• Deciphering mechanisms of DNA methylation regulation by depletion of the DNA methyltransferases and SETD2

      Tiedemann, Rochelle Lee; Department of Biochemistry and Molecular Biology / Cancer Center (2015)
      DNA methylation (5mC) is a stabile epigenetic mark that confers differential function for gene expression and chromatin accessibility dependent on the context and locality of the mark. Promoter regions populated by CpG islands (CGIs) are highly unmethylated while the remaining ∼80% of CpGs are methylated and distributed across gene bodies, repetitive and transposable elements, and intergenic regions of the genome. The presence and/or absence of particular histone modifications also dictate the patterning of 5mC genome-wide. In cancer, a reversal of 5mC patterns occur in which hypermethylation of tumor suppressor gene CGIs confers gene silencing, and hypomethylation of repetitive and transposable elements contribute to genomic instability. The mechanisms by which 5mC becomes aberrantly regulated in cancer remain unknown. In this study, direct and indirect mechanisms of 5mC regulation were investigated. To understand the direct regulation of 5mC genome-wide, we depleted cell line models of the DNA methyltransferases (DNMTs) that are responsible for establishing (DNMT3A, DNMT3B, DNMT3L) and maintaining (DNMT1) 5mC patterns. Profiling of 5mC patterns on the Illumina HumanMethylation450 BeadChip revealed a unique antithetical relationship between DNMT1 and DNMT3B for the regulation of both 5mC and DNA hydroxymethylation (5hmC) across gene bodies. DNMT3B mediated nonCpG methylation, while DNMT3L influenced the activity of DNMT3B toward nonCG versus CpG site methylation. DNMT3B depletion induced 5mC patterns that closely resemble those observed during cellular differentiation and occurred across gene bodies of highly expressed, H3K36me3-marked genes. SETD2, the histone methyltransferase responsible for H3K36me3 establishment across active gene bodies, was determined to influence the guidance of DNA methylation genome-wide through an indirect mechanism. SETD2 knockout induced widespread loss of H3K36me3 that did not coincide with changes in 5mC. However, paradoxical gains in H3K36me3 significantly induced hypermethylation and upregulation of underlying genes. Genes marked exclusively by the poised enhancer mark, H3K4me1, were commonly targeted for this epigenetic phenotype. DNA methylome profiling of loss-of-function SETD2 mutated clear cell renal cell carcinoma, papillary renal cell carcinoma, and lung adenocarcinoma tumors confirmed the predominance of the hypermethylation phenotype upon loss of SETD2. Collectively, these studies provide novel insight to understanding the regulatory mechanisms by which 5mC patterns are conferred.
    • Role of DNA methyltransferases in maintaining mammary stem/progenitor and cancer stem cells

      Pathania, Rajneesh; Department of Biochemistry and Molecular Biology (2015)
      Breast cancer is the leading cause of cancer death in women worldwide and it affects one in eight women in western countries. Like other human cancers, breast cancer also consists of cellular hierarchy, and heterogeneous. However, the cancer cell of origin and how a normal self-renewal pathway turns into abnormal self-renewal signaling are not known. DNA methylation provides a potential epigenetic mechanism for the cellular memory and heterogeneity, which needed to preserve the tumorigenic potential through repeated cell divisions. Further DNA methylation plays an essential role in stem/progenitor cell maintenance and provides a potential epigenetic mechanism for maintaining cellular memory and heterogeneity during self-renewal. However, the specific role of DNMTs in maintaining mammary stem cells (MaSC) and cancer stem cell (CSC) in a constantly replenishing organ, like mammary glands, is not yet known. Here, we show that Dnmt1 is essential for mammary gland development and indispensable for terminal end bud development and that mammary-gland specific Dnmt1 deletion in mice leads to significant reduction in mammary stem/progenitor cell formation. Moreover, Dnmt1 deletion almost completely abolishes Neu-Tg- and C3(1)-SV40-Tg- driven mammary tumor formation. The reduced tumor incidence observed in Dnmt1 deleted mouse is associated to significant reduction in cancer stem cell formation. These observations were recapitulated using pharmacological inhibitors of DNMTs in Neu-Tg mice in vivo. Further, we show that there is a substantial increase in DNMT1 expression when mammary stem/progenitor cells turn into tumor initiating cells. Using genome-scale methylation approach, we found that hypermethylation of genes involved in development and cell commitment pathways impart immortality and autonomous growth to the cancer stem cells. Moreover, our study provides evidence that stem cells, in addition to luminal progenitor cells, are susceptible for genetic and epigenetic modification and associated with chemotherapeutic resistance. Thus, combination of DNMT and HDAC inhibitors can be used as a therapeutic strategy to block mammary tumor formation and to overcome drug resistance by inhibiting CSCs. These findings improve our understanding of abnormal self-renewal associated with cell of origin, and highlight novel methylation markers that have the potential to serve as useful diagnostic tools and therapeutic targets in early detection of breast cancer.