In this study, based on the analysis of WGCNA and ceRNA network, we found that lnc-HLA-DQA1-5, lnc-RP11-127H5.1.1-1, and lnc-RTN2-1 participated in the mechanism of meniscus degeneration by regulating the expression of IGFBP4 and KLF2 through sponging miRNAs (miR-6799-5p, miR-1915-3p, miR-6764-5p, miR-6796-5p, and miR-6895-3p), which were related to the pathways of Staphylococcus aureus infection, complement and coagulation cascades, and cell adhesion molecules. This evidence concerns the gene HLA-DQA1 and staphylococcus aureus infection.