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

Tumor samples from 61 patients with the histopathological diagnosis AFX (n = 17), PDS (n = 15), cSCC (n = 19) and BCC (n = 10) were analyzed together with 11 skin melanomas and 156 soft tissue tumors. The latter comprised 11 angiosarcomas, 13 dermatofibrosarcomas protuberans, 9 extraskeletal myxoid chondrosarcomas, 11 leiomyosarcomas, 14 myxoid liposarcomas, 19 malignant peripheral nerve sheath tumors, 21 neurofibromas, 19 alveolar and 17 embryonal rhabdomyosarcomas, 10 schwannomas and 12 undifferentiated pleomorphic sarcomas of the deep soft tissue. The median age was 81 years for AFX, 83 years for PDS, 79 years for cSCC and 77 years for BCC. The AFX, PDS, cSCC and BCC cohort consisted of 58 primary tumor samples, two recurrent samples and one case with an unknown status. The predominant side of occurrence was the head region (n = 46) followed by the neck (n = 9). AFX and PDS had a much higher incidence in male patients compared to cSCC and BCC. Clinical data are summarized in Table 1.

Unsupervised hierarchical clustering and t-SNE analysis delineated tumors in methylation classes (Fig. 1), which also kept stable when varying the number of CpGs using for this analysis (data not shown). AFX and PDS were indistinguishable by clustering (Fig. 1a) and t-SNE analyses (Fig. 1b). cSCC and BCC grouped in close proximity to AFX and PDS. However, both formed homogeneous subgroups and therefore were distinct from these in both analyses, even though single cases overlapped (Fig. 1). Furthermore, we additionally analyzed 167 tumors encompassing 12 subtypes comprising different sarcoma entities and melanoma, which may mimic the phenotype of AFX and PDS. Each of these entities formed a subtype-specific methylation class. Interestingly, an obvious outlier case, initially diagnosed as PDS for lack of S100 and other melanoma specific staining (Additional file 2: Figure S1), repeatedly assigned to the methylation class of melanomas. Applying a targeted next generation sequencing panel the tumor demonstrated an activating TERT promoter mutation, a HRAS G12S mutation as well as a BRAF G466E mutation. Sequencing data are given in Additional file 3: Table S2.

We next generated copy number profiles derived from the DNA-methylation array data. AFX and PDS (Fig. 2a, b) revealed chromosomal imbalances that frequently involved losses of 9p (AFX 11/17; 65% vs. PDS 10/15; 66%) and 13q (AFX 11/17; 65% vs. PDS 14/15; 93%). A gain of chromosome arm 8q was slightly more frequent in PDS (5/15; 33%) compared to AFX (3/17; 18%). The homozygous deletion of the CDKN2A locus on 9p was more frequent in PDS (6/15; 40%) compared to AFX (2/17; 12%). Amplifications were rare in both AFX (3/15; 20%) and PDS (2/15; 13%). They were distributed in a non-recurrent pattern involving 5q21.3 (FER), 8p11.22-23 (FGFR1, TACC1) and 13q34 (LAMP1) in AFX, and 11q13.3 (CCND1) and 12q24.31 (KNTC1) in PDS (Additional file 4: Figure S2).

Copy number alterations in cSCC were distributed similarly to AFX and PDS (Fig. 2c). Chromosomal losses were frequently encountered on 3p (8/19; 42%), 13q (8/19; 42%) and 9p (12/19; 63%). Interestingly, the 19 cSCC demonstrated no homozygous deletions of the CDKN2A locus (9p). The most frequent gains involved 3q (4/19; 21%) and 8q (5/19; 26%). Amplifications were found in two cSCC involving MYC (8q24.21) and CCND1 (11q13.3), respectively.

The copy number profiles of the 10 BCCs showed overall less frequent chromosomal gains and losses compared to AFX, PDS and SCC (Fig. 2d). Obvious amplifications and deletions were absent in BCC.