In-patient hospice and rapid autopsy to interrogate tumor heterogeneity

通过快速尸检获取组织为研究原发和广泛转移部位的肿瘤生物学提供了一种有效的方法，这是任何其他方法都不可能实现的。除了肿瘤的异质性，尸检获得的组织还可以对与肿瘤进展相关的继发突变的频率和性质、新的生物标记物和耐药机制产生重要的生物学见解。肿瘤异质性的全面程度和后果可以通过对来自原发灶和转移灶的几个区域的同时核心活检的蛋白质水平的基因改变的深度测序和全局分析以及与临床结果的相关性来评估。据我们所知，在非小细胞肺癌中还没有进行过这样的研究。我们打算从多达十个不同的转移性疾病部位收集肿瘤组织，以研究肿瘤间的异质性。每个部位的最多六个不同的核心将被适当地存储，以询问肿瘤内的异质性。将对这些样本进行下一代测序和深入的基于质谱学的蛋白质组学分析，以分析肿瘤的异质性。我们还将尝试从患者的几个部位产生细胞系，这些细胞株有望成为研究肿瘤异质性和肿瘤生物学的独特试剂。到目前为止，我们已经对4例肺腺癌、1例间皮瘤患者和1例胸腺癌患者进行了快速尸检。我们已经从所有可能的疾病部位收集了肿瘤和正常组织。已从每个发病地点收集了多个岩芯。我们还成功地从其中两名患者的肿瘤组织中培养出了细胞系。我们已经对这六名患者中的一组样本进行了52个外显子组和30个转录组的测序。我们已经对这些数据进行了分析。我们发现每个患者的SNV和CNV具有显著的异质性。最即兴的是，我们发现APOBEC介导的突变是特定患者异质性的主要驱动因素。我们还对这些快速尸检样本进行了基于质谱学的蛋白质组学分析。我们现在正在关联我们的快速尸检患者队列中的基因组和蛋白质组的异质性(包括肿瘤内和肿瘤间)。

Tissue procurement by rapid autopsies provides an effective way to investigate tumor biology of primary and a broad range of metastatic sites in a manner not possible by any other means. In addition to tumor heterogeneity, tissue obtained at autopsy could yield important biologic insights into frequency and nature of secondary mutations associated with tumor progression, novel biomarkers and mechanisms of resistance to treatment. The full extent and consequences of tumor heterogeneity can be evaluated by deep sequencing and global analysis of genetic alterations at the protein level of simultaneous core biopsies from several areas of the primary tumor and metastases and correlation with clinical outcome. To our knowledge, no such studies have been done in NSCLC. We intend to collect tumor tissue from up to ten different sites of metastatic disease to study inter-tumor heterogeneity. Up to six different cores from each site will be stored properly to interrogate intra-tumor heterogeneity. Next generation sequencing and in-depth mass spectrometry-based proteomics analyses will be performed on these samples to assay tumor heterogeneity. We will also attempt to generate cell lines from several sites from a patient that are expected to be unique reagents to study tumor heterogeneity and tumor biology. We have so far performed rapid autopsies on four lung adenocarcinoma, one mesothelioma patient, and one thymic carcinoma patient. We have collected tumor and normal tissues from all possible sites of disease. Multiple cores have been collected from each site of disease. We have also been successful in generating cell lines from tumor tissue of two of these patients. We have completed 52 exome and 30 transcriptome sequencing of a subset of these samples among these six patients. We have analyzed this data. We have uncovered significant heterogeneity in SNV and CNV specific to each patient. Most improtantly, we have discovered that APOBEC-mediated mutagenesis was a major driver of heterogeneity in specific patients. We have also performed mass spectrometry-based proteomics analysis on a seuset of these rapid autopsy samples. We are now correlating the genomic and proteomic heterogeneity (both intra-tumor and inter-tumor) in our cohort of rapid-autopsy patients.