Integrated Bioinformatics and Experimental Analysis Revealed Crosstalk Between IL-6, Autophagy, Ubiquitination, and Key miRNAs in Female Infertility: Insights from Ovarian Endometriosis and PCOS

Female infertility, affecting millions worldwide, involves complex molecular mechanisms such as chronic inflammation, impaired cellular death, and protein regulation. This study explores how the inflammatory protein IL-6, autophagy marker LC3, ubiquitination processes, and small RNA molecules of miR-146a-5p, miR-9-5p, and miR-9-3p contribute to the control of ovarian function and female infertility. Two expression profile datasets (GSE199225 and GSE146856) were screened and downloaded from GEO. DEGs were screened using the GEO2R and ggVennDiagram tools. The three miRNAs were retrieved from datasets using the multiMiR tool, and IL6-targeted genes were retrieved from MSigDB. IL6, miRNAs interactions were constructed. Further, LC3, Ubiquitination, and their cross-relation with the DEGs associated miRNAs were demonstrated. Meanwhile, GO/KEGG pathway enrichment analyses, and molecular network interaction analysis were performed. Lastly, immunohistochemistry and quantitative PCR (qPCR) were used to confirm the expression of IL6, LC3, and miRNA in ovarian endometrial tissues compared to control. Results showed that IL-6 drives inflammation in conditions of PCOS and ovarian endometriosis, which then disrupt ovulation and embryo implantation. The miR-146a-5p reduced inflammation by targeting gene TRAF6, while miR-9-5p regulated protein degradation via SQSTM1. In agreement with the bioinformatic approach, experimental analysis revealed a reduced IL6 protein expression in ovarian endometriosis tissues while mRNA IL6 level was increased, suggesting the presence of post-transcriptional regulatory mechanisms that act to limit excessive inflammation, probably through miRNAs. Indeed, miR-146a-5 levels, which plays a role in immune modulation and inflammatory signaling were significantly upregulated. Interestingly, an induction of autophagic mechanism revealed by elevated LC3 was also observed. Aligned with these experimental data, bioinformatic analysis showed that autophagy genes LC3, ATG5 and ubiquitination processes were tightly linked to ovarian health, with disruptions accelerating follicle loss and oxidative damage. In conclusion, results showed that IL-6, miRNAs and autophagy work together to control inflammation and cellular repair in ovarian disorders. This study opens new avenues for targeted treatments to improve fertility outcomes by connecting molecular networks to clinical insights.