Cell-free DNA-Based Analysis for Diagnosis, Monitoring and Optimization of Therapy for Patients with Primary Central Nervous System Lymphomas

项目摘要 摘要原发性中枢神经系统淋巴瘤是一种罕见的侵袭性结外非霍奇金淋巴瘤。 这涉及到中枢神经系统(CNS)，而不是系统性疾病。大约1400例PCNSL病例是 在美国每年确诊一次，通常发生在45岁到65岁之间，但在#年发病率正在上升 代表需要有效治疗且副作用有限的老年患者[1，2]。标准 一线治疗包括大剂量甲氨蝶呤(HD-MTX)和自体干细胞移植作为巩固 心理治疗。然而，由于明显的神经毒性，这些方案并不是所有患者都能耐受[3]。即使到了那个时候，大约 三分之一的患者对一线治疗无效，高达60%的患者最终会复发[4]。疾病的预后 初治后难治或复发的患者较差，中位生存期仅为约1年失败 预先治疗[5]。由于长期效果不佳，迫切需要改进诊断和治疗。 医疗模式。进行临床试验以改善结果的一个相当大的障碍是缺乏可用的生物标记物 可可靠地用于诊断和监测疾病。因此，PCNSL的诊断通常需要神经外科手术。 活检具有侵入性，并与感染、出血和神经损伤的风险有关。许多患者最初 接受腰椎穿刺术(LP)，取脑脊液(CSF)进行细胞学和流式细胞术分析。这些 然而，方法缺乏敏感性，需要大量(10毫升)脑脊液，而且在许多情况下是非诊断性的。 对比剂增强MRI是疾病监测的金标准测试，而且不能发现早期复发或 微小残留病(MRD)导致无法检测出化疗耐药、完全缓解或复发。那里 存在一个未得到满足的需求，不仅需要为PCNSL患者提供更好的治疗选择，而且还需要生物标志物 协助诊断和监测治疗反应。这样的生物标志物在规划中将具有难以置信的重要性。 以及在PCNSL和相关疾病方面进行未来的临床试验。 最近，几种靶向治疗，包括布鲁顿酪氨酸激酶抑制剂(例如，伊布鲁替尼)以及 免疫调节剂(如来那度胺)可显著降低复发率[6-9]。分子 PCNSL对这些新型靶向药物的治疗耐药性的基础在很大程度上是未知的，没有特征性的，并且是一个关键的 翻译研究领域。Safe-SeqS和Real-SeqS技术，提供检测和量化的机会 脑脊液中的肿瘤DNA(CSF-tDNA)，为更好地定性中枢神经系统疾病提供了机会。在这项建议中，我们的目标是 建立可靠的Safe-SeqS和Real-SeqS检测肿瘤来源的循环游离DNA(cf-tDNA)的方法，这将 提高我们诊断和分型PCNSL、纵向监测疾病状态和执行完整外显子组的能力 测序(WES)以确定可以基于基因组识别靶向治疗的患者的分子特征 答复的签名。从完成拟议目标中获得的知识将使 Cf-tDNA作为PNCSL的第一个生物标记物，对于毁灭性的恶性肿瘤来说是一个亟需的进展。

Project Summary Primary central nervous system lymphoma (PCNSL) is a rare and aggressive extranodal non-Hodgkin lymphoma that involves the central nervous system (CNS) without systemic disease. Approximately 1400 cases of PCNSL are diagnosed in the United States annually, classically occurring between the ages of 45 and 65, but the incidence is rising in older patients who represent a population in need of effective therapies with limited adverse effect profiles[1, 2]. Standard frontline therapy consists of high-dose methotrexate (HD-MTX) with autologous stem cell transplant as consolidation therapy. However, these regimens are not tolerated by all patients due to significant neurotoxicity[3]. Even then, about a third of patients are refractory to first-line treatment, and up to 60% of the patients will eventually relapse[4]. Prognosis for patients who are refractory to or relapse after initial therapy is poor, with median survival of only about 1-year failure of upfront therapy[5]. Due to poor long term outcomes, there is a desperate need for improved diagnostic and therapeutic modalities. A considerable hurdle in conducting clinical trials to improve outcomes is the lack of available biomarkers that can be used reliably to diagnose and monitor disease. As such, the diagnosis of PCNSL frequently requires neurosurgical biopsies that are invasive and associated with risk of infection, bleeding and neurological injury. Many patients initially undergo a lumbar puncture (LP) for cerebrospinal fluid (CSF) that is analyzed by cytology and flow cytometry. These approaches, however, lack sensitivity, require large quantities (> 10 mL) of CSF, and are non-diagnostic in many cases. Contrast-enhanced MRI, the gold-standard test of disease monitoring, furthermore, cannot detect early recurrence or minimal residual disease (MRD) leading to an inability to detect chemo-resistance, complete remission, or recurrence. There exists an unmet need not only for better treatment options for patients with PCNSL, but also for biological biomarkers to aid in diagnosis and monitoring of therapeutic response. Such biomarkers would be of incredible importance in planning and executing future clinical trials in PCNSL and related diseases. Recently, several targeted therapies, including Bruton tyrosine kinase inhibitors (e.g., ibrutinib) as well as immunomodulatory agents (e.g., lenalidomide) have shown to dramatically decrease recurrence rate [6-9]. The molecular basis for treatment resistance to these novel targeted agents in PCNSL is largely unknown, uncharacterized and a critical area of translational research. Safe-SeqS and Real-SeqS, technologies that provide an opportunity to detect and quantify tumor DNA in CSF (CSF-tDNA), provide an opportunity to better characterize CNS disease. In this proposal, we aim to develop robust Safe-SeqS and Real-SeqS assays for detection of tumor-derived circulating free DNA (cf-tDNA) which will improve our ability to diagnose and genotype PCNSL, to longitudinally monitor disease status, and to perform whole-exome sequencing (WES) to identify molecular characteristics that can identify patients for targeted therapies based on genomic signatures of response. The knowledge gained from the completion of the proposed Aims would enable the development of cf-tDNA as the first biomarker in PNCSL, a much needed advance for a devastating malignancy.