SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis II

We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D solid-tumour models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq simultaneously reveals both inter- and intra-cellular signalling in tumour microenvironment organoids. SIGNAL-seq was performed on CRC patient derived organoids (PDOs) +/- CAFs in 3D, and treated +/- SN-38 chemotherapy. This patient-derived 3D model system provides a dynamic range of cell-fates driven by both inter-cellular communication and chemotherapy. Further information on the SIGNAL-seq barcoding layout and processed data can be found at: https://github.com/TAPE-Lab/SIGNAL-seq我们介绍了SIGNAL-seq（基于测序的分池索引信号分析，Split-pool Indexing siGNalling AnaLysis by sequencing）：一种多重分池组合条形码标记方法，可同时对3D实体瘤模型中固定后的单细胞内的RNA与翻译后修饰 (post-translational modifications, PTMs) 进行检测。SIGNAL-seq的翻译后修饰检测结果与质谱流式细胞术 (mass cytometry) 相当，其RNA基因检测则与分池组合条形码标记的单细胞RNA测序 (split-pool barcoding scRNA-seq) 类似。通过同时检测单细胞内的mRNA配体-受体对与翻译后修饰，SIGNAL-seq可同时揭示肿瘤微环境类器官中的细胞间与细胞内信号通路。本研究在3D培养体系下的结直肠癌 (colorectal cancer, CRC) 患者来源类器官 (patient derived organoids, PDOs) 中开展SIGNAL-seq实验，设置添加/不添加癌相关成纤维细胞 (cancer-associated fibroblasts, CAFs) 的组别，并分别施加添加/不添加SN-38化疗药物的处理。该患者来源的3D模型系统可提供由细胞间通讯与化疗共同调控的细胞命运动态变化范围。有关SIGNAL-seq条形码标记方案与处理后数据的更多信息，可访问以下链接：https://github.com/TAPE-Lab/SIGNAL-seq