Genome-wide profiling and analysis of microRNA expression in buffalo milk exosomes

Abstract

Milk microRNA are being studied as a bioactive component of milk. A major fraction of milk microRNA are encapsulated in the lipid bilayered nano-vesicles called exosomes which mediate cell-cell communication. Therefore, the present study was aimed to identify and characterize microRNA in buffalo milk exosomes. Milk exosomes were characterized and used for total RNA isolation. Small RNA sequencing identified 351 microRNA and 17 previously unannotated microRNA in the buffalo milk exosomes. Bta-miR-148a, bta-miR-30a-5p, bta-miR-21-5p, bta-miR-99a-5p, bta-miR-27b, bta-miR-200a, bta-miR-26a, bta-miR-26c, bta-let-7g and bta-let-7i were the 10 most abundant microRNA in buffalo milk exosomes. Out of 5 validated microRNA, bta-miR-148a and −30a-5p were differentially expressed whereas bta-miR-21-5p, bta-miR-200a and bta-let-7g were consistently expressed across lactation stages. Gene targets of the 10 most abundant microRNA were identified using TargetScan taking Homo sapiens as the reference genome. All the targets having context scores < −0.4 with a total of 1539 were taken for network and pathway analysis. In silico analyses predicted 9 significant gene clusters in buffalo milk exosomal microRNA, which were found to be involved in important cellular processes. Analyses of hub genes interactions, string and cytoscape network analysis indicated that ubiquitin proteasomal degradation is the most regulated cellular process by buffalo milk exosomal microRNA. In summary, the repertoire of microRNA identified along with in silico analysis has provided insights into the physiological functionality of bovine milk microRNA in humans.