课题组研究人员引入了周期杂交链反应（HCR），一种将多周期DNA条形码与HCR相结合的方法来克服这一限制。cycleHCR使RNA和蛋白质的高度多路成像成为统一的条形码系统。全胚胎转录组学成像在约310 μm的样品深度上实现了精确的三维基因表达和细胞命运定位。当与扩增显微镜相结合时，cycleHCR揭示了单母胚胎成纤维细胞中10个亚细胞结构的复杂网络。在同主题海马切片中，多重RNA和蛋白质成像揭示了复杂的基因表达梯度和细胞类型特异性核结构变化。cycleHCR为阐明深层组织背景下的空间调节提供了定量框架，用于研究和潜在的诊断应用。
据了解，荧光显微镜中有限的颜色通道长期限制了生物标本的空间分析。
附：英文原文
Title: Deep-tissue transcriptomics and subcellular imaging at high spatial resolution
Author: Valentina Gandin, Jun Kim, Liang-Zhong Yang, Yumin Lian, Takashi Kawase, Amy Hu, Konrad Rokicki, Greg Fleishman, Paul Tillberg, Alejandro Aguilera Castrejon, Carsen Stringer, Stephan Preibisch, Zhe J. Liu
Issue&Volume: 2025-02-20
Abstract: Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and potentially diagnostic applications.
DOI: adq2084
Source: https://www.science.org/doi/10.1126/science.adq2084