RNA-aware tissue preservation workflows for high-quality spatial transcriptomics
- 1Boston Children's Hospital
Abstract
Image-based transcriptomic approaches can define, discover, and chart cell types and states within an array of tissues. However, measurement quality depends on RNA integrity, and the modern tissue preservation toolbox was not designed to protect this highly labile molecule. Here we leverage MERFISH to show that tissue-dependent differences in endogenous RNase activity can shape spatial transcriptomics data quality for different preservation methods and that RNase-activity-guided protocol optimization can improve data quality. In parallel, we introduce an RNA-aware pan-tissue preservation approach, Rapid Inhibition and Permanent Inactivation of Nucleases (RIPIN), that rapidly stabilizes samples with a broad-spectrum RNase inhibitor while permitting slow, chemical inactivation. RIPIN produces high-quality MERFISH measurements in all profiled human and mouse tissues, is compatible with clinical workflows, and is easily integrated with frozen or paraffin sectioning. By highlighting how RNA integrity can be lost during tissue processing, our work may inspire the next generation of RNA-aware histology methods.
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BibTeX
@misc{cadinu2026rnaaware,
title = {{RNA-aware tissue preservation workflows for high-quality spatial transcriptomics}},
author = {P. Cadinu and C. A. Reardon-Lochbaum and H. Zhang and K. Kalemaki and B. R. Watson and S. Smirnakis and S. B. Snapper and A. B. Cantor and J. R. Moffitt},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.07.749899},
url = {https://www.biorxiv.org/content/10.64898/2026.09.07.749899v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - RNA-aware tissue preservation workflows for high-quality spatial transcriptomics
AU - P. Cadinu
AU - C. A. Reardon-Lochbaum
AU - H. Zhang
AU - K. Kalemaki
AU - B. R. Watson
AU - S. Smirnakis
AU - S. B. Snapper
AU - A. B. Cantor
AU - J. R. Moffitt
PY - 2026
DA - 2026/09/07
PB - bioRxiv
DO - 10.64898/2026.09.07.749899
UR - https://www.biorxiv.org/content/10.64898/2026.09.07.749899v1
AB - Image-based transcriptomic approaches can define, discover, and chart cell types and states within an array of tissues. However, measurement quality depends on RNA integrity, and the modern tissue preservation toolbox was not designed to protect this highly labile molecule. Here we leverage MERFISH to show that tissue-dependent differences in endogenous RNase activity can shape spatial transcriptomics data quality for different preservation methods and that RNase-activity-guided protocol optimization can improve data quality. In parallel, we introduce an RNA-aware pan-tissue preservation approach, Rapid Inhibition and Permanent Inactivation of Nucleases (RIPIN), that rapidly stabilizes samples with a broad-spectrum RNase inhibitor while permitting slow, chemical inactivation. RIPIN produces high-quality MERFISH measurements in all profiled human and mouse tissues, is compatible with clinical workflows, and is easily integrated with frozen or paraffin sectioning. By highlighting how RNA integrity can be lost during tissue processing, our work may inspire the next generation of RNA-aware histology methods.
ER -