Clinical Protocols in the Cancer Signaling Networks Section

方案1：局部消融治疗奥西替尼（AZD9291, Tagrisso）治疗后少进展、egfr突变的非小细胞肺癌（NSCLC）的试点研究项目摘要：我们在该方案中招募了34名患者。16例患者行LAT手术。由于我们在PFS1对奥西替尼耐药前后进行了强制性活组织检查，因此我们制定了蛋白质基因组学分析计划，以确定耐药的关键机制。我们对14例患者治疗前和进展后的肿瘤样本进行了全外显子组测序（WES）和转录组测序（RNAseq）。我们分析了这些数据，发现了对奥西替尼耐药的新机制。我们已经确定了MET扩增、C797S突变、SCLC转化等对奥西替尼耐药的机制。有趣的是，多区域测序揭示了MET扩增的显著异质性。关于这14名患者的数据的手稿正在准备中。方案2：非小细胞肺癌、小细胞肺癌、肺外小细胞癌、肺神经内分泌肿瘤和胸腺上皮肿瘤患者的组织获取和自然史研究。项目总结：本协议正在积极招募。共招募了296名患者。这是唯一一项在我们的胸部肿瘤学诊所为除间皮瘤以外的所有组织学患者进行组织获取的研究，即使患者没有参加NIH的任何治疗方案，他们也可以参加。间皮瘤有单独的治疗方案（PI- Hassan博士）。从该方案中获得的肿瘤组织将用于验证治疗反应和耐药性的潜在生物标志物。候选人将主要来自我们实验室进行的基础和临床前蛋白质组学研究。该方案也将允许在我们诊所进行的所有其他治疗方案的相关研究。方案3：在胸部恶性肿瘤患者中，住院安宁疗护与组织获取的初步研究。项目总结：我们已经根据该方案进行了六次尸检。从患者转移性疾病的不同部位获取肿瘤组织是非常具有挑战性的。然而，这样的组织库是各种研究的独特资源。快速解剖方案可以获得可行的组织，用于产生细胞系，创建患者来源的异种移植物（PDX），并为研究提供适当的储存和固定。这需要与病理学家、疼痛和姑息治疗专家、护士和社会工作者密切合作。美国国立卫生研究院临床中心拥有进行这样一项研究所需的所有资源。访问临床中心的患者也非常积极，经常希望在生命结束时为肿瘤学研究做出贡献。该方案的总体目标是检查各种胸部恶性肿瘤的肿瘤异质性程度及其如何影响靶向治疗反应。提出的蛋白质基因组研究正在我们和我们的合作者在校内项目的实验室中积极进行。我们对这些患者的52个外显子组和30个转录组进行了测序，以询问肿瘤内和肿瘤间的异质性。我们目前正在分析基因组数据。进行下一代测序的相同疾病位点将进行基于质谱的蛋白质组学，以检查蛋白质水平和信号通路的异质性。这些快速尸检样本的基因组学和蛋白质组学研究将相互关联，以获得异质性程度的综合分析以及它如何影响这些患者的治疗反应。我们已经成功地对18名病人进行了尸检。又有1名患者加入了这项研究并接受了随访。方案4：晚期非小细胞肺癌、小细胞肺癌和胸腺恶性肿瘤的分子分析和靶向治疗的试点试验。项目总结：目前，除潜在EGFR种系突变的患者外，所有治疗组的新患者已停止累积。这些患者被纳入并检测EGFR种系突变。我们正在跟踪携带EGFR种系突变T790M的两个家族的几名成员。种系EGFR突变的检测和突变家族的随访将很快成为一个独立的方案。这是一项生物标志物衍生的多臂、多组织学II期“篮子”试验。这项“篮子”试验设计的可行性在试验开始时没有得到适当的评估。该设计评估了靶向剂对特定分子畸变的影响，而不知道组织学背景。使用11个基因的突变或扩增将患者分配到5个生物标志物匹配治疗组中的1个。此外，还利用下一代测序（NGS）技术对200多个基因进行了突变检测。这种针对性测序分析的基础设施在校内项目中是可用的。测序研究在病理学实验室（Mark Raffeld博士）和遗传学分部（Paul Meltzer博士）进行。本方案中的种系EGFR突变患者构成了肺腺癌种系易感性患者的独特亚群。这个国家很少有针对这部分患者的临床方案。与其他地方的种系EGFR突变检测方案不同，我们的方案允许对这些患者进行年度高分辨率CT扫描的临床随访，包括所有必要的干预措施，以跟踪异常扫描。

Protocol 1: A Pilot Study of Local Ablative Therapy for Treatment of Oligoprogressive, EGFR-Mutated, Non-Small Cell Lung Cancer (NSCLC) After Treatment with Osimertinib (AZD9291, Tagrisso) Project summary: We have enrolled 34 patients in this protocol. 16 patients underwent LAT procedure. Since we have mandatory biopsies during PFS1 pre- and post-resistance to osimertinib, we have developed a proteo-genomics analysis plan to identify key mechanisms of resistance.We have conducted whole exome sequencing (WES) and transcriptome sequencing (RNAseq) on pre-treatment and post-progression tumor samples of 14 patients. We have analyzed this data and uncovered novel mechanisms of resistance to osimertinib. We have identified MET amplification, C797S mutation, SCLC transformation among the mechanisms of resistance to osimertinib. Interestingly, significant heterogeneity in MET amplification was uncovered by multi-region sequencing. A manuscript on the data from these 14 patients is in preparation. Protocol 2: Tissue Procurement and Natural History Study of Patients with Non-Small Cell Lung Cancer, Small Cell Lung Cancer, Extrapulmonary Small Cell Cancer, Pulmonary Neuroendocrine Tumors, and Thymic Epithelial Tumors. Project summary: This protocol is actively recruiting. 296 patients have been recruited. This is the only study for tissue procurement in our thoracic oncology clinic for patients of all histologies except mesothelioma in which patients can get enrolled even if they are not enrolled in any treatment protocol at the NIH. There is a separate such protocol for mesothelioma (PI- Dr. Hassan). The tumor tissue acquired from this protocol will be used for validation of potential biomarkers of treatment response and resistance. Candidates will primarily be from the basic and pre-clinical proteomics studies performed in our laboratory. This protocol will also allow correlative studies for all other treatment protocols conducted in our clinic. Protocol 3: A pilot study