Objective MicroRNAs (miRNAs) play important roles in various diseases’ development and progression. The aim of this study is to identify the differently expressed miRNAs (DEmiRNAs) and differently expressed genes (DEGs) between BPH and PCa.

Methods Selecting BPH and PCa tissues from GEO database (GSE118038 as test dataset; GSE30994 as validation dataset), we identified DEmiRNAs and DEGs between BPH and PCa using GEO2R online tool and “Deseq2” R package. We applied random forest method to select hub DEmiRNAs, combining age and BMI, to establish a nomogram model for BPH detection. Finally, GO and KEGG enrichment analyses were conducted to explore the underlying mechanisms and pathways of DEmiRNAs in BPH.

Results We found 26 DEmiRNAs between BPH and PCa, of which 21 DEmiRNAs were up-regulated and 5 DEmiRNAs were down-regulated. Via forest random method, we selected miR-636, miR-324-3p, miR-210-3p and miR-3615 as hub DEmiRNAs in BPH. Combing these four hub DEmiRNAs, age and BMI, we established a nomogram model to distinguish BPH from PCa. Through “miRWalk” online tool, we targeted 499 hub DEGs between BPH and PCa, and found most of genes enriched in muscle system process, muscle contraction, contractile fiber, myofibril, actin binding, passive transmembrane transporter activity, focal adhesion, axon guidance.

Conclusion Our results suggested that miR-636, miR-324-3p, miR-210-3p and miR-3615 might the hub DEmiRNAs between BPH and PCa, which may play a crucial role to distinguish BPH from PCa.