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. 2019 Feb 14:9:2.
doi: 10.1186/s13569-019-0113-6. eCollection 2019.

Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype

Christian Koelsche #  1 , Damian Stichel #  2   3   4 , Klaus G Griewank  5   6 , Daniel Schrimpf  2   3   4 , David E Reuss  2   3   4 , Melanie Bewerunge-Hudler  4   7 , Christian Vokuhl  8 , Winand N M Dinjens  9 , Iver Petersen  10 , Michel Mittelbronn  11   12   13   14 , Adrian Cuevas-Bourdier  12 , Rolf Buslei  15 , Stefan M Pfister  4   16   17   18 , Uta Flucke  19 , Gunhild Mechtersheimer  1 , Thomas Mentzel  20 , Andreas von Deimling  2   3   4
Affiliations

Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype

Christian Koelsche et al. Clin Sarcoma Res. .

Abstract

Background: Atypical fibroxanthomas (AFX) and pleomorphic dermal sarcomas (PDS) are lesions of the skin with overlapping histologic features and unspecific molecular traits. PDS behaves aggressive compared to AFX. Thus, a precise delineation, although challenging in some instances, is relevant.

Methods: We examined the value of DNA-methylation profiling and copy number analysis for separating these tumors. DNA-methylation data were generated from 17 AFX and 15 PDS using the Illumina EPIC array. These were compared with DNA-methylation data generated from 196 tumors encompassing potential histologic mimics like cutaneous squamous carcinomas (cSCC; n = 19), basal cell carcinomas (n = 10), melanoma metastases originating from the skin (n = 11), leiomyosarcomas (n = 11), angiosarcomas of the skin and soft tissue (n = 11), malignant peripheral nerve sheath tumors (n = 19), dermatofibrosarcomas protuberans (n = 13), extraskeletal myxoid chondrosarcomas (n = 9), myxoid liposarcomas (n = 14), schwannomas (n = 10), neurofibromas (n = 21), alveolar (n = 19) and embryonal (n = 17) rhabdomyosarcomas as well as undifferentiated pleomorphic sarcomas (n = 12).

Results: DNA-methylation profiling did not separate AFX from PDS. The DNA-methylation profiles of the other cases, however, were distinct from AFX/PDS. They reliably assigned to subtype-specific DNA-methylation clusters, although overlap occurred between some AFX/PDS and cSCC. Copy number profiling revealed alterations in a similar frequency and distribution between AFX and PDS. They involved losses of 9p (22/32) and 13q (25/32). Gains frequently involved 8q (8/32). Notably, a homozygous deletion of CDKN2A was more frequent in PDS (6/15) than in AFX (2/17), whereas amplifications were non-recurrent and overall rare (5/32).

Conclusions: Our findings support the concept that AFX and PDS belong to a common tumor spectrum. We could demonstrate the diagnostic value of DNA-methylation profiling to delineating AFX/PDS from potential mimics. However, the assessment of certain histologic features remains crucial for separating PDS from AFX.

Keywords: Atypical fibroxanthoma; Carcinomas; DNA methylation; Melanomas; Mimics; Pleomorphic dermal sarcoma; Profiling; Sarcomas.

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Figures

Fig. 1
Fig. 1
DNA-methylation profiling in atypical fibroxanthomas, pleomorphic dermal sarcomas and histologic mimics. Unsupervised hierarchical clustering (a) and t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis (b) of DNA-methylation data from atypical fibroxanthomas (AFX), pleomorphic dermal sarcomas (PDS) and histologic mimics shows a close epigenetic relation to cutaneous squamous cell carcinomas (cSCC). This AFX/PDS/SCC methylation cluster clearly separated from the methylation clusters of other diagnostic mimics
Fig. 2
Fig. 2
Cumulative copy number profiles. Frequency of copy number variations in 17 atypical fibroxanthomas (a), in 15 pleomorphic dermal sarcomas (b), in 19 cutaneous squamous cell carcinomas (c) and 10 basal cell carcinomas (d), assessed by automated aberrations profiling
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