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1.
Front Genet ; 13: 792165, 2022.
Article in English | MEDLINE | ID: mdl-35571061

ABSTRACT

Control of ribosome biogenesis is a critical aspect of the regulation of cell metabolism. As ribosomal genes (rDNA) are organized in repeated clusters on chromosomes 13, 14, 15, 21, and 22, trisomy of chromosome 21 confers an excess of rDNA copies to persons with Down syndrome (DS). Previous studies showed an alteration of ribosome biogenesis in children with DS, but the epigenetic regulation of rDNA genes has not been investigated in adults with DS so far. In this study, we used a targeted deep-sequencing approach to measure DNA methylation (DNAm) of rDNA units in whole blood from 69 adults with DS and 95 euploid controls. We further evaluated the expression of the precursor of ribosomal RNAs (RNA45S) in peripheral blood mononuclear cells (PBMCs) from the same subjects. We found that the rDNA promoter tends to be hypermethylated in DS concerning the control group. The analysis of epihaplotypes (the combination of methylated and unmethylated CpG sites along the same DNA molecule) showed a significantly lower intra-individual diversity in the DS group, which at the same time was characterized by a higher interindividual variability. Finally, we showed that RNA45S expression is lower in adults with DS. Collectively, our results suggest a rearrangement of the epigenetic profile of rDNA in DS, possibly to compensate for the extranumerary rDNA copies. Future studies should assess whether the regulation of ribosome biogenesis can contribute to the pathogenesis of DS and explain the clinical heterogeneity characteristic of the syndrome.

2.
Geroscience ; 43(3): 1283-1302, 2021 06.
Article in English | MEDLINE | ID: mdl-33870444

ABSTRACT

Ageing leaves characteristic traces in the DNA methylation make-up of the genome. However, the importance of DNA methylation in ageing remains unclear. The study of subtelomeric regions could give promising insights into this issue. Previously reported associations between susceptibility to age-related diseases and epigenetic instability at subtelomeres suggest that the DNA methylation profile of subtelomeres undergoes remodelling during ageing. In the present work, this hypothesis has been tested in the context of the European large-scale project MARK-AGE. In this cross-sectional study, we profiled the DNA methylation of chromosomes 5 and 21 subtelomeres, in more than 2000 age-stratified women and men recruited in eight European countries. The study included individuals from the general population as well as the offspring of nonagenarians and Down syndrome subjects, who served as putative models of delayed and accelerated ageing, respectively. Significant linear changes of subtelomeric DNA methylation with increasing age were detected in the general population, indicating that subtelomeric DNA methylation changes are typical signs of ageing. Data also show that, compared to the general population, the dynamics of age-related DNA methylation changes are attenuated in the offspring of centenarian, while they accelerate in Down syndrome individuals. This result suggests that subtelomeric DNA methylation changes reflect the rate of ageing progression. We next attempted to trace the age-related changes of subtelomeric methylation back to the influence of diverse variables associated with methylation variations in the population, including demographics, dietary/health habits and clinical parameters. Results indicate that the effects of age on subtelomeric DNA methylation are mostly independent of all other variables evaluated.


Subject(s)
Aging , DNA Methylation , Aged, 80 and over , Aging/genetics , Blood Cells , Cross-Sectional Studies , Europe , Female , Humans , Male
3.
Leukemia ; 35(2): 389-403, 2021 02.
Article in English | MEDLINE | ID: mdl-32409690

ABSTRACT

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer characterized by skewed epigenetic patterns, raising the possibility of therapeutically targeting epigenetic factors in this disease. Here we report that among different cancer types, epigenetic factor TET1 is highly expressed in T-ALL and is crucial for human T-ALL cell growth in vivo. Knockout of TET1 in mice and knockdown in human T cell did not perturb normal T-cell proliferation, indicating that TET1 expression is dispensable for normal T-cell growth. The promotion of leukemic growth by TET1 was dependent on its catalytic property to maintain global 5-hydroxymethylcytosine (5hmC) marks, thereby regulate cell cycle, DNA repair genes, and T-ALL associated oncogenes. Furthermore, overexpression of the Tet1-catalytic domain was sufficient to augment global 5hmC levels and leukemic growth of T-ALL cells in vivo. We demonstrate that PARP enzymes, which are highly expressed in T-ALL patients, participate in establishing H3K4me3 marks at the TET1 promoter and that PARP1 interacts with the TET1 protein. Importantly, the growth related role of TET1 in T-ALL could be antagonized by the clinically approved PARP inhibitor Olaparib, which abrogated TET1 expression, induced loss of 5hmC marks, and antagonized leukemic growth of T-ALL cells, opening a therapeutic avenue for this disease.


