Imaging Mass Cytometry Dataset of exhausted and non-exhausted breast cancer microenvironments

A cohort of human breast tumor samples were annotated as having an "exhausted" or "non-exhausted" immune environment based on CyTOF characterization of T cell phenotypes (see Wagner et al. 2019). 12 samples (6 exhausted, 6 non-exhausted) were then selected for further analysis by Imaging Mass Cytometry (IMC) with the goal to compare the two immune environment types and to comprehensively characterize exhaustion-associated spatial features of the tumor microenvironment. For IMC, two consecutive FFPE sections of each sample were stained with two different antibody panels (Protein Panel and RNAscope Panel), and 4-10 regions of interest (ROIs, 1mm x 1mm) were measured on each section. ROIs on consecutive sections were registered manually to be as spatially close as possible.

本研究队列的人类乳腺肿瘤样本基于T细胞表型的质谱流式细胞术（CyTOF）表征被注释为“耗竭型”或“非耗竭型”免疫微环境（详见Wagner等，2019）。随后选取12例样本（6例为耗竭型免疫微环境，6例为非耗竭型免疫微环境），通过成像质谱流式（Imaging Mass Cytometry, IMC）开展后续分析，以对比两类免疫微环境，并全面解析肿瘤微环境中与免疫耗竭相关的空间特征。在IMC检测流程中，每例样本的两张连续福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）切片分别使用两种不同的抗体标记组合（蛋白标记抗体组合与RNAscope检测组合）进行染色；每张切片上选取4~10个感兴趣区域（Regions of Interest, ROIs，尺寸为1mm×1mm）完成检测。连续切片上的感兴趣区域通过手动配准，以尽可能保证二者空间位置高度重合。