Spatial and single cell analysis of tumor microenvironment by seqFISH+

摘要 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 对化疗有抵抗力。有各种不同类型的细胞，可以在 肿瘤微环境，其中许多尚未完全列举。此外，几乎没有 了解肿瘤的“地理”和不同细胞类型的空间组织。 因此，迫切需要变革性的工具来实现深入的理解 TME在多种形式的恶性肿瘤中的表现。 空间基因组公司正在将seqFISH商业化(Eng等人，自然，2019)，它可以实现 具有空间信息的组织单细胞中10,000个基因在mRNA水平上的多重表达 保存完好。利用seqFISH转录组图谱，原位和空间上新的细胞类型 可以在肿瘤组织切片中直接识别和可视化组织。 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。在这个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。与安进和洛杉矶儿童医院(CHLA)合作，我们将申请 SeqFISH在小鼠模型系统和人类中成像肿瘤微环境 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.