Relating Drugs to Genotypes to Transform Precision Cancer Therapeutics with Tuba-seq - a Novel, Highly Scalable and Quantitative Preclinical Experimental Oncology Platform

项目总结 D2G肿瘤学公司建议开发一种新的临床前实验平台，该平台将有效地与 抗癌药物与基因型别(“D2G”)之间相互作用的预测。D2G肿瘤学的创新 该方法极大地改进了已建立的人类癌症的本土小鼠模型。这些都是经过验证的 模型允许受控的基因组改变在适当的免疫活性体内启动肿瘤 微环境和真实地概括了人类癌症的进展。D2G的创新方法 首次使这些动物模型变得真正可扩展和严格量化，从而实践- TIC支持药物发现。D2G的方法可以有效地询问大量的肿瘤基因型别 预测患者对治疗的不同反应。制药公司急于获得这一信息- 信息传递。D2G将极大地提高精准癌症治疗的水平，帮助制药公司 合理选择候选化合物以推进并使其更好地与患者匹配。D2G的肿瘤学平台 将提高临床试验的成功率，并导致更有效的个性化癌症治疗。 关键的创新是一种新的肿瘤条形码和测序(TUBA-SEQ)管道。每个克隆肿瘤都是 独特的条形码，因此每个肿瘤中的癌细胞的身份和数量都可以很容易地从 大块的荷瘤组织。结合慢病毒介导的CRISPR/Cas9体细胞基因组编辑，肿瘤 条形码允许在单个动物中同时产生许多预定义的肿瘤基因类型和 单独追踪。Tuba-seq支持数十个实验(每个实验通常需要单独 小鼠群)被多路传输到单个小鼠中。与传统的基因工程相比 鼠标模型，这种方法极大地增强了可伸缩性，引入了严格的量化，并减少了 变异的来源。 拟议的直接第二阶段SBIR项目的总体目标是将Tuba-Seq管道改造成一个坚固的 可以作为商业服务向制药公司销售的平台。具体目标是(1) 扩大该平台询问的肿瘤抑制基因小组，并仔细校准它们的效果 大小和(2)严格验证平台解决微小但具有临床意义的差异的能力 在肿瘤抑制基因-药物效应大小中具有很高的统计置信度，仅依赖于ANI-R的小队列。 公马。 D2G将创建第一个实用且可扩展的临床前实验建模方法，该方法可以评估 候选药物与多种精确设计的癌症基因相互作用以预测不同的患者 对治疗的反应。

PROJECT SUMMARY D2G Oncology, Inc. proposes to develop a novel preclinical experimental platform that will effectively relate cancer drugs to genotypes (“D2G”) to predict pharmacogenomic interactions. D2G Oncology's innovative approach dramatically improves on established autochthonous mouse models of human cancer. These proven models allow controlled genomic alterations to initiate tumors in vivo in an appropriate immune-competent microenvironment and faithfully recapitulate progression of human cancer. D2G's innovative methods for the first time enable these animal models to become truly scalable and rigorously quantitative, and hence prac- tical to support drug discovery. D2G's approach can efficiently interrogate a large matrix of tumor genotypes to predict differential patient responses to therapies. Pharmaceutical companies are eager to obtain this infor- mation. D2G will significantly advance the state of the art in precision cancer therapy by helping pharma to rationally select candidate compounds to advance and better match them to patients. D2G's oncology platform will increase the success rate of clinical trials and lead to more effective personalized cancer treatments. The key innovation is a novel tumor barcoding and sequencing (Tuba-seq) pipeline. Every clonal tumor is uniquely barcoded, so the identity and number of cancer cells in each tumor can be readily quantified from bulk tumor-bearing tissues. Combined with lentiviral-mediated CRISPR/Cas9 somatic genome editing, tumor barcoding allows many predefined tumor genotypes to be generated all at once in individual animals and tracked separately. Tuba-seq enables many tens of experiments (which would each ordinarily require separate cohorts of mice) to be multiplexed into a single mouse. Compared with conventional genetically engineered mouse models, this approach enormously enhances scalability, introduces rigorous quantification, and reduces sources of variation. The overall goal of the proposed Direct Phase 2 SBIR project is to transform the Tuba-seq pipeline into a robust platform that can be marketed as a commercial service to pharmaceutical companies. Specific aims are to (1) expand the panel of tumor suppressor genes that the platform interrogates and carefully calibrate their effect sizes and (2) rigorously validate the ability of the platform to resolve small but clinically meaningful differences in tumor suppressor gene-drug effect sizes with high statistical confidence, relying only on small cohorts of ani- mals. D2G will create the first practical and scalable preclinical experimental modeling approach that can assess how candidate drugs interact with diverse, precisely-engineered cancer genotypes to predict differential patient responses to therapy.