Yingqi Hua

Sarcomas are rare, genomically heterogeneous malignancies for which prognosis has remained poor and largely unchanged over recent decades. Patient‐derived xenograft (PDX) models are an important tool for cancer research, but their availability and utility remain limited in sarcoma. Here, we establish the SGH sarcoma PDX biobank, a living multi‐omics resource comprising 155 xenografts from 132 patients across 11 sarcoma histotypes, with osteosarcoma as the predominant subtype. This cohort is enriched for high‐risk sarcomas characterized by poor prognosis and widespread copy‐number alterations. Using this biobank, we show that extrachromosomal DNA (ecDNA) frequently drives high‐level oncogene amplification in osteosarcoma and that MYC ecDNA may underlie aggressive disease trajectories. Analyses of paired patient and PDX samples demonstrate that ecDNA is preferentially retained over intrachromosomal amplicons during engraftment and is stably maintained in PDX models. In addition, the PDX models largely recapitulate the histopathological and molecular features of their matched patient tumors while exhibiting distinct clonal evolutionary trajectories during engraftment. Finally, we identified potentially actionable genomic alterations within this PDX cohort, demonstrated genotype‐matched targeted therapy in a KRAS G12C‐mutant PDX model, and prioritized several candidate antibody–drug conjugate targets. Together, this resource provides a platform for biological discovery and preclinical precision oncology for sarcoma.

MYC‐amplified osteosarcoma, a poor‐prognosis molecular subtype, presents formidable therapeutic challenges due to its aggressive phenotype, chemoresistance, and the “undruggable” oncogenic driver MYC. A single‐molecule prodrug, DHU‐NO3, was developed to achieve precise synergy between photodynamic therapy (PDT) and nitric oxide (NO) gas therapy for the treatment of MYC‐amplified osteosarcoma. This prodrug covalently links the clinically approved photosensitizer methylene blue (MB) to an NO donor and undergoes a sequential activation cascade: reactive oxygen species‐triggered MB release, 405 nm light‐controlled NO generation, and PDT initiation under 650 nm laser irradiation. In 143B osteosarcoma cells, this temporally coordinated regimen efficiently induces apoptosis and potently suppresses the MYC signaling network. In the 143B osteosarcoma subcutaneous xenograft model, DHU‐NO3‐mediated sequential phototherapy demonstrated robust tumor growth inhibition with favorable biosafety. This work establishes a spatiotemporally programmable prodrug platform and provides a potent strategy to combat MYC‐amplified osteosarcoma by indirect pathway suppression.

Supplementary Figure S9. Pathway enrichment associated with UBA2 strata in the GEO_Integration_Cli cohort.

Supplementary Figure S8. UBA2 drives OS malignant phenotypes and impairs T-Cell cytotoxicity in vitro.

Supplementary Figure S12. UBA2 drives OS immune evasion in vivo.

Supplementary Figure S6: Construction and validation of a SUMOylation-related gene–based prognostic risk model across multiple cohorts.

Supplementary Table S3. Omics cohort.

Supplementary Figure S4: Identification of immune-related malignant osteosarcoma cell subpopulations and key SUMOylation genes at the single-cell level.

Osteosarcoma responds poorly to immune-checkpoint blockade (ICB), and the molecular drivers of its immune-cold state remain unclear. Using multi-omics analyses, we identified an immune-cold osteosarcoma subtype characterized by enrichment of protein SUMOylation and found the SUMO E1 subunit UBA2 as a key driver. UBA2 was anomalously upregulated in osteosarcoma cohorts and linked to worse outcomes. Functionally, UBA2 promoted autophagy, thereby exerting noncanonical protumor and immunosuppressive effects. Mechanistically, UBA2 catalyzed SUMO2-dependent SUMOylation of SESN2, enhancing autophagic flux. At the immune interface, UBA2 did not alter the expression of immune checkpoint molecules but reduced surface MHC-I through NBR1-mediated autophagy–lysosomal degradation, thereby limiting CD8+ T-cell infiltration. In vivo, pharmacologic UBA2 inhibition with ML-792 slowed tumor growth and sensitized tumors to ICB therapy. Together, these findings show that UBA2 links SUMOylation to autophagy-driven loss of antigen presentation and immune exclusion, highlighting the UBA2–autophagy–MHC-I axis as a therapeutic target and potential biomarker in osteosarcoma.