多种癌症类型的公开scRNA-seq数据集， 在人类肿瘤图谱网络上。