RASL-Seq CTC Assay

描述（由申请方提供）：本项目将证明通过使用靶向测序平台RASL-Seq检测分析基因表达特征来鉴定经历上皮-间充质转化（EMT）的循环肿瘤细胞（CTC）的可行性。已经经历EMT的CTC的存在是不良长期存活的预后。基因谱还将包括用于鉴定和计数EpCAM+和EpCAM-CTC以及用于鉴定治疗剂的靶标的表达的基因。因此，RASL-Seq CTC特征分析测定将提供当前Veridex CellSearch（R）测定所做的EpCAM+计数，但通过鉴定已经经历EMT的EpCAM-细胞提供显著的额外效用（未通过CellSearch评估）并且使患者处于风险中，以及为肿瘤学家提供这些细胞可能对什么疗法有反应的指示，总体而言，显著改善了患者护理和生存结局。本提案中使用的EMT和风险签名是MD安德森申请专利的主题。BioSpyder已经从UCSD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，确定单个CTC的基因表达谱是否 或者是否可以使用CTC池（例如EpCAM-和EpCAM+）进行测试。最初的开发和验证将使用细胞系，然后是一组30个患者样本，最后是一个 200个患者样本。将这些患者的CellSearch结果与RASL-Seq测定结果进行比较，以确定RASL-Seq测试对Epcam+ CTC的阳性预测值。该项目的结果将证明RASL-Seq分析测定不仅对CTC分析具有广泛的适用性，而且对活检分析具有广泛的适用性，并可用作伴随诊断。

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.