RNA-aware tissue preservation workflows for high-quality spatial transcriptomics

Image-based transcriptomic methods are capable of identifying, uncovering, and visualizing cell types and states within various tissues. However, the quality of these measurements is heavily influenced by the integrity of the RNA within the tissue sample. The current tissue preservation techniques were not specifically engineered to safeguard this delicate molecular component.

In this study, the authors utilized MERFISH to demonstrate that discrepancies in endogenous RNase activity, which varies among different tissues, can impact the spatial transcriptomics data quality based on the preservation method employed. Furthermore, they propose a protocol optimization strategy that takes into account the RNase activity to enhance the overall data quality.

Simultaneously, they introduce a novel, RNA-aware approach named Rapid Inhibition and Permanent Inactivation of Nucleases (RIPIN). This method swiftly stabilizes tissue samples by utilizing a broad-spectrum RNase inhibitor, while still allowing for a controlled, chemical inactivation process.

RIPIN is able to generate high-quality MERFISH measurements across a wide range of human and mouse tissue samples, making it compatible with clinical workflows and easily adaptable to frozen or paraffin sectioning techniques. By underscoring the potential loss of RNA integrity during tissue processing, this research suggests the need for future developments in RNA-aware histology methods.