RNA degradation compromises the reliability of microRNA expression profiling
Abstract
Background: MicroRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression and their expression is frequently altered in human diseases, including cancer. To correlate clinically relevant parameters with microRNA expression, total RNA is frequently prepared from samples that were archived for various time periods in frozen tissue banks but, unfortunately, RNA integrity is not always preserved in these frozen tissues. Here, we investigate whether experimentally induced RNA degradation affects microRNA expression profiles. Results: Tissue samples were maintained on ice for defined time periods prior to total RNA extraction, which resulted in different degrees of RNA degradation. MicroRNA expression was then analyzed by microarray analysis (miCHIP) or microRNA-specific real-time quantitative PCR (miQPCR). Our results demonstrate that the loss of RNA integrity leads to in unpredictability of microRNA expression profiles for both, array-based and miQPCR assays. Conclusion: MicroRNA expression cannot be reliably profiled in degraded total RNA. For the profiling of microRNAs we recommend use of RNA samples with a RNA integrity number equal to or above seven.
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RNA degradation due to prolonged inadequate tissue storage has a random effect on miRNAs and compromises the reliability of miRNA profiles, generating false positive deregulated miRNAs (15).
“Ibberson et al. found that RNA degradation due to prolonged inadequate tissue storage has a random effect on miRNAs and compromises the reliability of miRNA profiles, generating false positive deregulated miRNAs (15).”
From Distribution of miRNA expression across human tissues (2016) · cites this paper as [15]
Even samples with the most degraded RNAs still preserve a tissue-specific miRNA signature (15).
“But they also clearly state that ‘even samples with the most degraded RNAs still preserve a tissue-specific miRNA signature’.”
From Distribution of miRNA expression across human tissues (2016) · cites this paper as [15]
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Distribution of miRNA expression across human tissues
Ludwig, N., Leidinger, P., Becker, K., Backes, C., Fehlmann, T., Pallasch, C., Rheinheimer, S., Meder, B., Stähler, C., Meese, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw116 · Cited by 968 · see citing works
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Braza-Boïls, A., Marí-Alexandre, J., Gilabert, J., Sánchez-Izquierdo, D., España, F., Estellés, A., & Gilabert-Estellés, J. (2014) · Human Reproduction · doi:10.1093/humrep/deu019 · Cited by 164 · see citing works
- Authors
- Ibberson, D., Benes, V., Muckenthaler, M. U., & Castoldi, M.
- Venue
- BMC Biotechnology
- Published
- 2009-12
- Volume
- 9
- Issue
- 1
- ISSN
- 1472-6750
- PMC
- PMC2805631
- Cited by
- 90
- References
- 3
- Language
- en
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