Extended Data Fig. 2: Proteomic analysis of DMM mouse model post-K9 LNP treatment.

a, Volcano plot showing protein expression changes in knee joints following two doses of K9 LNP (mCas9 + sgTOM) treatment, as identified by LC-MS/MS. Significantly altered proteins are highlighted in red, identified using a two-sided Student’s t-test with Benjamini-Hochberg false discovery rate (FDR) correction in Spectronaut, and visualized as a volcano plot using the SRplot platform. b, KEGG pathway enrichment analysis of differentially expressed proteins between treated and untreated groups. c-h, GO enrichment analysis of differentially expressed proteins, displayed as cnetplots and bubble plots for (c, d) biological processes, (e, f) molecular functions, and (g, h) cellular components. i, j, Gene set enrichment analysis (GSEA) plots showing enriched pathways in DMM mice with or without K9 LNP treatment. KEGG and GO enrichment analyses were performed using two-sided hypergeometric tests with Benjamini-Hochberg FDR correction for multiple testing.