CroSeed: bioinformatics pipeline for the identification of miRNAs with nutraceutical activity in plants typical of the Mediterranean diet

The Mediterranean diet, rich in vegetables, is recognized for its health benefits, including protective roles against cancer, obesity, and type 2 diabetes. Recently, scientists have focused on plant microRNAs (miRNAs), small 16–24 base nucleic acids, for their potential cross-kingdom bioactivity and nutraceutical properties. These plant miRNAs, detectable in human tissues, are thought to regulate human metabolic activity by binding to specific messenger RNAs (mRNAs) or long non-coding RNAs (lncRNAs), thus influencing gene networks involved in chronic diseases. To predict this activity, a novel bioinformatics pipeline called CroSeed was developed. CroSeed compares the 5’end seed regions of plant miRNAs with human endogenous miRNA seed regions. The core assumption is that plant miRNAs that "mimic" human ones (plant functional analog miRNAs, or pfamiRs) can compete for the same mRNA binding sites, thereby exerting a cross-species effect. The CroSeed pipeline, which utilizes a mySQL relational database and Perl/Bash/SQL scripts, was applied to Brassica rapa miRNAs. The analysis identified 56 pfamiRs capable of cross-kingdom activity on human metabolism. Significantly, some of these Brassica miRNAs may regulate critical human oncogenes such as MYC, BCRA1, and TP53, which are often upregulated or mutated in various cancers.