Molecular, Cellular, and Tissue Characterization Unit

抽象--定性单位 特定股将负责对所采集的活体组织进行基因组和多尺度图像分析。 转移性乳腺癌和前列腺癌患者接受联合治疗前后的治疗情况 当代途径和免疫检查点靶向治疗。配对的活组织检查代表着敏感 而耐药损伤和对它们的比较分析使发现耐药机制成为可能。二十 将对来自三个治疗队列的样本进行分析。具体地说，(A)激素受体阳性 接受CDK4/6抑制剂联合内分泌治疗的乳腺癌(HRBC)，(B) 接受PARP抑制剂和免疫调节剂治疗的三阴性乳腺癌 (C)接受苯扎鲁胺治疗的耐阉割前列腺癌(CRPC)。目标1将 空间分离细胞的拓扑单细胞测序分析OCT冰冻活检组织 能够分析基因组拷贝数变化、突变、INDELs和单细胞的特定区域 组合索引atac-seq(sci-atac-seq)以阐明单个细胞中染色质的可及性。这些细胞 使用SCI-ATAC-SEQ进行分析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的基因序列。目标2将分析福尔马林固定石蜡包埋(FFPE) 切片采用多重免疫组织化学(MIHC)和细胞周期因子(CycIF)评估肿瘤和基质细胞成分。 位置及其分子状态。此外，下一代CycIF使用标记抗BOD的寡核苷酸- 将开发IES以实现高维CycIF染色和成像，使用常规和超 分辨率荧光显微镜。AIM 3将分析多聚甲醛固定树脂嵌入物(PFRE)- 用聚焦离子束扫描电子显微镜(FIB-SEM)观察MERS的超微结构变化 具有4纳米分辨率的2D图像和目标3D体积。此外，在这一目标方面的工作将评估 序列块面部成像扫描(SBFI)，以确定较大体积的3D超微结构变化，但在较低分辨率- 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.