Mapping circulating serum miRNAs to their immune-related target mRNAs
Authors Nosirov B, Billaud J, Vandenbon A, Diez D, Wijaya E, Ishii KJ, Teraguchi S, Standley DM
Received 5 September 2016
Accepted for publication 7 November 2016
Published 2 February 2017 Volume 2017:10 Pages 1—9
Checked for plagiarism Yes
Review by Single anonymous peer review
Peer reviewer comments 2
Editor who approved publication: Dr Juan Fernandez-Recio
Bakhtiyor Nosirov,1 Joël Billaud,1 Alexis Vandenbon,2 Diego Diez,3 Edward Wijaya,1 Ken J Ishii,4,5 Shunsuke Teraguchi,3 Daron M Standley1,6
1Systems Immunology Lab, 2Immuno-Genomics Research Unit, 3Quantitative Immunology Research Unit, 4Laboratory of Vaccine Science, WPI Immunology Frontier Research Center, Osaka University, Suita, 5Laboratory of Adjuvant Innovation, National Institute of Biomedical Innovation, Osaka, 6Lab of Integrated Biological Information, Institute for Virus Research Kyoto University, Kyoto, Japan
Purpose: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs.
Materials and methods: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA–mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related).
Results: Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent.
Conclusion: Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA–immune mRNA interactions than would be expected by chance.
Keywords: biomarker, posttranscriptional regulation, random forest, target prediction
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