Spatial and single cell analysis of tumor microenvironment by seqFISH+

总结 肿瘤微环境（TME）是肿瘤生长、疾病进展和预后的关键决定因素。 对化疗的抵抗力。存在不同细胞类型的多样性库， 肿瘤微环境，其中许多尚未完全枚举。此外， 已知肿瘤的“地理”和不同细胞类型的空间组织。 因此，迫切需要变革性工具，以便能够深入了解 TME在多种恶性肿瘤中的作用。 Spatial Genomics Inc正在商业化seqFISH+（Eng et al，Nature 2019），其可以实现 在具有空间信息的组织中的单个细胞中在mRNA水平上多路复用10，000个基因 保存。使用seqFISH+转录组谱，原位和空间的新细胞类型 组织可以在肿瘤组织切片中直接识别和可视化。 这些功能使seqFISH+成为检查不同细胞类型及其 肿瘤微环境中的相互作用。在这项SBIR提案中，我们将开发一种工具， 以及相关的软件和试剂，使研究人员能够在 肿瘤切片我们将与安进和洛杉矶儿童医院（CHLA）合作， seqFISH+对小鼠模型系统和人肿瘤微环境进行成像 儿童神经母细胞瘤样本。

SUMMARY Tumor microenvironment (TME) is a key determinant of tumor growth, disease progression and resistance to chemotherapy. There is a diverse repertoire of distinct cell type that are found in the tumor microenvironment, with many that have not been fully enumerated. In addition, little is known about the “geography” of the tumors and the spatial organization of the distinct cell types. There is therefore, an immediate need of transformative tools to enable in-depth understanding of the TME in many forms of malignancies. Spatial Genomics Inc is commercializing seqFISH+ (Eng et al, Nature 2019) which can achieves multiplexing of 10,000 genes at the mRNA level in single cells in tissues with spatial information preserved. Using the seqFISH+ transcriptome profiles, novel cells types in situ and spatial organizations can be directly identified and visualized in tumor tissue slices. These capabilities make seqFISH+ a powerful tool for examining the different cell types and their interactions in the tumor microenvironment. In this SBIR proposal, we will develop an instrument and the associated software and reagents that will allow researchers to perform seqFISH+ in tumor slices. In collaboration with Amgen and Children’s Hospital at LA (CHLA), we will apply seqFISH+ to image the tumor microenvironment in both mouse model systems and human pediatric neuroblastoma samples.