Widespread choroid plexus contamination in sampling and profiling of brain tissue

Area of Science:

• Neuroscience
• Molecular Biology
• Genomics

Background:

• The choroid plexus produces cerebrospinal fluid and is composed of vascularized, ciliated epithelial cells.
• Its complex structure can lead to contamination during brain tissue dissection for omic studies.
• Canonical choroid plexus markers include Ttr, Folr1, and Prlr.

Purpose of the Study:

• To investigate the prevalence and impact of choroid plexus contamination in transcriptomic brain tissue studies.
• To identify brain regions and datasets most susceptible to choroid plexus contamination.
• To provide recommendations for mitigating and addressing choroid plexus contamination in research.

Main Methods:

• Utilized the Ttr gene as a marker to query the Gene Expression Omnibus (GEO) database for transcriptome studies.
• Analyzed human transcriptomic datasets from the Allen Brain Atlas and Genotype-Tissue Expression (GTEx) database.
• Performed differential gene expression analysis between high and low contamination groups to identify enriched pathways.

Main Results:

• Identified likely choroid plexus contamination in numerous brain tissue transcriptome studies.
• Found abundant contamination in datasets from Allen Brain Atlas and GTEx, particularly in regions near the choroid plexus.
• Observed enrichment of choroid plexus marker genes and relevant gene ontology pathways in contaminated samples.

Conclusions:

• Choroid plexus contamination is a significant, unrecognized issue in neuroscience research that can confound data analysis and interpretation.
• Researchers should consider assessing and potentially removing contaminated samples or incorporating marker gene expression into statistical models.
• Simple validation methods like RT-qPCR or Western blot for choroid markers are recommended to prevent contamination in omic profiling.