Generating an atlas of Richter's Syndrome: from molecular understanding to outcome prediction, detection and monitoring

项目摘要：最近的治疗进展极大地改善了慢性阻塞性肺疾病患者的预后 淋巴细胞白血病(CLL)。然而，里希特综合征(RS)，即慢性淋巴细胞性白血病向非传染性疾病的转化。 侵袭性淋巴瘤(每年发生在0.5-1%的慢性淋巴细胞性白血病患者中)，通常对现有的治疗方法无效 接近了。在我们目前的P01成功创建了世界上最大的遗传驱动因素图谱的基础上 和亚型的CLL(n=~1100)，并使用它来建立预后模型，这个续订申请寻求应用 类似的(和新的)方法，全面定位RS的遗传基础。目前，以及在 与CLL相比，RS的遗传学、克隆组成、驱动因素和细胞电路知之甚少，因此 既没有基于分子的风险分层的框架，也没有治疗开发的目标。 因此，了解转化的分子(遗传、表观遗传学和蛋白质组)基础 从CLL到RS将为更有效的治疗干预、反应预测和 有可能及早发现，所有这些都是为了改善患者的预后。为了实现这些目标，我们建议 为了：(1)定义RS的驱动因素，描述RS与CLL和DLBCL的关系。使用完整外显子和 RNA测序，我们将研究&gt；300例RS病例的遗传和转录情况，包括分析 其转化前的CLL和RS样品。然后我们将进一步描绘出它们之间的遗传关系 CLL和RS使用病例子集的全基因组测序，并使用 染色质和组蛋白甲基化分析。此外，我们将追踪CLL细胞向RS和RS的进化 在单细胞分辨率下确定遗传、表观遗传和转录状态的不同模式。最后， 我们将结合这些数据来确定RS的分子亚型，并将它们与结果相关联。(2)界定 与CLL向RS转化相关的细胞回路的变化。我们将利用 用于识别细胞突起连接变化的微尺度蛋白质组和磷蛋白质组分析 与向RS的转化相关，并创建RS的全面蛋白质组学图谱。我们将确定 去调控的信号通路和潜在的治疗靶点。最后，我们将把蛋白质组数据整合到 提炼上述分子亚型，并建立高通量蛋白质组学分析 检测这些亚型的生物标志物，并在一组独立的RS患者中进行验证。(3)发展 遥感检测和监测的非侵入性工具。在我们对RS基因组的理解基础上，我们将建立 一种基于低通全基因组测序的可靠且廉价的无细胞DNA检测方法 血浆样本中RS特异性改变。我们将测试我们是否能在患者的血液中检测到RS克隆 监测RS的出现、进展和复发。这些目标加在一起将创建第一个全面的 RS图谱，确定关键途径和潜在的治疗目标，并建立可能影响临床的工具 做决定。

Project Summary: Recent therapeutic advances have dramatically improved patient outcomes in chronic lymphocytic leukemia (CLL). However, Richter's Syndrome (RS), which is the transformation of CLL to an aggressive lymphoma (that occurs in 0.5-1% of CLL patients annually), is often refractory to existing therapeutic approaches. Building on the success of our current P01 in creating the world's largest map of genetic drivers and subtypes of CLL (n=~1100) and using it to build prognostic models, this renewal application seeks to apply similar (and new) approaches to comprehensively map the genetic underpinnings of RS. Currently, and in contrast to CLL, little is known about the genetics, clonal composition, drivers and cell circuitry of RS, and hence there is neither a framework for molecularly based risk stratification nor targets for therapeutic development. Therefore, understanding the molecular (genetic, epigenetic and proteomic) underpinnings of the transformation from CLL to RS will create opportunities for more effective therapeutic interventions, prediction of response, and potentially early detection, all with the goal of improving patient outcome. To achieve these goals, we propose to: (1) Define the drivers of RS and delineate the relationship of RS to CLL and DLBCL. Using whole-exome and RNA sequencing, we will study the genetic and transcriptomic landscape of >300 RS cases, including analyzing their pre-transformation CLL and RS samples. We will then further delineate the genetic relationship between CLL and RS using whole-genome sequencing of a subset of cases, and chart their epigenetic landscape using chromatin and histone methylation profiling. Moreover, we will trace the evolution of the CLL cells to RS and determine distinct patterns of genetic, epigenetic, and transcriptomic states at a single-cell resolution. Finally, we will combine these data to identify molecular subtypes of RS and associate them with outcome. (2) Define the changes in cellular circuitry associated with transformation from CLL to RS. We will use the power of microscaled proteomic and phosphoproteomic analysis to identify changes in the wiring of cellular processes associated with transformation to RS and create a comprehensive proteomic map of RS. We will identify deregulated signaling pathways and potential therapeutic targets. Finally, we will integrate the proteomic data to refine the molecular subtypes identified above as well as develop a high-throughput proteomic assay for detecting biomarkers of these subtypes and validate them in an independent set of RS patients. (3) Develop a non-invasive tool for RS detection and monitoring. Building on our understanding of the RS genome, we will build a robust and inexpensive cell-free DNA assay based on low-pass whole-genome sequencing aimed at detecting RS-specific alterations in plasma samples. We will test whether we can detect RS clones in patients' blood to monitor the emergence, progression and relapse of RS. Together, these Aims will create the first comprehensive atlas of RS, identify key pathways and potential therapeutic targets and build tools that could impact clinical decision making.