Epigenetic transcriptional repression of tumor suppresor genes and its reversion by drugs.

Genetic alterations and deregulation of the epigenetic mechanisms collaborate in the initiation and progression of cancer. In contrast to the genetic defects, the epigenetic abnormalities are potentially reversible. This fact has driven the search for drugs that induce selectively changes in the epigenetic patterns of the tumor cells and thus lead to differentiation, cell death and/or cell growth arrest. Inhibitors of DNA (cytosine-5)-methyltransferases (DNMTs) and inhibitors of Zn(II)-dependent histone deacetylases (HDACs) have been developed with this purpose. The DNMTs inhibitors allow the reactivation of genes, including tumor-suppressor genes, silenced through hypermethylation of the CpG island at their promoter. The HDACs inhibitors allow the reexpression of genes silenced by ypoacetylation of the histones associated at their promoters. Despite all these chemicals have promising effects on cultured cancer cells, many of them have side-effects that limit their use in anticancer chemotherapy. Because of that, we analyzed the properties of the anesthetic procaine (4-aminobenzoic acid 2-diethylaminoethyl ester) as a new inducer of DNA demethylation and we also compared the effects of seven HDACs inhibitors. In both cases, the breast cancer cell line MCF7 was the model system. 1. Procaine reduces the proportion of 5-methylcytosine into global genomic DNA, achieving its maximum effect within 24-48 h of treatment. Low concentrations of procaine decrease the amount of 5- methylcytosine at RAR¦Â2 promoter, which is hypermethylated in MCF7 cells, and reactivate its expression with only small decrease in global DNA methylation. This fact could be an advantage, since global DNA hypomethylation leads to chromosomal instability. Finally, procaine reduces cell proliferation and arrests cell cycle in mitosis, but does not induce apoptosis in MCF7 cells after treatments 3 days long. 2. The seven inhibitors of Zn(II)-dependent HDACs chosen for comparison were: two carboxylic acids (butanoic and valproic acid); one N-(2¡¯-aminophenyl) benzamide (MS-275); and four hydroxamic acids(trichostatin A, suberoylanilide hydroxamic acid, CX and CY). The results of in vitro HDAC activity assays performed on MCF7 nuclear extracts show the existence of a relationship between the chemical structure of these compounds and their activity: low micromolar concentrations of hydroxamic acids are sufficient for inhibiting almost completely the deacetylase activity, whereas millimolar concentrations of carboxylic acids are required for similar effects. Also the alterations that the drugs cause on cell growth and cell cycle arrest depend on its chemical structure. The IC50 for cell treatments 24 h long is in the range of millimolar concentrations for butanoic and valproic acids and low micromolar for the rest of the chemicals. At the IC50, MS-275 induces cell growth arrest in G1/G0, whereas the hydroxamic acids stop cell cycle mostly at G2/M and the carboxylic acids seems to arrest the cycle at both G1/G0 and G2/M. Despite all these inhibitors induce similar changes in the global acetylation of H4 and H3 when employed at their respective IC50, not all of them are able of reactivate the expression of the same genes. Moreover, it seems that the induced expression levels of CDKN1A and GADD45¦Â determine the alterations induced by the drugs on cell cycle. The changes on histone modifications at the promoters of six genes ( CDKN1A, GADD45¦Â, JunD, IGFBP3, MT1X and MT2A) upon CY treatment were studied. HDACs inhibition induces an increase in histone H4 tetraacetylation and in dimethylation of lysine 4 in H3, as well as a decrease in dimethylation of lysine 9 in H3. Additionally, HDAC2 is released from the promoters upon CY treatment. These changes take place also in the promoters of MT1X and MT2A, the genes whose expression remains unaltered after the treatment with CY. __________________________________________________________________________________________________ RESUMEN Las alteraciones gen¨¦ticas y la desregulaci¨®n de los mecanismos epigen¨¦ticos colaboran en la iniciaci¨®n y progresi¨®n del c¨¢ncer. Los defectos epigen¨¦ticos son potencialmente reversibles, lo que ha suscitado la b¨²squeda de f¨¢rmacos que selectivamente causen cambios en los patrones epigen¨¦ticos de las c¨¦lulas tumorales, con la consiguiente diferenciaci¨®n, muerte y/o parada de crecimiento de las mismas. Se han estudiado especialmente inhibidores de metiltransferasas de DNA (DNMTs) e inhibidores de desacetilasas de histonas (HDACs) dependientes de Zn(II). Los inhibidores de DNMTs posibilitan la reactivaci¨®n de genes silenciados mediante hipermetilaci¨®n de la isla CpG de su promotor y los inhibidores de HDACs, de genes silenciados v¨ªa hipoacetilaci¨®n de las histonas asociadas a su promotor. A pesar de sus prometedores efectos en cultivos celulares, muchas de estas sustancias presentan inconvenientes que limitan su aplicaci¨®n en quimioterapia. Por ello, en esta tesis: 1. Se ha estudiado por primera vez la capacidad del anest¨¦sico proca¨ªna para reducir la metilaci¨®n de DNA gen¨®mico y la proliferaci¨®n de la l¨ªnea celular MCF7. Proca¨ªna reduce la cantidad de 5-metilcitosina en DNA, reactiva genes silenciados por hipermetilaci¨®n ( RAR¦Â2) e induce parada del ciclo celular en mitosis. 2. Se han comparado siete inhibidores de HDACs dependientes de Zn(II): ¨¢cido butanoico, ¨¢cido valproico, MS-275, tricostatina A (TSA), SAHA, CX y CY. Existe una relaci¨®n estructura-actividad para los efectos de estas sustancias en ensayos in vitro y en el crecimiento de MCF7. Adem¨¢s, aunque estos inhibidores inducen cambios similares en acetilaci¨®n global de histonas, no todos reactivan los mismos genes. Los niveles expresi¨®n de CDKN1A y GADD45¦Â parecen determinar los efectos de estos compuestos en el ciclo celular. En los promotores de los seis genes estudiados, la inhibici¨®n de HDACs aumenta la acetilaci¨®n de H4 y la dimetilaci¨®n de la lisina 4 de H3, mientras disminuye la dimetilaci¨®n de lisina 9 de H3

