Fig. 2: BPDCN DNA methylation in comparison to AML, CMML, t-ALL, and melanoma.

a Visualization of the first and second principal components of the 10,000 most variable DNA methylation sites (ellipses show 95% confidence intervals of multivariate normal distribution). b Partial-least squares discriminant analysis (PLS-DA) of adjusted beta values. c First and second principal components of the comparison between BPDCN and AML (RUNX1 wild-type and mutated samples highlighted differently). The four BPDCN cases falling inside the 95% confidence interval of the AML data are labeled. d–j a prototypical borderline case with both typical BPDCN as well as AML with pDC-like features. d Morphology of the neoplastic infiltrate within the lymph node resembles acute leukemia with polymorphic blast-like cells of variable size (H&E, 40×). e Uniform expression of CD123 initially led to the inclusion of BPDCN into the differential diagnosis (CD123, 40×). f Further immunophenotypic work-up revealed several atypical features, reminiscent of AML with partial pDC phenotype, including variable expression of CD33 in a significant fraction of the malignant infiltrate (CD33, 40×), yet only partial expression of CD56 (g; CD56, 200×) and CD117 (h; CD117, 200×). i The bi-phenotypic character of the infiltrate is further underlined by a strong CD34 expression of a minor fraction of the blast-like cells alongside the vascular structures, resembling the pDC-like AML phenotype component, whereas the majority of blasts resemble phenotypically characteristic BPDCN cells. j Two-dimensional density plots of average CpG site DNA methylation in BPDCN vs AML, CMML, t-ALL, and melanoma (low density: orchid; high density: yellow/orange). k Average genome-wide DNA methylation level (beta values) of BPDCN, AML, CMML, t-ALL, and melanoma; for BPDCN subcluster estimates are shown as well. l DNA-methylation-based mitotic clock (epiCMIT) estimates for each entity and BPDCN subtypes. m Network enrichment against REACTOME for DMRs between BPDCN and AML; fold changes are color-scaled (red: higher DNA methylation in BPDCN; blue: higher DNA methylation in AML) and gene sets are denoted by light-brown nodes. n Pathway enrichment against REACTOME gene sets of gene-associated CpGs between BPDCN (blue) and AML (orange). o Pathway enrichment against REACTOME gene sets of promotor-associated CpGs between BPDCN (blue) and AML (orange). If not stated differently, differences between BPDCN and the four other entities were assessed by unpaired Wilcoxon test, and significant levels are indicated by asterisks (*p < 0.05, **p < 0.01, and ***p < 0.001).