Molecular, Cellular, and Tissue Characterization Unit

摘要-表征单元 表征单元将负责对所采集的活检样本进行组学和多尺度图像分析 接受以下治疗的转移性乳腺癌和前列腺癌患者的治疗前和治疗中/治疗后 电流生成途径和免疫检查点靶向治疗。成对的活检代表了敏感的 和耐药病变，并对这些病变进行比较分析，可以发现耐药机制。二十 将分析来自三个治疗组的成对样品。具体而言，（a）受体阳性 接受CDK 4/6抑制剂与内分泌疗法联合治疗的乳腺癌（HRBC），（B） 接受PARP抑制剂和免疫调节剂治疗的三阴性乳腺癌（TNBC） 药剂，和（c）经受恩杂鲁胺治疗的去势抵抗性前列腺癌（CRPC）。目标1将 使用拓扑单细胞测序（TSCS）分析OCT冷冻活检，以从空间上分离的细胞 定义的区域，以便能够分析基因组拷贝数变化、突变和插入缺失， 组合索引ATAC-seq（sci-ATAC-seq），用于阐明单细胞中的染色质可及性。细胞 使用sci-ATAC-seq分析的细胞将被计算映射到循环免疫荧光（cycIF）染色的sec- 基于预测的基因表达模式。目的2分析福尔马林固定石蜡包埋（FFPE） 使用多重免疫组织化学（mIHC）和cycIF切片评估肿瘤和基质细胞成分， 位置及其分子状态。此外，使用寡核苷酸标记的抗体的下一代cycIF， 我们将开发出一种能够使用常规和超常规方法进行高维cycIF染色和成像的方法， 分辨率荧光显微镜。目的3将分析多聚甲醛固定，树脂包埋（PFRE）的物种， 使用聚焦离子束扫描电子显微镜（FIB-SEM）来识别 2D图像和目标3D体积，分辨率为4 nm。此外，这方面的工作将评估 连续块面成像SEM（SBFI），用于在较大体积中定义3D超微结构变化，但分辨率较低。 解决方案

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.