Identification and comparison of exosomal and non-exosomal microRNAs in mantle tissue of Pinctada fucata (Akoya pearl oyster)

MicroRNAs (miRNA) are a class of endogenous non-coding small RNA molecules that are widely found in tissues, biological fluids, and vesicles such as exosomes. Exosomes are extracellular vesicles released from multivesicular bodies of various cell types. They are involved in intercellular communication and transport and immune regulation and may serve as potential biomarkers for diagnosis and monitoring. The function of exosomal miRNAs and their potential applications as biomarkers are a topic of interest. However, identification and comparison of miRNA expression in different biological sample types have rarely been studied. Therefore, in this study, the miRNA profiles of tissue- and tissue-derived exosomes of Pinctada fucata were characterized and compared to screen for differentially expressed miRNAs. The miRNAs functioned within tissues and were also packaged into exosomes. Simultaneously, some miRNAs were preferentially exported to exosomes for their biological functions. Functional analyses suggested that the predicted genes targeted by these differentially expressed miRNAs were extensively involved in intracellular vesicle trafficking and vesicle-mediated substrate transport. Overall, our findings provide insights into the roles of tissue-derived miRNAs and circulating exosomal miRNAs in cell communication and gene regulation. Moreover, this study serves as an additional reference for sample type selection for P. fucata small RNA analysis.