The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.

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The transition from follicle to corpus luteum after ovulation is associated with profound morphological and functional changes and is accompanied by corresponding changes in gene expression. The gene encoding the α subunit of the dimeric reproductive hormone inhibin is maximally expressed in the granulosa cells of the preovulatory follicle, is rapidly repressed by the ovulatory LH surge, and is expressed at only very low levels in the corpus luteum. Although previous studies have identified transient repressors of inhibin α gene transcription, little is known about how this repression is maintained in the corpus luteum. This study examines the role of epigenetic changes, including DNA methylation and histone modification, in silencing of inhibin α gene expression. Bisulfite sequencing reveals that methylation of the inhibin α proximal promoter is low in preovulatory and ovulatory follicles but is elevated in the corpus luteum. Increased methylation during luteinization is observed within the cAMP response element in the promoter, and EMSA demonstrate that methylation of this site inhibits cAMP response element binding protein binding in vitro. Chromatin immunoprecipitation reveals that repressive histone marks H3K9 and H3K27 trimethylation are increased on the inhibin α promoter in primary luteal cells, whereas the activation mark H3K4 trimethylation is decreased. The changes in histone modification precede the alterations in DNA methylation, suggesting that they facilitate the recruitment of DNA methyltransferases. We show that the DNA methyltransferase DNMT3a is present in the ovary and in luteal cells when the inhibin α promoter becomes methylated and observe recruitment of DNMT3a to the inhibin promoter during luteinization.

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While medical ethics has been considered since the early days of civilization, it has come into prominence over the course of the last century due to medical advances that have an impact upon a broad array of health issues ranging from conception to the end-of-life and beyond. In light of the pace and scope of current technological developments in medicine, medical ethics now has an even greater level of importance and relevance to biomedical science and clinical practice as the amount and uses of medical information reach even further into the unknown.

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Acute myeloid leukemia (AML) is a disease of aberrant hematopoietic differentiation believed to mirror the hierarchical pattern of hematopoiesis with leukemia stem cells (LSC) serving as the originating cell population from which the tumor arises. Like hematopoietic stem cells (HSC), leukemia stem cells are believed to be largely quiescent and therefore impervious to conventional chemotherapeutics resulting in relapse of disease despite achievement of clinical remission. The DNA methylation profiles of bulk leukemia cells differ significantly from normal CD34+ cells; however, less is known about the potential differences between epigenetic profiles of purified LSC and normal HSC. Moreover, the stability of the methylome as the LSC differentiate into mature leukemia progenitor cells (LPC) has not been studied. In order to address this LSC, LPC, and HSC were sorted from the bone marrow of AML patients and normal controls based on CD34, CD38, CD45 and ALDH activity. LSC were defined as CD34+ CD38- ALDHmid; LPC as CD34+ CD38+; and HSC as CD34+ CD38- ALDHhigh. These isolated fractions were used for genome-wide DNA methylation analysis by the next-generation enhanced reduced representation bisulfite sequencing (ERRBS) assay, which allowed for the comparison of the methylation landscapes of LSC and HSC, as well as those of LSC and LPC. A total of thirteen AML samples were examined for the presence of LSC, six of which did not have an ALDHmid population but had instead an ALDHhigh population. Because of their phenotypic similarity to normal HSC, these samples were not included in the present comparison against HSC. The methylomes of six independent LSC samples were compared to methylomes of five HSC. Sequenced ERRBS libraries were aligned against the human genome (hg19) and differentially methylated regions (DMR) were identified using a beta-binomial model and selecting regions with absolute mean methylation difference of >25% and false discovery rate (FDR) < 10%. The methylation profiles of LSC showed widespread genome wide differences relative to HSC; 39,162 regions were found to be hypermethylated in LSC while 5,408 regions were hypomethylated. DMRs were enriched at CpG islands as well as intra- and intergenic enhancers. Functional annotation of the DMRs to gene sets in the MSigDb database revealed enrichment for genes marked by the Polycomb repressive mark H3K27me3 (FDR = 1.86×10-49). In order to determine whether epigenetic abnormalities observed at the LSC level were distinct from the epigenetic profiles observed in the more mature LPC fraction, we compared paired LSC and LPC specimens from 6 AML patients. Notably, LPC did not significantly differ in their epigenetic profiles from LSC, indicating that epigenetic abnormalities acquired at the LSC stage are stably transmitted through leukemic expansion to the more mature LPC fraction. In summary, we have identified widespread epigenetic abnormalities acquired at the LSC stage, of greater magnitude than was previously recognized by performing comparisons of leukemic cells to unfractionated CD34+ controls. Genes targeted by aberrant methylation in LSC are significantly enriched in Polycomb target genes, suggesting a potential role for Polycomb proteins in leukemic transformation. By contrast, no significant epigenetic differences were observed between the LSC and LPC fractions in AML, indicating that epigenetic abnormalities acquired at the LSC level are static through multiple cell generations. Disclosures Gore: Celgene: Consultancy, Honoraria, Research Funding.