Molecular, Cellular, and Tissue Characterization Unit

分子、细胞和组织表征单元

基本信息

批准号：
10246896
负责人：
JOE W. GRAY
金额：
$ 74.64万
依托单位：
OREGON HEALTH & SCIENCE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-19 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10246896
关键词：
3-Dimensional ATAC-seq Aftercare Antibodies Antigen Presentation Architecture Atlases Biopsy CDK4 gene Cells Chemicals Chromatin Collection Cost Control Detection Disseminated Malignant Neoplasm Drug Targeting Event Extracellular Matrix Face Fluorescence Fluorescence Microscopy Formalin Freezing Gene Expression Profile Generations Genome Genomic Instability Genomics Goals Human Image Image Analysis Immune Immune checkpoint inhibitor Immunofluorescence Immunologic Immunohistochemistry Immunomodulators Individual Ions Label Lesion Malignant Neoplasms Malignant neoplasm of prostate Maps Mechanics Metastatic breast cancer Molecular Mutation Oligonucleotides Paraffin Embedding Pathway interactions Patients Periodicity Pharmaceutical Preparations Plant Resins Primary Neoplasm Production Radiology Specialty Resistance Resolution Sampling Scanning Electron Microscopy Signal Transduction Specimen Stains Stromal Cells Technology Therapeutic Time Tissues Work base cancer cell castration resistant prostate cancer cohort combinatorial comparative drug efficacy epigenome epigenomics exhaustion high dimensionality hormone receptor-positive hormone therapy immune checkpoint improved indexing individual patient inhibitor/antagonist insertion/deletion mutation malignant breast neoplasm molecular imaging neoplastic cell next generation paraform prospective resistance mechanism single cell sequencing targeted treatment technology development triple-negative invasive breast carcinoma tumor tumor-immune system interactions

项目摘要

ABSTRACT – Characterization Unit The Characterization Unit will be responsible for omic and multiscale image analyses of pairs of biopsies taken pre- and on/post treatment from patients with metastatic breast and prostate cancer undergoing treatment with current generation pathway and immune checkpoint targeted treatments. The paired biopsies represent sensitive and resistant lesions and comparative analyses of these enable discovery of mechanisms of resistance. Twenty pairs of samples each from three treatment cohorts will be analyzed. Specifically, (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 resistant prostate cancer (CRPC) undergoing treatment with enzalutamide. Aim 1 will analyze OCT frozen biopsies using Topographic Single Cell Sequencing (TSCS) to cells isolated from spatially defined regions to enable analysis of genomic copy number changes, mutations, and indels and Single-cell Combinatorial Indexing ATAC-seq (sci-ATAC-seq) to elucidate chromatin accessibility in single cells. The cells analyzed using sci-ATAC-seq will be computationally mapped to cyclic immunofluorescence (cycIF) stained sec- tions based on predicted gene expression patterns. Aim 2 will analyze formalin-fixed paraffin embedded (FFPE) sections using multiplex immunohistochemistry (mIHC) and cycIF to assess the tumor and stromal cell compo- sition and the molecular states thereof. In addition, next generation cycIF using oligonucleotide labeled antibod- ies will be developed to enable high dimension cycIF staining and imaging using both conventional and super resolution fluorescence microscopy. Aim 3 will analyze paraformaldehyde fixed, resin embedded (PFRE) speci- mens using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) to identify ultrastructural changes in 2D images and targeted 3D volumes with 4-nm resolution. In addition, work in this aim will assess the utility of Serial Block Face Imaging SEM (SBFI) to define 3D ultrastructural changes in larger volumes, but at lower res- olution.

摘要 - 表征单元表征单元将负责对成对的活检对的OMIC和多尺度图像分析接受转移性乳腺癌和前列腺癌患者的治疗前后/治疗当前一代途径和免疫检查点目标治疗。配对的活检表示敏感这些抗性病变以及这些能够发现抗性机制的比较分析。二十将分析来自三个治疗队列的样品对。具体而言，（a）同性受体阳性乳腺癌（HRBC）接受CDK4/6抑制剂与内分泌疗法结合治疗，（b）三重阴性乳腺癌（TNBC）接受PARP抑制剂和免疫调节治疗药物，（c）接受enzalutamide治疗的抑制前列腺癌（CRPC）。目标1意志使用地形单细胞测序（TSC）分析OCT冷冻活检到从空间分离的细胞定义的区域以启用基因组拷贝数变化，突变和indels和单细胞的分析组合索引ATAC-SEQ（SCI-ATAC-SEQ）阐明单个细胞中的染色质可及性。细胞使用SCI-ATAC-SEQ分析将在计算上映射到环状免疫荧光（CYCIF）染色的SEC- 基于预测的基因表达模式。 AIM 2将分析福尔马林固定石蜡嵌入（FFPE）使用多重免疫组织化学（MIHC）和CYCIF的切片评估肿瘤和基质细胞综合此外，使用寡核苷酸标记的抗体 - 将开发IE，以实现使用常规和超级的高维cycif染色和成像分辨率荧光显微镜。 AIM 3将分析固定固定的嵌入树脂（PFRE）的多聚甲醛（PFRE）。使用聚焦离子束扫描电子显微镜（FIB-SEM）的男士确定超微结构的变化 2D图像和针对4 nm分辨率的目标3D体积。此外，以此目的的工作将评估串行块面成像SEM（SBFI）以定义较大体积的3D超微结构变化，但在较低的res- outure。