DNA methylation polymorphisms precede any histological sign of atherosclerosis in mice lacking apolipoprotein E

The present work investigates the occurrence and significance of aberrant DNA methylation patterns during early stages of atherosclerosis. To this end, we asked whether the genetically atherosclerosis-prone APOE-null mice show any changes in DNA methylation patterns before the appearance of histologically detectable vascular lesion. We exploited a combination of various techniques: DNA fingerprinting, in vitro methyl-accepting assay, 5-methylcytosine quantitation, histone post-translational modification analysis, Southern blotting, and PCR. Our results show that alterations in DNA methylation profiles, including both hyper- and hypomethylation, were present in aortas and PBMC of 4-week-old mutant mice with no detectable atherosclerotic lesion. Sequencing and expression analysis of 60 leukocytic polymorphisms revealed that epigenetic changes involve transcribed genic sequences, as well as repeated interspersed elements. Furthermore, we showed for the first time that atherogenic lipoproteins promote global DNA hypermethylation in a human monocyte cell line. Taken together, our results unequivocally show that alterations in DNA methylation profiles are early markers of atherosclerosis in a mouse model and may play a causative role in atherogenesis

Developmental regulation of N-terminal H2B methylation in Drosophila melanogaster

Histone post-translational modifications play an important role in regulating chromatin structure and gene expression in vivo. Extensive studies investigated the post-translational modifications of the core histones H3 and H4 or the linker histone H1. Much less is known on the regulation of H2A and H2B modifications. Here, we show that a major modification of H2B in Drosophila melanogaster is the methylation of the N-terminal proline, which increases during fly development. Experiments performed in cultured cells revealed higher levels of H2B methylation when cells are dense, regardless of their cell cycle distribution. We identified dNTMT (CG1675) as the enzyme responsible for H2B methylation. We also found that the level of N-terminal methylation is regulated by dART8, an arginine methyltransferase that physically interacts with dNTMT and asymmetrically methylates H3R2. Our results demonstrate the existence of a complex containing two methyltransferases enzymes, which negatively influence each other’s activity

Release of hypoacetylated and trimethylated histone H4 is an epigenetic marker of early apoptosis

