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

基本信息

批准号：
10627906
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
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-06-12 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10627906
关键词：
ATAC-seq Aneuploidy Atlases Basement membrane Biological Markers Breast Breast Cancer Patient Carcinoma Cell Line Cell Separation 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 Invaded Knowledge Lead Lesion Macrophage Malignant Neoplasms 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 Tumor Promotion United States National Institutes of Health Work breast cancer progression cancer cell cancer invasiveness cell type clinical diagnostics cohort epigenomics human tissue improved infiltrating duct carcinoma malignant breast neoplasm migration neoplastic cell premalignant programs single cell sequencing single-cell RNA sequencing transcriptional reprogramming transcriptome sequencing transcriptomics tumor tumor initiation tumor microenvironment tumor progression tumor-immune system interactions

项目摘要

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.

项目摘要导管癌原位（DCIS）和非典型导管增生（ADH）是早期早期最常见的形式乳腺癌阶段，是侵入性导管癌（IDC）的非渗透前体。基因组研究乳腺癌前肿瘤的启动和侵袭是知识的主要差距，并且具有由于几个技术障碍，包括管道中的肿瘤细胞数量有限，获得新鲜或冷冻组织的后勤挑战，并且缺乏标准基因组的空间分辨率方法。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具有空间分辨率的DNA，RNA和表观基因组学。我们也有在MD Anderson建立了一个独特的新鲜DCIS组织收集计划，以从DCI中采购可行的细胞手术后直接进行单细胞测序，以克服样品来源中的后勤挑战。在以前的工作中，我们应用了这些方法来研究入侵期间拷贝数的演变同步DCIS-IDC患者，该患者确定了管道中的标点拷贝数演化（PCNE），并且揭示了一种侵袭的多克隆模型（Casasent等，2018，细胞）。该提议将大大扩展这些建议研究肿瘤细胞和乳腺癌前癌进展过程中的微环境。我们的中心假设是进化预先病变的病变需要启动突变和标点的拷贝数演化（PCNE），这是然后在肿瘤细胞中进行转录和表观基因组重编程以及导致的微环境入侵。 AIM1将研究ADH和DCIS中的乳腺肿瘤的启动，而AIM2将重点放在肿瘤上 DCIS和IDC的侵袭以及AIM3将研究肿瘤微环境在DCIS进展中的作用。这些目标中确定的候选突变将在体外功能验证。这些目标的完成将大大提高我们对肿瘤启动和入侵乳腺癌的基本知识进展，可能导致新的生物标志物和诊断方式，以识别ADH和DCIS 将发展为侵入性疾病并且未满足临床需求的患者。我们的长期目标是将单细胞测序技术转化为诊所，在那里它们有望对诊断和治疗前乳腺癌患者。提出的目标是直接对齐的 NIH的任务是减少发病率并改善乳腺癌患者的生活质量早期检测。