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Myelodysplastic syndrome (MDS) is a hematopoietic stem cell disorder. Several genetic/epigenetic abnormalities are deeply associated with the pathogenesis of MDS. Although bone marrow (BM) aspiration is a common strategy to obtain MDS cells for evaluating their genetic/epigenetic abnormalities, BM aspiration is difficult to perform repeatedly to obtain serial samples because of pain and safety concerns. Here, we report that circulating cell-free DNAs from plasma and serum of patients with MDS can be used to detect genetic/epigenetic abnormalities. The plasma DNA concentration was found to be relatively high in patients with higher blast cell counts in BM, and accumulation of DNA fragments from mono-/di-nucleosomes was confirmed. Using serial peripheral blood (PB) samples from patients treated with hypomethylating agents, global methylation analysis using bisulfite pyrosequencing was performed at the specific CpG sites of the LINE-1 promoter. The results confirmed a decrease of the methylation percentage after treatment with azacitidine (days 3-9) using DNAs from plasma, serum, and PB mono-nuclear cells (PBMNC). Plasma DNA tends to show more rapid change at days 3 and 6 compared with serum DNA and PBMNC. Furthermore, the TET2 gene mutation in DNAs from plasma, serum, and BM cells was quantitated by pyrosequencing analysis. The existence ratio of mutated genes in plasma and serum DNA showed almost equivalent level with that in the CD34+/38- stem cell population in BM. These data suggest that genetic/epigenetic analyses using PB circulating DNA can be a safer and painless alternative to using BM cells.

Although rituximab is a critical monoclonal antibody therapy for CD20-positive B-cell lymphomas, rituximab resistance showing a CD20-negative phenotypic change has been a considerable clinical problem. Here we demonstrate that CD20 mRNA and protein expression is repressed by recruitment of a histone deacetylase protein complex to the MS4A1 (CD20) gene promoter in CD20-negative transformed cells after treatment with rituximab. CD20 mRNA and protein expression were stimulated by decitabine (5-Aza-dC) in CD20-negative transformed cells, and was enhanced by trichostation A (TSA). Immunoblotting indicated that DNMT1 expression was first downregulated 1 day after treatment with 5-Aza-dC, but IRF4 and Pu.1, the transcriptional regulators of MS4A1, were still expressed with or without 5-Aza-dC. Interestingly, CpG methylation of the MS4A1 promoter was not observed in CD20-negative transformed cells without 5-Aza-dC. A chromatin immunoprecipitation (ChIP) assay indicated that the Sin3A-HDAC1 co-repressor complex was recruited to the promoter and dissociated from the promoter with 5-Aza-dC and TSA, resulting in histone acetylation. Under these conditions, IRF4 and Pu.1 were continually recruited to the promoter with or without 5-Aza-dC and TSA. These results suggest that recruitment of the Sin3A-HDAC1 complex is related to downregulation of CD20 expression in CD20-negative B-cells after treatment with rituximab.

PML-RARalpha is a chimeric transcription factor tightly associated with acute promyelocytic leukemia. PML-RARalpha plays an important role in the aberrant transcription repression on the target genes of wild-type retinoic acid receptors. Here, we demonstrated that HDAC3, one component of the N-CoR transcription repressor complex, is a key regulator of the transcription repression by PML-RARalphain vivo. Using immunoprecipitation, we demonstrated that PML-RARalpha interacts with N-CoR/HDAC3 in vivo without ligand. Next, using chromatin immunoprecipitation (ChIP) assay, this N-CoR/HDAC3 co-repressor complex was recruited to the endogenous target promoters (RARbeta and CYP26) through PML-RARalpha. The neighboring histones were de-acetylated and gene expression was repressed. When HDAC3 protein was knocked down by RNA interference in PML-RARalpha-expressing cells, the endogenous target genes were significantly activated, which was also confirmed by promoter-luciferase reporter assay. These results provide evidence to show that the N-CoR/HDAC3 co-repressor complex is involved in the aberrant transcription regulation in PML-RARalpha-expressing cells.