Distinct IDH1/2-associated Methylation Profile and Enrichment ofTP53andTERTMutations Distinguish Dedifferentiated Chondrosarcoma from Conventional Chondrosarcoma

Abstract

Dedifferentiated chondrosarcoma (DDCS) is a rare high-grade chondrosarcoma characterized by a well-differentiated chondrosarcoma (WDCS) component that abruptly transitions to a high-grade, non-cartilaginous sarcomatous component. To date, the molecular pathogenesis of DDCS and its distinction from conventional chondrosarcoma remain poorly understood. By targeted sequencing, we examined the mutational and copy number profiles of 18 DDCS, including macrodissected WDCS components, compared to 55 clinically sequenced conventional chondrosarcomas. In conjunction with publicly available external data, we analyzed the methylation and expression profiles of 34 DDCS and 94 conventional chondrosarcomas. IDH1/IDH2 mutations were present in 36% conventional chondrosarcomas and 71% DDCS. Compared to conventional chondrosarcomas, DDCS had higher frequencies of TP53 and TERT promoter mutations and CDKN2A/B copy number losses. Paired analysis of macrodissected WDCS and the high-grade components revealed TERT promoter mutations as early events. Despite phenotypic similarities, the percentage of genome with copy number alterations in DDCS was significantly lower than that in other high-grade sarcomas. Differential methylation analysis revealed reduction of IDH1/IDH2-associated global hypermethylation characteristically seen in conventional chondrosarcoma and a distinct methylation profile in DDCS. The WDCS and high-grade components in DDCS showed similar methylation profiles. These CpG sites were associated with upregulated expression of genes involved in G2M checkpoints and E2F targets. Genomic profiling revealed enrichment of TP53, TERT promoter and CDKN2A/B alterations in DDCS. Integrated methylation and gene expression analysis revealed distinct IDH1/IDH2-associated methylation and transcriptional profiles as early events in DDCS, which may underly the pathogenesis of dedifferentiation in chondrosarcomas.

A personalized medicine approach identifies enasidenib as an efficient treatment for IDH2 mutant chondrosarcoma

“…Considering the genes of the E1/E2 signatures, we can hypothesize that the inhibitor produces a negative regulation of those genes linked to the cell cycle, proliferation and division, which would explain the general repression of E2F-controlled targets in T-CDS17#1 cells. Relevant to this finding, a recent study found that mutant IDH -induced methylation profiles in dedifferentiated chondrosarcomas were associated with upregulated expression of genes involved in G2/M checkpoints and E2F targets 57 . Among the E2F targets that we found repressed by enasidenib there are key mediators of progression through the G2/M phase of the cell cycle such as CDK1 , AURKA , PLK1 , WEE1 or CHK1 , while the expression of other inhibitors of proliferation such as TP53 , CDKN2A or CDKN1B increases after treatment with the inhibitor.…”

“…In line with these non-canonical cases, we have not found changes in the methylation levels of the CDS17 chondrosarcoma models after treatment with enasidenib. The relevance of IDH mutant-induced epigenetic changes in chondrosarcoma has been revealed in previous studies showing a global hypermethylated status of IDH mutant cases 53, 57 . Although there could be technical biases arising from the comparison of epigenetic features in tissue samples and cultured cell lines, our methylome analysis of normal cartilage samples and chondrosarcoma cell lines also showed a high rate of hypermethylated genes in IDH2 mutated cells.…”

The spectrum and significance of secondary (co‐occurring) genetic alterations in sarcomas: the hallmarks of sarcomagenesis

“…Although not associated with progression‐free or overall survival, the presence of TERT promoter mutations is hypothesized to be crucial for telomere maintenance during early stages of tumorigenesis. In dedifferentiated chondrosarcoma, by comparing microdissected well‐differentiated and dedifferentiated chondrosarcomatous components to conventional chondrosarcomas, a recent genomic profile showed that TERT promoter mutations were an early event in dedifferentiated chondrosarcoma [72].…”

“…Introduction of mutant IDH generated USARCs in vivo [102]. Interestingly, global hypermethylation is reduced/reversed in dedifferentiated chondrosarcoma [72]. Further, downregulation of miR‐22, a downstream negative regulator of TET1, has been reported in both USARC and osteosarcoma, with a strong association with poor disease‐free survival [26,103].…”

Dedifferentiated Chondrosarcoma from Molecular Pathology to Current Treatment and Clinical Trials

“…Genomic examination identified an overrepresentation of TP53, TERT promoter, and CDKN2A/B alterations in DDCS but copy-number alterations in DDCS was significantly lower. Integrating methylation and gene expression analysis revealed that distinctive methylation and transcriptional profiles related to IDH1/IDH2 were early events in DDCS [80,81]. SRY-box transcription factor 9 (SOX-9) is the master regulator of chondrogenesis and increases in chondrosarcoma tissue and is directly targeted by miR-145 [82].…”