Omic and Multidimensional Spatial Atlas of Metastatic Breast and Prostate Cancers

摘要--总体 我们建议创建一个有机和多维空间(OMS)地图集，使人们能够发现 转移性乳腺癌和前列腺癌患者个体耐药机制的研究 使用当代靶向治疗组合和免疫检查点抑制剂进行治疗。这个 OMS Atlas的动机是这些治疗通常只对转移性肿瘤短暂有效 布景。可能的耐药机制可能是肿瘤细胞固有的或源自不同的 肿瘤细胞生存的微环境。OMS地图集将侧重于阐明这些抗性 三种特定当代临床情景的机制：(A)激素受体阳性的乳腺癌 正在接受CDK4/6抑制剂联合内分泌治疗的(HRBC)，(B)三阴性 接受PARP抑制剂和免疫调节剂治疗的乳腺癌(TNBC)，以及(C) 接受苯扎鲁胺治疗的去势抵抗前列腺癌(CRPC)。我们会做到这一点的 通过四个方面的工作。一个生物检疫单位将前瞻性地收集、管理和纵向分发 临床资料、血液和活组织检查分别来自两个转移性乳腺癌队列和 一个前列腺癌队列将被分析以创建三个OMS图谱。活组织检查将被保存到 启用使用多个表征模式的分析。一个表征股将分析(A)OCT冻结 利用地形单细胞测序(TSCS)和单细胞组合索引ATAC的标本- SEQ(SCI-ATAC-SEQ)以阐明单个细胞中空间定义的基因组变化和染色质可及性， (B)福尔马林固定石蜡包埋(FFPE)标本，采用多重免疫组织化学(MIHC) 评估免疫微环境和循环免疫荧光(CycIF)以评估其成分和 肿瘤细胞及其微环境的分子状态，以及(C)多聚甲醛固定，树脂包埋 用聚焦离子束扫描电子显微镜(FIB-SEM)鉴定(PFRE)样品 4 nm分辨率的2D图像和靶向3D图像的超微结构变化。植物基因组学特征的研究 SMMART计划将提供相同的肿瘤样本。将开发和部署一个数据分析股 用于(A)管理、分析和可视化由原始序列数据和图像组成的第1层数据以生成 单峰Tier 2结果，(B)通过横向映射集成组学和成像数据，以创建单一 时间点肿瘤地图和量化系统肿瘤细胞亚群的生物学功能以生成Tier 3个结果，以及(C)探讨治疗前和治疗后/治疗后肿瘤地图的差异，以揭示 构成第4层结果的阻力。我们将与私营部门合作伙伴合作，评估和采用 提高分析能力和速度并降低成本的下一代技术。行政部门 该股将协助协调、运作、互动和评价海洋监测系统地图集和 在OMS Atlas科学家和Htan之间。

ABSTRACT - Overall We propose to create an Omic and Multidimensional Spatial (OMS) Atlas that will enable discovery of mechanisms of resistance that arise in individual patients with metastatic breast and prostate cancer during treatment with current generation targeted therapeutic combinations and immune checkpoint inhibitors. The OMS Atlas is motivated by the fact that these treatments typically are only transiently effective in the metastatic setting. Possible resistance mechanisms may be intrinsic to the tumor cells or derive from the diverse microenvironments in which the tumor cells live. The OMS Atlas will focus on elucidating these resistance mechanisms in three specific current generation clinical scenarios: (a) hormone-receptor positive breast cancer (HRBC) undergoing treatment with a CDK4/6 inhibitor in combination with endocrine therapy, (b) triple negative breast cancer (TNBC) undergoing treatment with a PARP inhibitor and an immunomodulatory agent, and (c) castration resistance prostate cancer (CRPC) undergoing treatment with enzalutamide. We will accomplish this through work in four areas. A Biospecimen Unit will prospectively collect, manage, and distribute longitudinal clinical information, blood, and biopsies from 20 patients from each of two metastatic breast cancer cohorts and one prostate cancer cohort that will be analyzed to create three OMS Atlases. The biopsies will be preserved to enable analyses using multiple characterization modalities. A Characterization Unit will analyze (a) OCT frozen specimens using Topographic Single Cell Sequencing (TSCS) and Single-cell Combinatorial Indexing ATAC- seq (sci-ATAC-seq) to elucidate spatially defined genomic changes and chromatin accessibility in single cells, (b) formalin fixed, paraffin embedded (FFPE) specimens using multiplex immunohistochemistry (mIHC) to assess the immune microenvironment and cyclic Immunofluorescence (cycIF) to assess the composition and molecular states of tumor cells and their microenvironments, and (c) paraformaldehyde fixed, resin embedded (PFRE) specimens using a Focused Ion Beam Scanning Electron Microscope (FIB-SEM) to identify ultrastructural changes in 2D images and targeted 3D images with 4-nm resolution. Omic characterization of the same tumor samples will be provided by the SMMART Program. A Data Analysis Unit will develop and deploy tools to (a) manage, analyze, and visualize Tier 1 data comprised of raw sequence data and images to generate unimodal Tier 2 results, (b) integrate omics and imaging data through crosswise mapping to create single timepoint tumor maps and quantify systems biological functions of tumor cellular subpopulations to generate Tier 3 results, and (c) explore differences between pre- and on/post-treatment tumor maps to reveal mechanisms of resistance that comprise Tier 4 results. We will collaborate with private sector partners to evaluate and adopt next generation technologies that increase analytical power and speed and reduce costs. The Administrative Unit will facilitate the coordination, operation, interaction, and evaluation of activities within the OMS Atlas and between OMS Atlas scientists and the HTAN.