Optimization of Brain Tissue Preservation for Nucleic Acid Stability

Postmortem human brain tissue is an important resource for brain research. Spatial transcriptomics is a novel technology that utilizes formalin-fixed, paraffin-embedded (FFPE) or cryosections, with the former having good cytoarchitecture but poor RNA quality and vice versa for frozen tissue. Sheep brains (n=16) were used to test various protocols that simulate the conditions around the preparation and dissemination of human postmortem FFPE and frozen brain tissue to optimize for future spatial transcriptomic work. FFPE and frozen tissues were investigated for RNA quality, while hematoxylin and eosin-stained cryosections were analyzed by quantifying tissue voids as a proxy for cytoarchitectural integrity. Postmortem interval reduced the RNA integrity number equivalent (RIN^e) of frozen tissue from 7.2 (24 hr) to 4.8 (168 hr). In FFPE tissue, the percentage of RNA fragments greater than 200 nucleotides (DV200) values ranged from 18.9% to 69.01%, with the highest values observed in samples fixed for less than 24 hr. Pretreatment with liquid nitrogen before -80°C storage resulted in the lowest voids (11.6%) in cryosections, but cryoprotectants had little effect. These findings provide researchers with guidelines for tissue preparation in spatial transcriptomics. However, freezing protocols require further refinement to approach the cytoarchitecture of FFPE tissue.