Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics

The advent of transcriptomics technologies compatible with formalin-fixed paraffin-embedded tissues has enabled greater opportunities for scientists to interrogate the transcriptome of archived tissues, especially those from rare neurodegenerative diseases. Tissues from brain banks are often placed in fixative for weeks or years due to limitations in resources and storage space. We investigated the impact of long-term fixation for sequencing-based transcriptomics in human formalin-fixed paraffin-embedded lumbar spinal cord and hypothalamic tissues sourced from the Sydney Brain Bank. Extended fixation times were not associated with RNA quality metrics, RNA integrity number or DV200. However, fixation duration was associated with poorer ligation of transcriptome probes, leading to poorer detection of RNA molecules. This led to lower measured central nervous system gene expression, severely impacting the interpretability of the transcriptome. The findings of this study underscore the importance of adaptability and standardization among brain banks, especially in the face of rapid technological advancements. There is a need to foster collaborative efforts between researchers, technology providers and brain banks worldwide to ensure tissue compatibility with emerging technologies.