Selective under-representation of transcripts encoding membrane-integrated architectures following neural tissue vitrification

Cryopreservation is essential for long-term storage of biological tissues. Yet, surprisingly, the impact of cryopreservation on tissue transcriptomes remains poorly defined. This study used bulk RNA sequencing to examine how preservation method (snap freezing or vitrification) affects transcriptomes in mouse cerebral cortex and hippocampus. Tissues processed under vitrification condition showed selective under-representation of a small but structurally coherent group of transcripts, with the hippocampus exhibiting greater vulnerability than the cortex. UniProt annotation revealed that affected transcripts were strongly enriched for proteins with membrane-associated, secretory-pathway, and multi-pass topologies, indicating that structurally complex membrane-integrated architectures could be disproportionately sensitive to vitrification. Pathway-level analysis using iPANDA further showed that negative preservation scores in vitrified tissue clustered primarily within signal transduction and metabolic pathways, suggesting coordinated pathway-level disruption rather than global transcript loss. This work highlights molecular vulnerability during vitrification and emphasizes the need for transcript-level evaluation when optimizing cryopreservation approaches for neural system.