Elucidating the dependencies of tumor initiating and drug-resistant niches in human malignancies by genome- wide molecualr profiling of single cells

 描述（由申请人提供）：肿瘤从易处理发展为难治性耐药形式，可能是在肿瘤生物学机制的基本阐明及其转化和临床意义方面最艰巨的挑战。即使不是所有的肿瘤都会自发地进展到转移性耐药阶段，我们识别进展风险更大的患者的能力也非常有限。对于注定要发展的肿瘤，挑战提出了两个不同但高度互补的观点。从宏观上看，进展的发生是因为特定恶性肿瘤的可消除机制尚不存在，或者由于遗传和表观遗传机制导致的耐药性增强。例如，虽然70%的HER 2+乳腺腺癌最初对曲妥珠单抗有反应，但其中70%最终会复发为曲妥珠单抗耐药肿瘤。同样令人沮丧的结果反映在大多数靶向治疗中。然而，从微观上看，耐药性的出现根源于癌症的极端异质性，无论是在个体之间（肿瘤间），还是更重要的是在个体肿瘤细胞之间（肿瘤内）。该提案的目标是开发一种新的方法框架，将实验和计算方法相结合，以系统地阐明肿瘤异质性驱动肿瘤进展和耐药性出现的机制。它将特别关注单细胞水平上肿瘤内异质性的研究，以确定导致亚克隆扩增和耐药小生境出现的独立分子事件的范围。从这些研究中获得的方法学进展将被广泛传播，并将适用于任何人类恶性肿瘤的无偏分析，其中有适当的数据。这些方法将是假设生成，产生高可能性的分子机制，将实验验证的全面剧目。在这一更广泛的背景下，拟议研究的主要重点将是扩展基于网络的方法，这些方法已成功应用于多细胞样本，以研究肿瘤异质性对单细胞水平进展和耐药性的影响。我们将关注异质性的三个来源：（a）遗传上不同的肿瘤亚克隆，（B）表观遗传上重编程但同基因的肿瘤亚群，和（c）正常细胞（例如基质或免疫系统相关），其存在调节肿瘤细胞的行为和对治疗药物的反应。我们的假设是，阐明单细胞中的肿瘤相关机制对于开发更好的预防，诊断和治疗疾病的策略至关重要。

 DESCRIPTION (provided by applicant): Tumor progression from a tractable to an intractable, drug-resistant form represents perhaps the most formidable challenge both in terms of basic elucidation of tumor biology mechanisms and in terms of its translational and clinical implications. Even though not all tumors will spontaneously progress to a metastatic drug-resistant stage; our ability to identify the patients at greater risk of progression is extremely limited. For tumors destined to progress, the challenge presents two distinct, yet highly complementary perspectives. Macroscopically, progression occurs because either pharmacologically actionable mechanisms do not yet exist for a specific malignancy or because drug resistance ensues, due to genetic and epigenetic mechanisms. For instance, while 70% of HER2+ breast adenocarcinomas initially respond to trastuzumab, 70% of these will eventually relapse to trastuzumab-resistant tumors. The same dismal outcome is reflected across most targeted therapeutics. Microscopically, however, emergence of drug resistance is rooted in the exceedingly heterogeneous nature of cancer, both across individuals (inter-tumor) and, more importantly, across individual tumor cells (intra-tumor). The goal of this proposal is the development of a novel methodological framework integrating both experimental and computational approaches to systematically elucidate the mechanisms by which tumor heterogeneity drives tumor progression and emergence of drug resistance. It will focus specifically on the study of intra-tumor heterogeneity at the single cell level to identify the rane of independent molecular events contributing to sub-clonal expansion and emergence of drug-resistant niches. The methodological advances resulting from these studies will be broadly disseminated and will be applicable to the unbiased analysis of any human malignancy for which appropriate data is available. These methodologies will be hypothesis generating, producing comprehensive repertoire of high-likelihood molecular mechanisms that will be experimentally validated. Within this broader context, the primary focus of the proposed research will be on extending network-based methodologies, which were successfully applied to multicellular samples, to study the impact of tumor heterogeneity on progression and drug resistance, at the single cell level. We will focus on three sources of heterogeneity: (a) genetically distinct tumor subclones, (b) epigenetically reprogrammed yet isogenic tumor sub-populations, and (c) normal cells (e.g. stromal or immune system related), whose presence modulates tumor cell behavior and response to therapeutic agents. Our hypothesis is that elucidating tumor-related mechanisms in single cells is critical to the development of better strategies for prevention, diagnosis, and treatment of the disease.