Subject(s)
DNA Methylation , DNA-Binding Proteins/physiology , Gene Expression Regulation, Leukemic , Mixed Function Oxygenases/metabolism , Phthalazines/pharmacology , Piperazines/pharmacology , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins/physiology , Animals , Apoptosis , Cell Proliferation , Histones , Humans , Mice , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , Mixed Function Oxygenases/genetics , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/metabolism , Promoter Regions, Genetic , Proto-Oncogene Proteins/genetics , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
4.
Nutrients ; 11(12)2019 Dec 06.
Article in English | MEDLINE | ID: mdl-31817660

ABSTRACT

Alu hypomethylation promotes genomic instability and is associated with aging and age-related diseases. Dietary factors affect global DNA methylation, leading to changes in genomic stability and gene expression with an impact on longevity and the risk of disease. This preliminary study aims to investigate the relationship between nutritional factors, such as circulating trace elements, lipids and antioxidants, and Alu methylation in elderly subjects and offspring of healthy nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly recruited age-stratified individuals from the general population) and thirty-two GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project. Factor analysis revealed a different clustering between Alu CpG1 and the other CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO subjects in the same age class. Moreover, Alu CpG1 methylation was associated with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper. The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a potential marker of aging. Our preliminary investigation shows that Alu methylation may be affected by food rich in fibers and antioxidants, or circulating LDL subfractions and plasma copper.


Subject(s)
Aging/genetics , Alu Elements , DNA Methylation , Nutrients/blood , Adult , Aged , Aging/blood , Antioxidants/analysis , CpG Islands , Diet , Female , Healthy Volunteers , Humans , Italy , Lipoproteins/blood , Lipoproteins/genetics , Longevity/genetics , Male , Middle Aged , Nutritional Status , Trace Elements/blood
5.
Front Oncol ; 9: 198, 2019.
Article in English | MEDLINE | ID: mdl-31001470

ABSTRACT

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive blood cancer caused by the deregulation of key T-cell developmental pathways, including Notch signaling. Aberrant Notch signaling in T-ALL occurs by NOTCH1 gain-of-function mutations and by NOTCH3 overexpression. Although NOTCH3 is assumed as a Notch1 target, machinery driving its transcription in T-ALL is undefined in leukemia subsets lacking Notch1 activation. Here, we found that the binding of the intracellular Notch3 domain, as well as of the activated Notch1 fragment, to the NOTCH3 gene locus led to the recruitment of the H3K27 modifiers JMJD3 and p300, and it was required to preserve transcriptional permissive/active H3K27 marks and to sustain NOTCH3 gene expression levels. Consistently, pharmacological inhibition of JMJD3 by GSKJ4 treatment or of p300 by A-485 decreased the levels of expression of NOTCH3, NOTCH1 and of the Notch target genes DELTEX1 and c-Myc and abrogated cell viability in both Notch1- and Notch3-dependent T-cell contexts. Notably, re-introduction of exogenous Notch1, Notch3 as well as c-Myc partially rescued cells from anti-growth effects induced by either treatment. Overall our findings indicate JMJD3 and p300 as general Notch1 and Notch3 signaling co-activators in T-ALL and suggest further investigation on the potential therapeutic anti-leukemic efficacy of their enzymatic inhibition in Notch/c-Myc axis-related cancers and diseases.