Nuclear events such as chromatin condensation, DNA cleavage at internucleosomal sites, and histone release from chromatin are recognized as hallmarks of apoptosis. However, there is no complete understanding of the molecular events underlying these changes. It is likely that epigenetic changes such as DNA methylation and histone modifications that are involved in chromatin dynamics and structure are also involved in the nuclear events described. In this report we have shown that apoptosis is associated with global DNA hypomethylation and histone deacetylation events in leukemia cells. Most importantly, we have observed a particular epigenetic signature for early apoptosis defined by a release of hypoacetylated and trimethylated histone H4 and internucleosomal fragmented DNA that is hypermethylated and originates from perinuclear heterochromatin. These findings provide one of the first links between apoptotic nuclear events and epigenetic markers

Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells

The nucleolus is the site of ribosome synthesis in the nucleus, whose integrity is essential. Epigenetic mechanisms are thought to regulate the activity of the ribosomal RNA (rRNA) gene copies, which are part of the nucleolus. Here we show that human cells lacking DNA methyltransferase 1 (Dnmt1), but not Dnmt33b, have a loss of DNA methylation and an increase in the acetylation level of lysine 16 histone H4 at the rRNA genes. Interestingly, we observed that SirT1, a NAD+-dependent histone deacetylase with a preference for lysine 16 H4, interacts with Dnmt1; and SirT1 recruitment to the rRNA genes is abrogated in Dnmt1 knockout cells. The DNA methylation and chromatin changes at ribosomal DNA observed are associated with a structurally disorganized nucleolus, which is fragmented into small nuclear masses. Prominent nucleolar proteins, such as Fibrillarin and Ki-67, and the rRNA genes are scattered throughout the nucleus in Dnmt1 deficient cells. These findings suggest a role for Dnmt1 as an epigenetic caretaker for the maintenance of nucleolar structure

Histone deacetylases as new therapy targets for platinum-resistant epithelial ovarian cancer

Introduction: In developed countries, ovarian cancer is the fourth most common cancer in women. Due to the nonspecific symptomatology associated with the disease many patients with ovarian cancer are diagnosed late, which leads to significantly poorer prognosis. Apart from surgery and radiotherapy, a substantial number of ovarian cancer patients will undergo chemotherapy and platinum based agents are the mainstream first-line therapy for this disease. Despite the initial efficacy of these therapies, many women relapse; therefore, strategies for second-line therapies are required. Regulation of DNA transcription is crucial for tumour progression, metastasis and chemoresistance which offers potential for novel drug targets. Methods: We have reviewed the existing literature on the role of histone deacetylases, nuclear enzymes regulating gene transcription. Results and conclusion: Analysis of available data suggests that a signifant proportion of drug resistance stems from abberant gene expression, therefore HDAC inhibitors are amongst the most promising therapeutic targets for cancer treatment. Together with genetic testing, they may have a potential to serve as base for patient-adapted therapies

Histone deacetylase inhibition results in a common metabolic profile associated with HT29 differentiation

Cell differentiation is an orderly process that begins with modifications in gene expression. This process is regulated by the acetylation state of histones. Removal of the acetyl groups of histones by specific enzymes (histone deacetylases, HDAC) usually downregulates expression of genes that can cause cells to differentiate, and pharmacological inhibitors of these enzymes have been shown to induce differentiation in several colon cancer cell lines. Butyrate at high (mM) concentration is both a precursor for acetyl-CoA and a known HDAC inhibitor that induces cell differentiation in colon cells. The dual role of butyrate raises the question whether its effects on HT29 cell differentiation are due to butyrate metabolism or to its HDAC inhibitor activity. To distinguish between these two possibilities, we used a tracer-based metabolomics approach to compare the metabolic changes induced by two different types of HDAC inhibitors (butyrate and the non-metabolic agent trichostatin A) and those induced by other acetyl-CoA precursors that do not inhibit HDAC (caprylic and capric acids). [1,2-13C2]-d-glucose was used as a tracer and its redistribution among metabolic intermediates was measured to estimate the contribution of glycolysis, the pentose phosphate pathway and the Krebs cycle to the metabolic profile of HT29 cells under the different treatments. The results demonstrate that both HDAC inhibitors (trichostatin A and butyrate) induce a common metabolic profile that is associated with histone deacetylase inhibition and differentiation of HT29 cells whereas the metabolic effects of acetyl-CoA precursors are different from those of butyrate. The experimental findings support the concept of crosstalk between metabolic and cell signalling events, and provide an experimental approach for the rational design of new combined therapies that exploit the potential synergism between metabolic adaptation and cell differentiation processes through modification of HDAC activity

