Tumor DNA in CSF and novel modeling decode breast cancer - brain metastases

 描述（由申请人提供）：CSF中的肿瘤DNA和新模型解码乳腺癌脑转移项目概述描述：转移到中枢神经系统（CNS）的癌症治疗的进展需要诊断和科学工具的范式转变，具有重现人类疾病的忠实模型。我正在开发一种创新的，侵入性较小的方法来识别脑肿瘤突变，并跟踪肿瘤转移到CNS的遗传谱如何随时间和治疗而变化。肿瘤细胞和无细胞DNA（cfDNA）作为指纹，允许检测标记疾病变化和进展的遗传改变。脑脊髓液（CSF）中的肿瘤DNA将建议基于脑内实体和软脑膜（LM）乳腺癌转移中包含的突变进行靶向治疗。CSF中新发现的肿瘤突变将详细说明脑转移瘤如何在治疗后获得有利的突变。与LM疾病扩散一致的突变将揭示这种脑转移亚型的潜在病理生理学，并提出有效的靶向治疗。乳腺癌向脑的实体和LM转移研究不足，部分原因是缺乏可靠反映人类疾病的细胞培养和动物异种移植模型。我将创建一个新的、可移植的异种移植模型，包括脑内移植直接来自人脑转移瘤的乳腺癌细胞的原代培养物。这些主要的人脑胶质瘤特异性工具将允许通过对CSF中的肿瘤DNA进行测序来进行新药筛选和遗传靶点的验证。具体目标1：为了创建一种鉴定和表征实体和LM乳腺癌脑转移患者CSF中脑肿瘤特异性突变的方法，在CSF中，我将：a）对原发性乳腺肿瘤中已知突变的肿瘤细胞和cfDNA进行测序，并确定突变体分数，B）对脑肿瘤DNA应用全外显子组测序以鉴定另外的突变基因，和c）开发由乳腺癌中已知的可靶向突变组成的癌症测序组。具体目标二：为了确定乳腺癌原发性肿瘤、实体性脑肿瘤转移和软脑膜转移在肿瘤生物学和对药物治疗的反应方面的差异，我将利用来自乳腺癌CNS转移的新型原代细胞培养和颅内异种移植模型来验证CSF中鉴定的肿瘤突变并筛选治疗方法。总结：所提出的目标是互补的，但不相互依赖，如果成功结合，将有巨大的潜力以指数级方式推进我们对转移到中枢神经系统的最常见癌症之一的了解。我们的研究结果将提出潜在的治疗途径，以改善这些患者的治疗。识别和跟踪患者CSF中的脑肿瘤DNA指纹将最终实现更复杂，个性化和靶向治疗。我们的转化研究将彻底改变实体和LM转移的识别和治疗，并加深我们对转移性癌症进展的理解。测试脑转移瘤的新疗法的假设需要更特异、快速和可转化的细胞培养和动物模型。通过开发细胞系和将人乳腺癌脑肿瘤植入颅内的小鼠异种移植物模型，我们可以测试治疗方法并促进我们对实体和LM CNS肿瘤的理解。我是一名执业神经外科医生，在我职业生涯的早期阶段，临床实践主要集中在脑肿瘤患者的手术治疗上。我的实验室专注于神经肿瘤学的基础科学，项目重点是直接影响患者护理，并揭示脑肿瘤生物学研究的新领域。我在手术室和诊所照顾脑肿瘤患者，在实验室努力了解驱动CNS肿瘤发生的遗传和表观遗传机制。这个指导培训奖对于保护我的研究时间至关重要，并使我能够进一步发展我的实验室对CSF中细胞和cfDNA的关注，并推进已建立的颅内转移的工作模型。我的系主任为我提供了50%的受保护的研究时间，我完全致力于这个项目。

 DESCRIPTION (provided by applicant): Tumor DNA in CSF and novel modeling decode breast cancer brain metastases Project Summary DESCRIPTION: Advances in the treatment of cancer metastatic to the central nervous system (CNS) require paradigm shifts in diagnostic and scientific tools, with faithful models recapitulating the human disease. I am developing an innovative, less invasive method to identify brain tumor mutations and track how the genetic spectrum of tumors metastatic to the CNS changes over time and with therapy. Tumor cellular and cell-free DNA (cfDNA) acts as a fingerprint, allowing detection of genetic alterations that mark the variation and progression of disease. Tumor DNA in cerebral spinal fluid (CSF) will suggest targeted therapies based on the mutations contained in solid and leptomeningeal (LM) breast cancer metastases within the brain. Newly identified tumor mutations in CSF will detail how brain metastases acquire advantageous mutations in response to therapy. Mutations consistent with LM spread of disease will unveil the underlying pathophysiology of this brain metastasis subtype, and suggest effective, targeted therapies. Solid and LM metastases to the brain from breast cancer are woefully understudied, in part due to a lack of cell culture and animal xenograft models that reliably reflect the human disease. I will create a novel, translatable, xenograft model, involving the intracerebral transplantation of primary cultures of breast cancer cells derived directly from human brain metastases. These primary, human brain metastases-specific tools will allow for novel drug screens and validation of genetic targets identified through sequencing of tumor DNA in CSF. Specific Aim 1: To create a method of identifying and characterizing brain tumor-specific mutations in the CSF of patients with solid and LM breast cancer brain metastases, in CSF I will: a) sequence tumor cellular and cfDNA for known mutations in the primary breast tumor, and determine the mutant fraction, b) apply whole exome sequencing to brain tumor DNA to identify additional mutated genes, and c) develop a cancer sequencing panel consisting of known, targetable mutations in breast cancer. Specific Aim 2: To determine how breast cancer primary tumors, solid brain tumor metastases, and leptomeningeal metastases differ in tumor biology and response to medical therapy, I will utilize novel primary cell culture and intracranial xenograft models from breast cancer CNS metastases to validate tumor mutations identified in CSF and screen therapeutics. Summary: The proposed aims are complimentary yet not reliant on each other, and if successful in combination have substantial potential to exponentially advance our understanding of one of the most common cancers to metastasize to the CNS. Our findings would propose potential therapeutic avenues to improve treatment for these patients. Identifying and following the brain tumor DNA fingerprint in patient CSF will ultimately enable more sophisticated, personalized, and targeted therapies. Our translational study will revolutionize the recognition and treatment of solid and LM metastases, and deepen our understanding of metastatic cancer progression. Testing hypotheses of novel therapeutics for brain metastases requires more specific, rapid, and translatable cell culture and animal models. By developing cell lines and implanting mouse xenograft models intracranial with human breast cancer brain tumors we can test therapeutics and advance our understanding of solid and LM CNS tumors. I am a practicing neurosurgeon, in the early stage of my career, with a clinical practice focused on the surgical treatment of patients with brain tumors. My laboratory focuses on the basic science of neuro-oncology, with a project focus to directly impact patient care and unveil new areas of study in brain tumor biology. I care for brain tumor patients in the operating room and in the clinic, striving in the laboratory to understand the genetic and epigenetic mechanisms that drive tumor genesis in the CNS. This mentored training award is crucial to protect my research time and allow me to further develop my laboratory focus on cellular and cfDNA in CSF, and to advance a working model for established intracranial metastases. My department chair has provided me with 50% protected research time, and I am fully committed to this project.