INVESTIGATING TUMOR INITIATION AND INVASION IN PREMALIGNANT BREAST CANCER WITH SPATIAL SINGLE CELL GENOMICS

利用空间单细胞基因组学研究癌前乳腺癌的肿瘤发生和侵袭

• 批准号: 10407042
• 负责人: Nicholas Navin
• 金额: $ 35.87万
• 依托单位: UNIVERSITY OF TX MD ANDERSON CAN CTR
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-12 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10407042
• 关键词: ATAC-seq; Aneuploidy; Atlases; Basement membrane; Biological Markers; Breast; Breast Cancer Patient; Carcinoma; Cell Line; Cell Survival; Cells; Clinic; Clinical; Clinical Research; Complex; DNA; DNA Sequence Alteration; DNA sequencing; Diagnosis; Diagnostic; Diploidy; Disease; Duct (organ) structure; Early Diagnosis; Ecosystem; Endothelial Cells; Epithelial Cells; Event; Evolution; Fibroblasts; Freezing; Genes; Genetic Transcription; Genome; Genomics; Goals; Grant; Immune; In Situ Lesion; In Vitro; Intraductal Hyperplasia; Knowledge; Lead; Lesion; Logistics; Mammary Neoplasms; Methods; Mission; Modality; Modeling; Molecular; Morbidity - disease rate; Mutation; Myoepithelial cell; Noninfiltrating Intraductal Carcinoma; Operative Surgical Procedures; Patients; Phenotype; Process; Quality of life; RNA; Research Personnel; Resolution; Role; Sampling; Source; Spatial Distribution; Stromal Cells; T-Lymphocyte; Technology; Tissue Banks; Tissues; Translating; Tumor Cell Invasion; United States National Institutes of Health; Work; XCL1 gene; breast cancer progression; cancer cell; cancer invasiveness; cell type; clinical diagnostics; cohort; epigenomics; human tissue; improved; infiltrating duct carcinoma; macrophage; malignant breast neoplasm; neoplastic cell; premalignant; programs; single cell sequencing; transcriptional reprogramming; transcriptome sequencing; transcriptomics; tumor; tumor initiation; tumor microenvironment; tumor progression; tumor-immune system interactions

PROJECT SUMMARY Ductal Carcinoma in situ (DCIS) and Atypical Ductal Hyperplasia (ADH) are the most common forms of early- stage breast cancer and are non-obligatory precursors to invasive ductal carcinoma (IDC). Genomic studies of tumor initiation and invasion in premalignant breast cancer represents a major gap in knowledge and have been challenging due to several technical barriers, including the limited number of tumor cells in the ducts, the logistical challenge of obtaining fresh or frozen tissues, and the lack of spatial resolution in standard genomic methods. To overcome these challenges, we have developed cutting-edge single cell sequencing methods to profile DNA, RNA and Epigenomics with spatial-resolution in human tissue sections. We have also established a unique fresh DCIS tissue collection program at MD Anderson to procure viable cells from DCIS patients directly after surgery for single cell sequencing to overcome logistical challenges in sample sources. In our previous work, we applied these methods to study copy number evolution during invasion in synchronous DCIS-IDC patients, which identified punctuated copy number evolution (PCNE) in the ducts and revealed a multi-clonal model of invasion (Casasent et al. 2018, Cell). This proposal will greatly extend these initial studies to study mutational, epigenomic and transcriptional reprogramming in the tumor cells and the microenvironment during premalignant breast cancer progression. Our central hypothesis is that the evolution of premalignant lesions requires initiating mutations and punctuated copy number evolution (PCNE), which is followed by transcriptional and epigenomic reprogramming in tumor cells and the microenvironment that leads to invasion. AIM1 will investigate breast tumor initiation in ADH and DCIS, while AIM2 will focus on tumor invasion in DCIS and IDC, and AIM3 will study role of the tumor microenvironment in DCIS progression. Candidate mutations identified in these aims will be functionally validated in vitro. Completion of these aims will greatly improve our fundamental knowledge of tumor initiation and invasion in premalignant breast cancer progression, which may lead to new biomarkers and diagnostic modalities for identifying ADH and DCIS patients that will progress to invasive disease and is critical unmet clinical need. Our long-term goal is to translate single cell sequencing technologies into the clinic, where they are poised to make a major impact on the diagnosis and treatment of premalignant 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 through early detection.

项目概要 导管原位癌 (DCIS) 和非典型导管增生 (ADH) 是早期最常见的形式 分期乳腺癌，并且是浸润性导管癌 (IDC) 的非必然前兆。基因组研究 癌前乳腺癌的肿瘤发生和侵袭代表了知识上的重大差距，并且已经 由于一些技术障碍，包括导管中肿瘤细胞数量有限、 获取新鲜或冷冻组织的后勤挑战，以及标准基因组缺乏空间分辨率 方法。为了克服这些挑战，我们开发了尖端的单细胞测序方法 在人体组织切片中以空间分辨率分析 DNA、RNA 和表观基因组学。我们还有 在 MD 安德森建立了独特的新鲜 DCIS 组织采集计划，以从 DCIS 获取活细胞 手术后直接对患者进行单细胞测序，以克服样本来源的后勤挑战。 在我们之前的工作中，我们应用这些方法来研究入侵过程中的拷贝数进化 同步 DCIS-IDC 患者，识别导管中的间断拷贝数进化 (PCNE) 揭示了一种多克隆入侵模型（Casasent et al. 2018，Cell）。该提案将大大扩展这些 初步研究肿瘤细胞中的突变、表观基因组和转录重编程以及 乳腺癌癌前进展期间的微环境。我们的中心假设是进化 癌前病变的发生需要起始突变和间断拷贝数进化（PCNE），这是 其次是肿瘤细胞中的转录和表观基因组重编程以及导致的微环境 来入侵。 AIM1 将研究 ADH 和 DCIS 中的乳腺肿瘤起始，而 AIM2 将重点研究肿瘤 DCIS 和 IDC 的侵袭，AIM3 将研究肿瘤微环境在 DCIS 进展中的作用。 在这些目标中确定的候选突变将在体外进行功能验证。完成这些目标 将极大地提高我们对癌前乳腺癌肿瘤发生和侵袭的基础知识 进展，这可能会产生新的生物标志物和诊断模式来识别 ADH 和 DCIS 将进展为侵袭性疾病且临床需求未得到满足的关键患者。我们的长期目标是 将单细胞测序技术转化为临床，它们有望对以下领域产生重大影响： 乳腺癌患者的癌前诊断和治疗。拟议的目标直接一致 NIH 的使命是通过以下方式降低乳腺癌患者的发病率并提高其生活质量 及早发现。