PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Chang, T.; Zhao, S.; Deng, K.; Liao, Z.; Tang, M.; Zhu, Y.; Han, W.; Yu, C.; Fan, W.; Jiang, M.; Wang, G.; Liu, D.; Peng, J.; Pang, Y.; Fei, P.; Wang, J.; Zheng, C.; Huang, Y.

doi:10.1101/2024.06.29.601330

bioRxiv · 10.1101/2024.06.29.601330

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Chang, T.·Zhao, S.·Deng, K.·Liao, Z.·Tang, M.·Zhu, Y.·Han, W.·Yu, C.·Fan, W.·Jiang, M.·Wang, G.·Liu, D.·Peng, J.·Pang, Y.·Fei, P.·Wang, J.·Zheng, C.·Huang, Y.

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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 (FISH) 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 PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

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Chang, T., Zhao, S., Deng, K., Liao, Z., Tang, M., Zhu, Y., Han, W., Yu, C., Fan, W., Jiang, M., Wang, G., Liu, D., Peng, J., Pang, Y., Fei, P., Wang, J., Zheng, C., Huang, Y.. 2024-07-02. PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue. https://doi.org/10.1101/2024.06.29.601330

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