Comprehensive microRNA Profiling Reveals Novel Regulatory Networks in Human Osteoarthritis Articular Cartilage MiRNA Regulatory Networks in Osteoarthritis

Abstract

Knee osteoarthritis (KOA) is a highly prevalent degenerative joint disease. To investigate its molecular mechanisms, we performed high-throughput sequencing to compare miRNA expression profiles in articular cartilage from KOA patients and healthy controls. We identified differentially expressed miRNAs, predicted their target genes, and conducted functional enrichment analysis. Total RNA was extracted from both sample groups, and miRNA libraries were constructed for PE-150 sequencing on the HiSeq/MiSeq platform. Raw data were subjected to fastq quality control and kcUID deduplication, after which 18-30 nt short RNAs were retained for alignment against the human reference genome, known miRNAs were annotated via MiRBase, novel miRNAs were predicted using mREvo and mirdeep2, differential expression analysis was performed with DESeq2, target genes were predicted by combining miRanda and RNAhybrid, and subsequent GO and KEGG enrichment analyses were carried out. The sequencing data showed high quality with a clean read coverage over 90% and a Q30 score above 85%； a total of 701–783 known miRNAs and 64–85 novel miRNAs were annotated, among which 131 differentially expressed miRNAs were identified, and the target genes of these differentially expressed miRNAs displayed significant enrichment in GO functional categories and KEGG pathways. These miRNAs play a potential role in KOA progression.