DELINEATING THE EVOLUTION AND ECOLOGY OF CHEMORESISTANCE IN BREAST CANCER WITH SINGLE CELL GENOMICS

项目总结 三阴性乳腺癌(TNBC)是一种侵袭性亚型，患者表现为广泛的肿瘤内。 基因组异质性和经常(50%)对新辅助化疗(NAC)产生耐药性 会导致转移性疾病和死亡。由于缺乏激素受体和靶向治疗， 患有难治性疾病的TNBC患者的治疗选择往往有限。目前，我们的理解是 肿瘤细胞基因组进化和肿瘤微环境在化疗耐药疾病中的作用 在初级和转移性器官部位，这是这项提案旨在解决的知识方面的一个重大差距。 我们团队已经开发出尖端的单细胞DNA和RNA测序技术，可以克服 以往研究基因组和蛋白质组的“批量”基因组方法的技术障碍和局限性 肿瘤细胞对化疗反应的表型演变。我们的初步数据中有一小部分 TNBC患者提示，化疗耐药的基因组进化是通过适应性选择 先前存在的突变和拷贝数改变，随后是转录重新编程，以 获得耐药表型(Kim等人)。2018年，细胞)。我们进一步假设转录 肿瘤微环境中细胞类型的重新编程发生在化疗耐药疾病中， 耐药性程序是在远处转移的器官部位克隆遗传的。全面排查 在大型新辅助化疗中来自TNBC患者的配对纵向样本中的这些问题 试验(Artemis)，我们提出了三个协同目标：目标1将决定拷贝数偏差(CNA) 与化疗耐药相关的亚克隆突变是预先存在的，并在响应中适应性地选择 去接受治疗。Aim 2将研究微环境中的肿瘤细胞和细胞类型是否经历转录 在难治性疾病中重新编程。目标3将确定原代细胞中的抗性细胞亚群 肿瘤播撒转移灶，并在远处器官部位提供耐药方案.完成这些工作 AIMS将确定TNBC患者化疗耐药的基因组和进化基础，并将提供新的 克服化疗耐药疾病的诊断生物标志物和治疗目标，这是一个关键的未实现的目标 临床需要。我们的长期目标是将单细胞测序技术转化为临床，在那里他们 将对乳腺癌患者的诊断和治疗产生重大影响。建议数 目标直接与NIH减少发病率和提高乳房生活质量的使命相一致 癌症患者。

PROJECT SUMMARY Triple-negative breast cancer (TNBC) is an aggressive subtype in which patients display extensive intratumor genomic heterogeneity and frequently (50%) develop resistance to neoadjuvant chemotherapy (NAC) which leads to metastatic disease and death. Due to the absence of hormonal receptors and targeted therapies, TNBC patients with refractory disease are often left with limited treatment options. Currently, our understanding of the genomic evolution of tumor cells and the role of the tumor microenvironment in chemoresistant disease at primary and metastatic organ sites represents a major gap in knowledge that this proposal aims to address. Our group has developed cutting-edge single cell DNA and RNA sequencing technologies that can overcome previous technical barriers and limitations with `bulk' genomic methods for studying the genomic and phenotypic evolution of tumor cells in response to chemotherapy. Our preliminary data in a small number of TNBC patients suggests that genomic evolution of chemoresistance occurs through the adaptive selection of pre-existing mutations and copy number alterations, which is followed by transcriptional reprogramming, to achieve a chemoresistant phenotype (Kim et al. 2018, Cell). We further hypothesize that transcriptional reprogramming of cell types in the tumor microenvironment occurs in chemoresistant disease and that resistance programs are clonally inherited at distant metastatic organ sites. To comprehensively investigate these questions in matched longitudinal samples from TNBC patients in a large neoadjuvant chemotherapy trial (ARTEMIS), we propose three synergistic aims: Aim 1 will determine if copy number aberrations (CNAs) and subclonal mutations associated with chemoresistance are pre-existing and adaptively selected in response to therapy. Aim 2 will investigate if tumor cells and cell types in the microenvironment undergo transcriptional reprogramming in refractory disease. Aim 3 will determine if subpopulations of resistant cells in the primary tumor seed the metastatic lesions and confer resistance programs at distant organ sites. Completion of these aims will define the genomic and evolutionary basis of chemoresistance in TNBC patients and will provide new diagnostic biomarkers and therapeutic targets for overcoming chemoresistant disease, which is a critical unmet clinical need. Our long-term goal is to translate single cell sequencing technologies into the clinic, where they are poised to have a major impact on the diagnosis and treatment of breast cancer patients. The proposed aims are directly aligned with the mission of NIH to reduce morbidity and improve the quality of life for breast cancer patients.