6.
Mech Ageing Dev ; 174: 3-17, 2018 09.
Article in English | MEDLINE | ID: mdl-29268958

ABSTRACT

DNA methylation is currently the most promising molecular marker for monitoring aging and predicting life expectancy. However, the mechanisms underlying age-related DNA methylation changes remain mostly undiscovered. Here we discuss the current knowledge of the dynamic nature of DNA epigenome landscape in mammals, and propose putative molecular mechanisms for aging-associated DNA epigenetic changes. Specifically, we describe age-related variations of methylcytosine and its oxidative derivatives in relation to the dynamics of chromatin structure, histone post-translational modifications and their modulators. Finally, we are proposing a conceptual framework that could explain the complex nature of the effects of age on DNA methylation patterns. This combines the accumulation of DNA methylation noise and also all of the predictable, site-specific DNA methylation changes. Gathering information in this area would pave the way for future investigation aimed at establishing a possible causative role of epigenetic mechanisms in aging.


Subject(s)
Aging/physiology , Chromatin/metabolism , DNA Methylation/physiology , Epigenesis, Genetic/physiology , Histones/metabolism , Protein Processing, Post-Translational/physiology , Animals , Chromatin/genetics , Histones/genetics , Humans
7.
J Gerontol A Biol Sci Med Sci ; 73(6): 737-744, 2018 05 09.
Article in English | MEDLINE | ID: mdl-29069286

ABSTRACT

Down syndrome (DS) is caused by the presence of part or an entire extra copy of chromosome 21, a phenomenon that can cause a wide spectrum of clinically defined phenotypes of the disease. Most of the clinical signs of DS are typical of the aging process including dysregulation of immune system. Beyond the causative genetic defect, DS persons display epigenetic alterations, particularly aberrant DNA methylation patterns that can contribute to the heterogeneity of the disease. In the present work, we investigated the levels of 5-hydroxymethylcytosine and of the Ten-eleven translocation dioxygenase enzymes, which are involved in DNA demethylation processes and are often deregulated in pathological conditions as well as in aging. Analyses were carried out on peripheral blood mononuclear cells of DS volunteers enrolled in the context of the MARK-AGE study, a large-scale cross-sectional population study with subjects representing the general population in eight European countries. We observed a decrease in 5-hydroxymethylcytosine, TET1, and other components of the DNA methylation/demethylation machinery in DS subjects, indicating that aberrant DNA methylation patterns in DS, which may have consequences on the transcriptional status of immune cells, may be due to a global disturbance of methylation control in DS.


Subject(s)
Aging/blood , Aging/genetics , DNA Methylation , Down Syndrome/blood , Down Syndrome/genetics , Leukocytes, Mononuclear/metabolism , 5-Methylcytosine/analogs & derivatives , 5-Methylcytosine/blood , Adult , Aged , Cross-Sectional Studies , Epigenesis, Genetic , Europe , Female , Humans , Immunoblotting , Italy , Male , Middle Aged , Mixed Function Oxygenases/blood , Proto-Oncogene Proteins/blood , RNA, Messenger/blood
8.
J Gerontol A Biol Sci Med Sci ; 73(6): 745-753, 2018 05 09.
Article in English | MEDLINE | ID: mdl-29045571

ABSTRACT

Metallothionein (MT) family are cysteine-rich proteins that regulate zinc (Zn) homeostasis and protect against oxidative damage. Studies in transgenic mice have shown that MT favorably influence longevity, although their role in human aging is not completely understood. Within the European multicenter study MARK-AGE, we analyzed MT induction after Zn treatment in peripheral blood mononuclear cells (PBMCs) and its relation with redox biomarkers in 2,936 age-stratified subjects (35-75 years) including the general population (RASIG), centenarian offspring (GO), and their spouses (SGO). We found that the lymphocyte capability to induce MT in response to Zn is not affected by aging. However, GO participants showed lower Zn-induced MT and increased basal expression of MT1A, MT1X, and ZnT-1 genes than RASIG subjects. Moreover, Zn-induced MT levels were found to be inversely related with oxidative stress markers (plasma protein carbonyls, 3-nitrotyrosine, and malondialdehyde) in the whole population, but not in GO subjects. In conclusion, our results support the hypothesis that the response to Zn is attenuated in PBMCs of centenarian offspring compared to the general population as a consequence of a tighter control of Zn homeostasis which is likely to provide them constant protection against stress stimuli over the whole lifespan.


