Limiting or filtering – what’s the better strategy for microRNA discovery?


Mature microRNAs are the master regulators of gene expression and exhibit prominent roles in both normal and disease biologic processes. Since Victor Ambros and colleagues discovered the first miRNA in 1993, the microRNA universe has rapidly expanded. As of miRBase ( V21, there are 35,828 microRNAs across 223 species! For human alone, there are an astounding 2588 annotated mature microRNAs. As one microRNA can target multiple mRNAs or one mRNA can be targeted by multiple microRNAs, one can truly appreciate the diverse and complex contribution of miRNA to human biology, and understand at the same time that there is still great potential for novel discoveries.

This brings up an important question. In discovery-based microRNA experiments, such as circulating biomarker studies, should you first limit the microRNAs you are looking for or simply filter your results once you’ve “cast your broadest net”? To be on the cutting-edge in a continually growing field, it’s best to cast the broadest net possible and then filter your results, giving yourself the greatest opportunity to make novel discoveries. For instance, if the critical panel of microRNAs for your disease, pathway, or treatment of interest was annotated in miRBase V19, why would you only look at the microRNAs annotated through miRBase V10 or V11, cutting out the more recently discovered microRNAs? Instead, first look at the entire up-to-date miRNome and then filter your results for followup studies by only looking at expressed/differentially expressed microRNAs.

An example of the success of this approach was published in Clinical Chemistry, looking at microRNA markers of acute kidney injury (AKI) in the urine. The authors profiled the entire human miRNome using the QIAGEN miRNome qPCR array, updated through miRBase V18 at the time (currently updated through miRBase V21), and found several important microRNAs for assessing AKI. One of these, miR-4640, had only been identified in 2011, the same year as the miRBase V18 update. Therefore, it would’ve been missed if an older version of miRBase had been used to generate their miRNome profile.

Overall, taking the “limiting approach” may mean missing your critical microRNAs as well as the chance for the next great microRNA discovery. Even if you do realize that you’ve missed important microRNAs later on, it’s not always easy to simply add assays; often you may no longer have enough sample material or time. The best approach is to cast a wide net early, ensuring that you don’t miss a thing.

Science is an exciting field to be in because of the pioneers that have pushed the envelope and ventured into the unknown. For discovery-based microRNA studies, take this approach and never limit the potential of your experiments!

Jonathan M. Shaffer, Ph.D.

Dr. Shaffer joined QIAGEN in 2009 and has since worked with various technology development groups, the most recent being miRNA technologies. He received his Ph.D. in biochemistry and molecular genetics from the University of Pittsburgh School of Medicine in 2008 where his research focused on determining the mechanisms that regulate non-receptor tyrosine kinase expression and activity. Dr. Shaffer did his postdoctoral training at SABiosciences Corporation, now part of QIAGEN. Currently, Dr. Shaffer is a Senior Scientist in R&D at QIAGEN.

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