of inpatient hospice with procurement of tissue on expiration in thoracic malignancies. Project summary: We have performed six autopsies on this protocol. It is quite challenging to acquire tumor tissue from various sites of metastatic disease in patients. However, such a tissue bank is a unique resource for various research studies. A rapid autopsy protocol enables viable tissue procurement for generation of cell lines, creation of patient-derived xenografts (PDX), and proper storage and fixation for research studies. This requires a close collaboration with pathologists, pain and palliative care specialists, nurses and social workers. The NIH Clinical Center has all the resources needed to conduct such a study. The patients who visit the Clinical Center are also very motivated and often want to contribute to research in oncology at the end of their life. The overall goal of this protocol is to examine the extent of tumor heterogeneity in various thoracic malignancies and how it influences targeted treatment response. The proteo-genomic studies proposed are actively being conducted in our and in our collaborators' laboratories within the intramural program. We have performed sequencing of 52 exomes and 30 transcriptomes to interrogate both intra-tumor and inter-tumor heterogeneity in these patients. We are currently analyzing the genomics data. The same sites of disease that underwent next-generation sequencing will undergo mass spectrometry-based proteomics to examine the heterogeneity at the protein level and in signaling pathways. The genomics and the proteomics studies on these rapid autopsy samples will be correlated to get a comprehensive analysis of the extent of heterogeneity and how it may have influenced treatment response in these patients. We have successfully conducted autopsies in 18 patients. 1 more patient is enrolled in this study and being followed. Protocol 4: Pilot trial of molecular profiling and targeted therapy for advanced Non-Small Cell Lung Cancer, Small Cell Lung Cancer, and Thymic malignancies. Project summary: Currently this is closed to accrual for new patients on all treatment arms, except for patients with potential EGFR germline mutations. Such patients are enrolled and tested for EGFR germline mutations. We are following several members of two families harboring the EGFR germline mutation, T790M. The detection of germline EGFR mutation and follow up of families with the mutation will soon be a stand-alone protocol. This is a biomarker derived multi-arm, multi-histology phase II "basket" trial. The feasibility of this "basket" trial design was not assessed properly when this trial was started. This design assesses the effects of a targeted agent against a specific molecular aberration while agnostic of the histologic context. Mutations or amplifications in 11 genes were used to assign patients to 1 of 5 biomarker matched treatment groups. In addition, around 200 genes were tested for mutations by next generation sequencing (NGS) technology. The infrastructure for such targeted sequencing analysis is available in the intramural program. The sequencing studies were performed in the Laboratory of Pathology (Dr. Mark Raffeld) and the Genetics Branch (Dr. Paul Meltzer). Germline EGFR mutant patients in this protocol constitute a unique subset of patients with germline predisposition of lung adenocarcinoma. There are few clinical protocols of this subset of patients in this country. Unlike other protocols elsewhere for germline EGFR mutation detection, our protocol allows clinical follow up of these patients with annual high resolution CT scan, including all interventions necessary to follow abnormal scans.