RASL-Seq CTC Assay

描述(由申请人提供)：该项目将通过使用靶向测序平台RASL-Seq分析基因表达特征来证明识别经历了上皮-间充质转化(EMT)的循环肿瘤细胞(CTC)的可行性。接受EMT的CTC的存在预示着较差的长期存活率。基因图谱还将包括用于识别和计数EpCAM+和EpCAM-CTCs的基因，以及用于识别治疗剂靶标表达的基因。因此，RASL-Seq CTC Profiling Signature分析将提供当前Veridex CellSearch(R)分析所能提供的EpCAM+计数，但通过识别已接受EMT(未经CellSearch评估)并将患者置于危险境地的EpCAM-细胞，并为肿瘤学家提供这些细胞可能对何种治疗有效的指示，总体上显著改善患者的护理和生存结果。本提案中使用的EMT和风险签名是MD Anderson申请的专利的主题。BioSpyder已经从UCSD那里单独获得了RASL-Seq技术的许可，它将在第一阶段证明其可行性，即确定单个CTC的基因表达谱 或者(例如，EpCAM-和EpCAM+)CTC池是否可用于测试。最初的开发和验证将是细胞系，然后是一组30个患者样本，最后是 一组200个患者样本。这些患者的细胞搜索结果将与RASL-Seq测试结果进行比较，以确定RASL-Seq测试对Epcam+CTCs的阳性预测价值。该项目的结果将证明，RASL-Seq图谱分析不仅适用于CTC分析，而且还适用于活检组织的分析，并可用作辅助诊断。

DESCRIPTION (provided by applicant): This project will demonstrate the feasibility of identifying circulating tumor cells (CTCs) that have undergone an epithelial-mesenchymal transition (EMT) by profiling a gene expression signature using a targeted sequencing platform, the RASL-Seq assay. The presence of CTCs that have undergone EMT is prognostic of poor long term survival. The gene profile will also include genes for identifying and counting EpCAM+ and EpCAM- CTCs, and for identifying the expression of targets for therapeutic agents. Thus, the RASL-Seq CTC Profiling signature assay will deliver the EpCAM+ counts that the current Veridex CellSearch(R) assay does, but provide significant additional utility by identifying EpCAM- cells that have undergone EMT (not assessed by CellSearch) and which put the patient at risk, as well as provide the oncologist with an indication of what therapy these cells may be responsive to, overall significantly improving patient care and survival outcome. The EMT and risk signature used in this proposal is the subject of patents filed by MD Anderson. BioSpyder, which has separately licensed the RASL-Seq technology from UCSD, will demonstrate its feasibility in Phase I, determining if gene expression profiling of individual CTCs is required or if pools of (e.g. EpCAM- and EpCAM+) CTCs can be used for testing. Initial development and validation will be with cell lines, then a set of 30 patient samples, and finally a set of 200 patient samples. CellSearch results for these patients will be compared to the RASL-Seq assay results to determine the positive predictive value of the RASL-Seq test for Epcam+ CTCs. The results of this program will demonstrate that the RASL-Seq profiling assay has broad applicability not just to CTC analysis, but to analysis of biopsies, and for use as a companion diagnostic.