Revolutionizing Deep-Tissue Analysis: High-Resolution Transcriptomics and Subcellular Imaging with cycleHCR

Deep-Tissue Transcriptomics and Subcellular Imaging at Unprecedented Resolution

Understanding the intricate architecture of biological tissues requires advanced imaging techniques capable of providing precise spatial information. Traditional fluorescence microscopy, however, has been limited by the availability of color channels, restricting the simultaneous analysis of multiple molecular targets. Overcoming this significant challenge, researchers have developed the cycle Hybridization Chain Reaction (cycleHCR)—a groundbreaking method that combines multicycle DNA barcoding with the Hybridization Chain Reaction (HCR).

What is cycleHCR?

cycleHCR represents a new era in deep-tissue imaging. By integrating a unified DNA barcode system with HCR, this technique allows the highly multiplexed imaging of both RNA and proteins. The result is a comprehensive, three-dimensional view of gene expression and protein distribution across complex tissue samples. Unlike traditional methods limited by spectral overlap, cycleHCR uses iterative labeling and stripping cycles, significantly expanding the number of molecular targets that can be visualized in a single specimen.

Key Breakthroughs with cycleHCR

1. Whole-Embryo Transcriptomics with 3D Precision:

cycleHCR has been successfully used to perform whole-embryo imaging, mapping gene expression patterns and cell fate decisions with remarkable three-dimensional accuracy. This was achieved across a specimen depth of approximately 310 μm, highlighting the method’s potential for deep-tissue applications previously unattainable with conventional imaging techniques.

2. Subcellular Structure Visualization:

When paired with expansion microscopy—a process that physically enlarges biological samples—cycleHCR enabled researchers to visualize an intricate network of ten distinct subcellular structures within mouse embryonic fibroblasts. Such detailed subcellular imaging provides critical insights into cellular organization and function, which could advance our understanding of developmental biology and disease mechanisms.

3. Insights into Brain Tissue Organization:

In another application, cycleHCR was used to study mouse hippocampal brain slices. This revealed complex gene expression gradients and cell-type-specific nuclear structural variations, offering a window into the spatial organization of neural tissues. Such insights are invaluable for neuroscience research, where understanding the molecular and structural diversity of brain cells is essential for deciphering neural function and dysfunction.

Potential Research and Diagnostic Applications

The ability of cycleHCR to provide quantitative, high-resolution spatial maps of gene and protein expression opens new avenues in both basic and applied biomedical research. In the realm of diagnostics, this technique could facilitate the identification of disease-specific spatial biomarkers, enabling early detection and personalized treatment strategies for complex diseases such as cancer and neurological disorders.

Conclusion

The development of cycleHCR marks a pivotal moment in the field of biological imaging. By overcoming the longstanding limitations of fluorescence microscopy, cycleHCR provides a robust, scalable, and highly multiplexed approach for deep-tissue transcriptomics and subcellular imaging. With its potential to unravel complex spatial regulatory mechanisms in tissues, cycleHCR is poised to become a vital tool for advancing research and improving diagnostic precision in the years to come.

Source : https://www.science.org/doi/10.1126/science.adq2084