Subject(s)
Biomarkers/metabolism , Leukocytes, Mononuclear/metabolism , Metallothionein/metabolism , Zinc/pharmacology , Adult , Aged , Aged, 80 and over , Cell Culture Techniques , Cross-Sectional Studies , Europe , Female , Flow Cytometry , Humans , Male , Middle Aged , Oxidative Stress , RNA/metabolism , Real-Time Polymerase Chain Reaction
9.
Semin Cell Dev Biol ; 63: 123-134, 2017 03.
Article in English | MEDLINE | ID: mdl-27908606

ABSTRACT

Epigenetic events include reversible modifications of DNA and histone tails driving chromatin organization and thus transcription. The epigenetic regulation is a highly integrated process underlying the plasticity of the genomic information both in the context of complex physiological and pathological processes. The global regulatory aspects of epigenetic events are largely unknown. PARylation and PARP1 are recently emerging as multi-level regulatory effectors that modulate the topology of chromatin by orchestrating very different processes. This review focuses in particular on the role of PARP1 in epigenetics, trying to build a comprehensive perspective of its involvement in the regulation of epigenetic modifications of histones and DNA, contextualizing it in the global organization of chromatin domains in the nucleus.


Subject(s)
Chromatin/metabolism , Epigenesis, Genetic , Poly(ADP-ribose) Polymerases/metabolism , ADP-Ribosylation , Animals , Humans , Models, Biological
10.
Aging (Albany NY) ; 8(9): 1896-1922, 2016 08 29.
Article in English | MEDLINE | ID: mdl-27587280

ABSTRACT

Gradual changes in the DNA methylation landscape occur throughout aging virtually in all human tissues. A widespread reduction of 5-methylcytosine (5mC), associated with highly reproducible site-specific hypermethylation, characterizes the genome in aging. Therefore, an equilibrium seems to exist between general and directional deregulating events concerning DNA methylation controllers, which may underpin the age-related epigenetic changes. In this context, 5mC-hydroxylases (TET enzymes) are new potential players. In fact, TETs catalyze the stepwise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), driving the DNA demethylation process based on thymine DNA glycosylase (TDG)-mediated DNA repair pathway. The present paper reports the expression of DNA hydroxymethylation components, the levels of 5hmC and of its derivatives in peripheral blood mononuclear cells of age-stratified donors recruited in several European countries in the context of the EU Project 'MARK-AGE'. The results provide evidence for an age-related decline of TET1, TET3 and TDG gene expression along with a decrease of 5hmC and an accumulation of 5caC. These associations were independent of confounding variables, including recruitment center, gender and leukocyte composition. The observed impairment of 5hmC-mediated DNA demethylation pathway in blood cells may lead to aberrant transcriptional programs in the elderly.


Subject(s)
5-Methylcytosine/metabolism , Aging/genetics , DNA Methylation , Dioxygenases/genetics , Gene Expression Regulation , Mixed Function Oxygenases/genetics , Proto-Oncogene Proteins/genetics , Adult , Aged , Aging/metabolism , Dioxygenases/metabolism , Female , Gene Expression , Humans , Leukocytes, Mononuclear/metabolism , Male , Middle Aged , Mixed Function Oxygenases/metabolism , Proto-Oncogene Proteins/metabolism
11.
Aging Cell ; 15(4): 755-65, 2016 08.
Article in English | MEDLINE | ID: mdl-27169697

