Accurate Prediction of Central Conventional Chondrosarcoma Risk and Outcome Using Methylation Profiling: CHROME

Chondrosarcomas are malignant cartilage-forming bone tumors with heterogeneous behavior, making prognostication and clinical management challenging. Histological grading is the primary tool for predicting clinical outcomes in conventional chondrosarcoma. However, its high interobserver variability limits reliable distinction between low- and high-risk patients, potentially leading to suboptimal clinical management. Given the increasing use of DNA methylation profiling as a valuable tool in surgical pathology for tumor classification, we investigated its prognostic value in central conventional chondrosarcoma. We generated methylation data from 69 primary central conventional chondrosarcomas profiled with Illumina's Human MethylationEPIC Array (850 k sites), and identified methylation sites individually linked to patient outcome. A LASSO Cox regression model was applied to these methylation sites to identify an optimal set of eight informative sites. With the regression coefficients of these methylation sites, we constructed a risk score that predicts central conventional Chondrosarcoma Risk Outcome from Methylation (CHROME). CHROME stratifies patients into High or Low risk groups for disease recurrence, onset of metastasis and disease-specific mortality. Survival analysis in an independent validation cohort (n = 68) demonstrated strong discriminatory performance of CHROME, with complete separation of outcomes and no adverse events observed in the Low risk group. Overview of the clinico-pathological information showed that a low grade (ACT/G1) case with an event was correctly assigned to the High risk group, while nine high grade cases without events were classified as Low risk. CHROME provides accurate risk stratification in central conventional chondrosarcoma and may represent a valuable tool for improving its prognostication and clinical management.