Fine Mapping of Posttranslational Modifications of the Linker Histone H1 from Drosophila melanogaster

The linker histone H1 binds to the DNA in between adjacent nucleosomes and contributes to chromatin organization and transcriptional control. It is known that H1 carries diverse posttranslational modifications (PTMs), including phosphorylation, lysine methylation and ADP-ribosylation. Their biological functions, however, remain largely unclear. This is in part due to the fact that most of the studies have been performed in organisms that have several H1 variants, which complicates the analyses. We have chosen Drosophila melanogaster, a model organism, which has a single H1 variant, to approach the study of the role of H1 PTMs during embryonic development. Mass spectrometry mapping of the entire sequence of the protein showed phosphorylation only in the ten N-terminal amino acids, mostly at S10. For the first time, changes in the PTMs of a linker H1 during the development of a multicellular organism are reported. The abundance of H1 monophosphorylated at S10 decreases as the embryos age, which suggests that this PTM is related to cell cycle progression and/or cell differentiation. Additionally, we have found a polymorphism in the protein sequence that can be mistaken with lysine methylation if the analysis is not rigorous

CpG methylation potentiates pixantrone and doxorubicin-induced DNA damage and is a marker of drug sensitivity

DNA methylation is an epigenetic modification of the mammalian genome that occurs predominantly at cytosine residues of the CpG dinucleotide. Following formaldehyde activation, pixantrone alkylates DNA and particularly favours the CpG motif. Aberrations in CpG methylation patterns are a feature of most cancer types, a characteristic that may determine their susceptibility to specific drug treatments. Given their common target, DNA methylation may modulate the DNA damage induced by formaldehyde-activated pixantrone. In vitro transcription, mass spectrometry and oligonucleotide band shift assays were utilized to establish that pixantrone–DNA adduct formation was consistently enhanced 2–5-fold at discrete methylated CpG doublets. The methylation-mediated enhancement was exquisitely sensitive to the position of the methyl substituent since methylation at neighboring cytosine residues failed to confer an increase in pixantrone–DNA alkylation. Covalent modification of DNA by formaldehyde-activated doxorubicin, but not cisplatin, was augmented by neighbouring CpG methylation, indicating that modulation of binding by CpG methylation is not a general feature of all alkylators. HCT116 colon cancer cells vastly deficient in CpG methylation were 12- and 10-fold more resistant to pixantrone and doxorubicin relative to the wild-type line, suggesting that these drugs may selectively recognize the aberrant CpG methylation profiles characteristic of most tumour types

Epigenetics provides a new generation of oncogenes and tumour-suppressor genes

Cancer is nowadays recognised as a genetic and epigenetic disease. Much effort has been devoted in the last 30 years to the elucidation of the ‘classical' oncogenes and tumour-suppressor genes involved in malignant cell transformation. However, since the acceptance that major disruption of DNA methylation, histone modification and chromatin compartments are a common hallmark of human cancer, epigenetics has come to the fore in cancer research. One piece is still missing from the story: are the epigenetic genes themselves driving forces on the road to tumorigenesis? We are in the early stages of finding the answer, and the data are beginning to appear: knockout mice defective in DNA methyltransferases, methyl-CpG-binding proteins and histone methyltransferases strongly affect the risk of cancer onset; somatic mutations, homozygous deletions and methylation-associated silencing of histone acetyltransferases, histone methyltransferases and chromatin remodelling factors are being found in human tumours; and the first cancer-prone families arising from germline mutations in epigenetic genes, such as hSNF5/INI1, have been described. Even more importantly, all these ‘new' oncogenes and tumour-suppressor genes provide novel molecular targets for designed therapies, and the first DNA-demethylating agents and inhibitors of histone deacetylases are reaching the bedside of patients with haematological malignancies