Comparative Molecular Analysis of Clear Cell Sarcoma and Cutaneous Melanomas: Key Genetic Insights for diagnosis
Authors
- BostonGene, Corp., Waltham, USA
Abstract
A rare and aggressive form of soft tissue sarcoma, clear cell sarcoma (CCS), is difficult to diagnose and treat because it shares diagnostic markers (S100, SOX10, HMB45, MelanA, PRAME) with cutaneous melanoma (CM) as detected by immunohistochemistry. Here, we examined a CCS cohort and a CM cohort (both internal) by pathological assessment coupled with molecular profiling in order to identify molecular distinctions between them that may help improve diagnostic accuracy and treatment specificity for CCS.
Methods
CCS samples (n=10) and CM samples (n=72) underwent whole exome and RNA sequencing. Differential gene expression and subsequent GO gene enrichment analysis, gene fusions, mutations, and copy number alterations were analyzed. Independent histomorphological analysis was performed by 3 pathologists to document the most distinctive growth patterns and cytological traits for CCS.
Results
Histological assessment of all CCS samples verified 4 key CCS features: thick hyalinized septa (n=9) and nested growth pattern, epithelioid appearance and focal cytoplasmic clearing (n=8 for the latter 3 features). An EWSR1 gene translocation was detected in 8 CCS cases but was absent in all CM cases. While the BRAF V600E mutation that is common in melanomas was absent in the CCS cohort, we found one CCS sample with D594N and P334S mutations, both unusual in melanomas. Amplification of 8q (where MYC is located) was present in 8 CCS cases, consistent with elevated MYC, RPLP0, PABPC1, and AATF expression (U-test, FDR correction, p-val. adj. < 0.05 for all). We also observed a greater extent of elevated MITF expression associated with melanocytic differentiation in CCS than in CM. Increased FOXC2 expression, while not observed in the CM cohort, was present in the CCS cohort. Overall, the expression of 1,324 and 2,725 non-overlapping genes were significantly higher in CCS and in CM, respectively, when compared to each other (p-val. adj.< 0.05). Pathways involved in chondroblastic and osteogenic differentiation and collagen fiber organization were enriched in CCS compared to CM, with CCS showing significantly higher expression of fibrillar collagens (Fisher test, FDR correction, p-val. adj. < 0.01 for all). As such, our findings suggest similarities between CCS and extraskeletal myxoid chondrosarcoma.
Conclusion
Our study confirmed the diagnostic value of EWSR1 translocation and BRAF mutations in CCS, and revealed elevated FOXC2 expression as a potential diagnostic marker for CCS. We also detected distinct bone and chondroblastic differentiation signatures in CCS, revealing insights into the mechanism of CCS development. Our findings warrant the evaluation of the clinical utility of these new features in diagnosing CCS and facilitating treatment selection.
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