北京大学黄岩谊研究小组提出了使用彩色强度条形码的常规显微镜进行一轮高plex空间RNA成像。2025年10月30日出版的《自然—生物技术》杂志发表了这项成果。

该团队介绍了“通过单轮成像对RNA进行原位分析”（PRISM），这是一种通过颜色强度分级扩大编码容量的方法。PRISM使用径向矢量滤波策略来确保码字在颜色空间中的可分辨性，在常规显微镜的单个成像轮中实现多达64位彩色条形码RNA成像。为了验证PRISM在不同组织中的多功能性，课题组人员制作了从E12.5到E14.5的同位胚胎发育的三维图谱、人肝癌肿瘤-正常过渡的准三维图谱以及同位大脑的三维细胞图谱和亚细胞RNA定位图谱。此外，该研究组展示了癌症相关成纤维细胞在肿瘤微环境内和肿瘤微环境之间介导免疫浸润和免疫反应异质性中的关键作用。

据介绍，空间RNA成像尚未被广泛采用，因为传统的荧光显微镜仅限于几个通道，并且在诸如序列荧光原位杂交等技术中增加多路复用所需的循环反应需要复杂的仪器。

附：英文原文

Title: High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes

Author: Chang, Tianyi, Zhao, Shihui, Deng, Kunyue, Liao, Zhizhao, Tang, Mingchuan, Zhu, Yanxi, Han, Wuji, Yu, Chenxi, Fan, Wenyi, Jiang, Mengcheng, Wang, Guanbo, Liu, Dongfang, Peng, Jirun, Pang, Yuhong, Fei, Peng, Wang, Jianbin, Zheng, Chunhong, Huang, Yanyi

Issue&Volume: 2025-10-30

Abstract: Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in situ hybridization require sophisticated instrumentation. Here, we introduce ‘profiling of RNA in situ through single-round imaging’ (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISM’s versatility across various tissues by generating a three-dimensional (3D) atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor–normal transition landscape of human hepatocellular carcinoma and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

DOI: 10.1038/s41587-025-02883-7

Source: https://www.nature.com/articles/s41587-025-02883-7