CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma

Amplification of the MDM2 and CDK4 genes on chromosome 12 is commonly associated with low-grade osteosarcomas. In this study, we conducted high-resolution genomic and transcriptomic analyses on 33 samples from 25 osteosarcomas, encompassing both high- and low-grade cases with MDM2 and/or CDK4 amplification. We identified four major subgroups: (i) low-grade osteosarcoma with chromosome 12 amplicons as the sole acquired alteration, (ii) high- and low-grade tumours with CDK4 and MDM2 amplification along with few changes affecting other chromosomes, (iii) high-grade osteosarcomas with heavily rearranged genomes including either CDK4 and MDM2 amplification or (iv) CDK4 amplification and TP53 structural alterations. The amplicons involving MDM2 exhibited signs of an initial chromothripsis event affecting chromosome 12. In contrast, there was no indication of a chromothripsis event on chromosome 12 in TP53-rearranged cases. Instead, the initial disruption of the TP53 locus resulted in breakage and repair processes that co-amplified the CDK4 locus. Furthermore, our investigation revealed recurring promoter swapping events that involved the regulatory regions of the FRS2, PLEKHA5, and TP53 genes. These events led to the ectopic expression of partner genes, with the ELF1 gene being upregulated by the FRS2 and TP53 promoter regions, respectively, in two distinct cases.