S1 File - Single-cell and spatial transcriptomics reveal post-translational modifications in osteosarcoma progression and tumor microenvironment

S1 Table. Post-translational modifications-related genes list. S2 Table: Sequences for siRNA. S3 Table: RT-qPCR primer sequences. S1 Fig. Gene set enrichment analysis (GSEA) based on dysregulated genes of the osteoblastic cells. (A, B) GSEA analysis of dysregulated genes in osteoblastic cells based on PTMshighos and PTMslowos. S2 Fig. Intercellular communication analyses. (A) Intercellular communication pathways among PTMs-associated osteoblastic cells. (B) Correlation circle plots illustrating interactions between different cell types. (C) Heatmap showing cell–cell ligand-receptor correlations. (D) Sankey diagram visualizing ligand-receptor-transcription factor interactions in fibroblasts with higher PTMs expression. S3 Fig. Clinical practice value of CMDPTMS. (A, B) Comparison of CMDPTMS with 16 other published models in the TARGET-OS and GEO-OS cohorts. S4 Fig. Prognostic significance of CMDPTMS. (A) Nomogram predicting 1-, 3-, and 5-year overall survival in OS patients. (B) Kaplan-Meier survival analysis comparing high- and low-score groups. (C-E) Decision curve analysis assessing the clinical utility of the nomogram for 1-, 3-, and 5-year survival predictions. S5 Fig. GSEA-KEGG pathway enrichment analysis in the low CMDPTMS and high CMDPTMS groups. A. GSEA-KEGG analysis of metabolic-related pathways in the low CMDPTMS and high CMDPTMS groups. (B, C). GSEA-KEGG analysis in different CMDPTMS groups. S6 Fig. The predictive value of CMDPTMS in immunotherapy response among OS patients. (A) Differences in restricted mean survival (RMS) time at 6 months and 1-year post-treatment. (B) Differences in long-term survival (LTS) at 3 months post-treatment. (C) Distribution of CMDPTMS across immunotherapy response groups. (D) Variations in TIP process activation levels. (E) Immunotherapy response predictions based on the TIDE algorithm. (F) Immunotherapy response predictions based on the subclass mapping algorithm. (G) Distribution of CMDPTMS across immunotherapy response groups in the GSE91061 dataset. (H, I) Survival analysis in the GSE78220 and GSE135222 datasets. S7 Fig. Pseudotime analysis of core genes of CMDPTMS in scRNA-seq data. (A, B) Core genes were divided into three evolutionary branches. S8 Fig. Pseudotime analysis of core genes of CMDPTMS in ST data. (A, B) Core genes were divided into four evolutionary branches. S9 Fig. Validation of VIM role in OS. (A) Cellular localization of VIM in U2-OS cell lines. (B) qRT-PCR analysis of VIM expression in normal osteoblast and OS cell lines. (C, D) The level of VIM transfection with siRNA was analyzed by qRT-PCR. (E, F) CCK-8 assays were performed to examine the potential proliferation of siVIM cells or negative control cells. (G, H) Transwell assays were performed to assess the migratory potential of siVIM cells and negative control cells. (ZIP)