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Chemotherapy is an important treatment modality for osteosarcoma (OS), but the development of chemoresistance limits the therapeutic efficacy of OS and results in a poor prognosis. Thus, a better understanding of the mechanisms underlying chemoresistance in OS is essential. We previously demonstrated that COPS3/CSN3 (COP9 signalosome subunit 3) functions as an oncogene to promote OS cells lung metastasis, which is closely related to chemoresistance. Here, we showed that COPS3 was significantly upregulated in OS tissues with poor response to preoperative chemotherapy. Moreover, COPS3 depletion made OS cells more sensitive to cisplatin treatment in vitro and in vivo, implicating COPS3 as a driver of cisplatin resistance. Mechanistic investigations showed that COPS3 induced a cytoprotective macroautophagy/autophagy in response to cisplatin. Specifically, we identified FOXO3 as a critical target of COPS3, as high expression of COPS3 enhanced the nuclear abundance of FOXO3 and increased the expression of FOXO3-responsive genes, promoting autophagosome formation and maturation. In turn, FOXO3 regulated COPS3 levels by inhibiting ubiquitin-mediated degradation and attenuating SKP2-mediated COPS3 inhibition, cooperatively maintaining a high level of COPS3. In both COPS3-expressing OS cells and a murine xenograft model, inhibition of autophagy could also overcome resistance to cisplatin. Collectively, our results offer insights into the mechanisms of cisplatin resistance and suggest that targeting COPS3-mediated autophagy is a promising therapeutic strategy for overcoming the cisplatin resistance of OS. Abbreviations: 3-MA: 3-methyladenine; BECN1: beclin 1; ChIP: chromatin immunoprecipitation; CHX: cycloheximide; COPS3/CSN3: COP9 signalosome subunit 3; CQ: chloroquine; DEGs: differentially expressed genes; FOXO3: forkhead box O3; GFP: green fluorescent protein; IC50: 50% inhibitory concentration; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; mRFP: monomeric red fluorescent protein; OS: osteosarcoma; PBS: phosphate-buffered saline; qRT-PCR: quantitative real-time PCR; RAB7: RAB7, member RAS oncogene family; RPS6KB1/p70S6K1: ribosomal protein S6 kinase B1; SEM: standard error of the mean; shRNA: short hairpin RNA; siRNA: small interfering RNA; SKP2: S-phase kinase associated protein 2; TEM: transmission electron microscopy; UPS: ubiquitin-proteasome system

Additional file 1: Fig. S1. Synteny breaks identified by setting different minimal number of syntenic genes (5, 8, 10, 20, and 30) enclosed in colinear syntenic blocks in paired comparisons (G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii). Fig. S2. Genomic gene synteny identified in G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii genomes. Fig. S3. Characterization of synteny breaks in diploid Gossypieae species. Fig. S4. Reproducibility and resolution of Hi-C data. Fig. S5. Genome-wide Hi-C contact maps constructed in G. arboreum, G. raimondii, and G. kirkii. Fig. S6. Relative distribution of orthologous chromosomes that were not involved in inter-chromosomal rearrangements mediating the descending dysploidy in Gossypioides kirkii. Fig. S7. The chromosomal landscape of genomic and epigenomic features within identified A/B compartments in G. kirkii, G. arboreum, and G. raimondii. Fig. S8. DNA methylation and histone modification near (±2 kb) the gene body of stable (A/B compartment status stable) and switched genes (A/B compartment status switching/transitions). Fig. S9. Representative IGV snapshots illustrating the A/B compartment, epigenetic features (DNA methylation and histone modifications), and gene models around the synteny break in G. arboreum vs. G. kirkii (top) and G. raimondii vs. G. kirkii (bottom). Fig. S10. Profile of TADs identified in G. kirkii, G. arboreum, and G. raimondii, respectively. Fig. S11. No statistically significant co-localization between synteny breaks and TADs interior bodies and intervals. Fig. S12. Fractions of TAD boundaries overlapping with breakpoints of inversion and translocation identified in comparisons of G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii are statistically higher than those randomization controls, which involve groups of shuffled TAD boundaries, shuffled breakpoints, and both TAD boundaries and breakpoints shuffled simultaneously. Fig. S13. Abundance of transposable element (TEs) in boundaries of TAD groups (large and small TADs) in G. kirkii, G. arboreum, and G. raimondii, respectively. Fig. S14. Open-chromatin epigenetic and active transcriptional features of TAD boundaries co-localizing with synteny breaks. Fig. S15. The relationships between genomic rearrangements and epigenetic modifications of syntenic genes for conserved TADs. Table S1. Summary of clean Hi-C reads. Table S2. Summary of uniquely mapped Hi-C reads. Table S3. Summary of valid Hi-C reads. Table S4. Pearson correlations of overall chromosomal distributions in G. kirkii, G. arboreum, and G. raimondii. Table S5. Epigenetic data from public databases.