Intimal sarcomas and undifferentiated cardiac sarcomas carry mutually exclusive MDM2, MDM4, and CDK6 amplifications and share a common DNA methylation signature

Abstract

Undifferentiated mesenchymal tumors arising from the inner lining (intima) of large arteries are classified as intimal sarcomas (ISA) with MDM2 amplification as their molecular hallmark. Interestingly, undifferentiated pleomorphic sarcomas (UPS) of the heart have recently been suggested to represent the cardiac analog of ISA due to morphological overlap and high prevalence of MDM2 amplifications in both neoplasms. However, little is known about ISAs and cardiac UPS without MDM2 amplifications and molecular data supporting their common classification is sparse. Here, we report a series of 35 cases comprising 25 ISAs of the pulmonary artery, one ISA of the renal artery and 9 UPS of the left atrium. Tumors were analyzed utilizing the Illumina Infinium MethylationEPIC BeadChip array, enabling copy number profile generation and unsupervised DNA methylation analysis. DNA methylation patterns were investigated using t-distributed stochastic neighbor embedding (t-SNE) analysis. Histologically, all ISAs and UPS of the left atrium resembled extra-cardiac UPS. All cases exhibited highly complex karyotypes with overlapping patterns between ISA and UPS. 29/35 cases showed mutually exclusive amplifications in the cell-cycle associated oncogenes MDM2 (25/35), MDM4 (2/35), and CDK6 (2/35). We further observed recurrent co-amplifications in PDGFRA (21/35), CDK4 (15/35), TERT (11/35), HDAC9 (9/35), and CCND1 (4/35). Sporadic co-amplifications occurred in MYC, MYCN, and MET (each 1/35). The tumor suppressor CDKN2A/B was frequently deleted (10/35). Interestingly, DNA methylation profiling (t-SNE) revealed an overlap of ISA and cardiac UPS. This "ISA" methylation signature was distinct from potential histologic and molecular mimics. In conclusion, our data reveal MDM4 and CDK6 amplifications in ISAs and UPS of the left atrium, lacking MDM2 amplification. We further report novel co-amplifications of various oncogenes, which may have therapeutic implications. Finally, the genetic and epigenetic concordance of ISAs and UPS of the left atrium further supports a shared pathogenesis and common classification.

Fig. 1. Examples of characteristic architectural patterns in intimal sarcomas.

At low magnification this case illustrates the endoluminal growth of a polypoid tumor within an artery (a). Intimal sarcomas typically overgrow fibrin layers attached at the vessel wall (b). Tumor cells spread lateral within the intimal space (c). Some cases show focal infiltration and penetration of the tunica media (d). Scale bars equal 200 µm.

Fig. 2. Histologic features in intimal sarcomas.

Intimal sarcomas often exhibited a loose storiform growth pattern (a). Single cases showed an epithelioid cytomorphology with tumor cells focally forming diffuse sheets and solid areas (b). Some cases showed focal stromal sclerosis, hemosiderin deposits and dystrophic calcifications (c). Case 141642 exhibited a prominent myxoid stroma with elongated, thin-walled vessels and increased perivascular tumor cell density (d). Case 141634 showed variable-sized pseudocystic spaces containing homogeneous eosinophilic material or blood. These spaces are lined by tumor cells. Hemosiderin is present (e). Case 129604 showed a prominent component of aggregating plasma cells (f). Scale bars equal 100 µm.

Fig. 3. Copy number profiles in intimal sarcomas.

Exemplary copy number profiles of intimal sarcomas carrying a 12q14-q15 amplification including MDM2 and CDK4 (upper left), carrying a 1q32.1 amplification including MDM4 (upper right), carrying a 7q21.2 amplification including CDK6 (lower left) and one example case lacking one of these gene amplifications (lower right).

Fig. 4. MDM4 and CDK6 amplifications demonstrated by FISH.

2-color FISH for CDK6 (green signal) or MDM4 (red signal) in MDM2 balanced intimal sarcomas. The upper image (case 163852) shows tight clustered green signals (CDK6) and almost balanced red signals (MDM4). The lower image (case 129602) shows the opposite constellation with abundant red signals (MDM4) and almost balanced green signals (CDK6).

Fig. 5. Summary of copy number variations in intimal sarcomas.

Shown are the the most prominent copy number alterations identified. The color code is indicated in the figure.

Fig. 6. Unsupervised DNA methylation analysis of intimal sarcomas, undifferentiated pleomorphic sarcomas of the left atrium and potential mimics.

Unsupervised t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis of DNA methylation data from intimal sarcomas. The study cohort was compared with methylation data of prototypical soft tissue sarcomas that may histologically or molecularly mimic intimal sarcomas.