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

Stephanie Howe1, Heather McCann2, Zherui Xiong3

  • 1Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.

Brain Communications
|November 20, 2025
PubMed
Summary
This summary is machine-generated.

Long-term tissue fixation impacts RNA molecule detection for transcriptomics. Extended fixation hinders gene expression analysis in archived brain tissues, affecting neurodegenerative disease research.

Keywords:
FFPERNAbrain banktissue fixationtranscriptomics

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Area of Science:

  • Neuroscience
  • Molecular Biology
  • Genomics

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are valuable for studying rare diseases.
  • Archived tissues are often stored for extended periods due to practical constraints.

Purpose of the Study:

  • To investigate the impact of long-term tissue fixation on sequencing-based transcriptomics.
  • To assess RNA quality and gene expression in human FFPE tissues with varying fixation durations.

Main Methods:

  • Analysis of human lumbar spinal cord and hypothalamic FFPE tissues from the Sydney Brain Bank.
  • Evaluation of RNA quality metrics (RNA integrity number, DV200) and probe ligation efficiency.
  • Measurement of central nervous system gene expression levels.

Main Results:

  • Extended fixation did not correlate with RNA quality metrics (RNA integrity number, DV200).
  • Fixation duration negatively impacted transcriptome probe ligation and RNA molecule detection.
  • This resulted in reduced measured gene expression, compromising transcriptome interpretability.

Conclusions:

  • Long-term tissue fixation can hinder transcriptomic analysis, impacting the reliability of gene expression data.
  • Standardization and adaptability in brain banking practices are crucial for compatibility with advanced technologies.
  • Collaboration is needed to ensure archived tissues remain suitable for future research.