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Assessing Discrepancies in miRNA Profiles of Mouse Blood-Derived Extracellular Vesicles: A Systematic Review of
Md Sorwer Alam Parvez1, Erika Hayakawa2,3, Yoritsugu Iida2
1Department of Psychiatry and Behavioral, Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
Abstract:
We systematically reviewed published studies to assess reproducibility in miRNA expression profiles from extracellular vesicles (EVs) isolated from mouse serum. Our search specifically targeted mouse studies employing precipitation methods for EV isolation from blood and small RNA sequencing of EV-miRNAs in control groups. Out of 53 identified studies, approximately half lacked publicly available raw data, leaving four eligible studies containing sequencing data from a total of 11 mice. miRNA expression counts were standardized using z-scores for comparability. Within individual studies, miRNA profiles showed reasonable consistency; however, significant variability was observed across different studies. Principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and Spearman correlation consistently demonstrated study-specific clustering rather than biological similarity. Methodological discrepancies in EV isolation, RNA extraction protocols, and unreported confounders such as platelet contamination or blood-handling procedures likely contributed to this variability. Our findings emphasize substantial reproducibility challenges in EV-miRNA research across murine studies, highlighting an urgent need for standardized methodologies and transparent reporting to improve reliability of miRNA biomarker discovery and facilitate meta-analytic integration in preclinical research.
Insights
Reproducibility of microRNA (miRNA) profiles from mouse extracellular vesicles (EVs) is challenging. Significant variability across studies hinders reliable biomarker discovery, necessitating standardized methods for preclinical research.
Area of Science:
- Biomedical Research
- Molecular Biology
- Extracellular Vesicle Research
Background:
- MicroRNAs (miRNAs) in extracellular vesicles (EVs) are promising biomarkers.
- Reproducibility of miRNA profiling from mouse serum EVs is critical for preclinical research.
- Current methodologies exhibit significant variability, impacting data reliability.
Purpose of the Study:
- To systematically review and assess the reproducibility of miRNA expression profiles from mouse serum EVs.
- To identify challenges and sources of variability in current EV isolation and miRNA sequencing protocols.
- To emphasize the need for standardized methods in EV-miRNA research.
Main Methods:
- Systematic literature review of mouse serum EV isolation and miRNA sequencing studies.
- Inclusion criteria focused on precipitation methods and control groups.
- Standardization of miRNA expression counts using z-scores for comparability.
- Analysis of data using Principal Component Analysis (PCA), t-SNE, and Spearman correlation.
Main Results:
- Only four eligible studies with data from 11 mice were identified out of 53.
- While within-study consistency was reasonable, significant variability existed across studies.
- Data analysis revealed study-specific clustering, not biological similarity.
- Methodological discrepancies in EV isolation and RNA extraction were identified as likely contributors to variability.
Conclusions:
- Substantial reproducibility challenges exist in mouse EV-miRNA research.
- Variability stems from inconsistent methodologies in EV isolation, RNA extraction, and potential confounders.
- Standardized protocols and transparent reporting are urgently needed for reliable miRNA biomarker discovery and meta-analysis in preclinical studies.
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