ABSTRACT

Aging is associated with alterations in the content and patterns of DNA methylation virtually throughout the entire human lifespan. Reasons for these variations are not well understood. However, several lines of evidence suggest that the epigenetic instability in aging may be traced back to the alteration of the expression of DNA methyltransferases. Here, the association of the expression of DNA methyltransferases DNMT1 and DNMT3B with age has been analysed in the context of the MARK-AGE study, a large-scale cross-sectional study of the European general population. Using peripheral blood mononuclear cells, we assessed the variation of DNMT1 and DNMT3B gene expression in more than two thousand age-stratified women and men (35-75 years) recruited across eight European countries. Significant age-related changes were detected for both transcripts. The level of DNMT1 gradually dropped with aging but this was only observed up to the age of 64 years. By contrast, the expression of DNMT3B decreased linearly with increasing age and this association was particularly evident in females. We next attempted to trace the age-related changes of both transcripts to the influence of different variables that have an impact on changes of their expression in the population, including demographics, dietary and health habits, and clinical parameters. Our results indicate that age affects the expression of DNMT1 and DNMT3B as an almost independent variable in respect of all other variables evaluated.


Subject(s)
Aging/genetics , DNA (Cytosine-5-)-Methyltransferases/genetics , Gene Expression Regulation, Developmental , Gene Expression Regulation, Enzymologic , Leukocytes, Mononuclear/enzymology , White People/genetics , Adult , Aged , Body Mass Index , DNA (Cytosine-5-)-Methyltransferase 1 , DNA (Cytosine-5-)-Methyltransferases/metabolism , Female , Gene Ontology , Humans , Life Style , Male , Middle Aged , RNA, Messenger/genetics , RNA, Messenger/metabolism , Regression Analysis , Risk Factors , DNA Methyltransferase 3B
12.
PLoS One ; 10(12): e0144287, 2015.
Article in English | MEDLINE | ID: mdl-26636673

ABSTRACT

Poly(ADP-ribosyl)ation (PARylation) is a posttranslational protein modification catalyzed by members of the poly(ADP-ribose) polymerase (PARP) enzyme family. PARylation regulates a wide variety of biological processes in most eukaryotic cells including energy metabolism and cell death, maintenance of genomic stability, chromatin structure and transcription. Inside the nucleus, cross-talk between PARylation and other epigenetic modifications, such as DNA and histone methylation, was already described. In the present work, using PJ34 or ABT888 to inhibit PARP activity or over-expressing poly(ADP-ribose) glycohydrolase (PARG), we show decrease of global histone H3 and H4 acetylation. This effect is accompanied by a reduction of the steady state mRNA level of p300, Pcaf, and Tnfα, but not of Dnmt1. Chromatin immunoprecipitation (ChIP) analyses, performed at the level of the Transcription Start Site (TSS) of these four genes, reveal that changes in histone acetylation are specific for each promoter. Finally, we demonstrate an increase of global deacetylase activity in nuclear extracts from cells treated with PJ34, whereas global acetyltransferase activity is not affected, suggesting a role for PARP in the inhibition of histone deacetylases. Taken together, these results show an important link between PARylation and histone acetylation regulated transcription.


Subject(s)
Histones/metabolism , Poly Adenosine Diphosphate Ribose/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Transcription, Genetic , Acetylation , Animals , Benzimidazoles/pharmacology , DNA (Cytosine-5-)-Methyltransferase 1 , DNA (Cytosine-5-)-Methyltransferases/biosynthesis , E1A-Associated p300 Protein/biosynthesis , Genomic Instability , Mice , NIH 3T3 Cells , Phenanthrenes/pharmacology , Tumor Necrosis Factor-alpha/biosynthesis , p300-CBP Transcription Factors/biosynthesis
13.
Oncotarget ; 6(27): 24333-47, 2015 Sep 15.
Article in English | MEDLINE | ID: mdl-26136340

ABSTRACT

5-hydroxymethylcytosine is a new epigenetic modification deriving from the oxidation of 5-methylcytosine by the TET hydroxylase enzymes. DNA hydroxymethylation drives DNA demethylation events and is involved in the control of gene expression. Deregulation of TET enzymes causes developmental defects and is associated with pathological conditions such as cancer. Little information thus far is available on the regulation of TET activity by post-translational modifications. Here we show that TET1 protein is able to interact with PARP-1/ARTD1 enzyme and is target of both noncovalent and covalent PARylation. In particular, we have demonstrated that the noncovalent binding of ADP-ribose polymers with TET1 catalytic domain decreases TET1 hydroxylase activity while the covalent PARylation stimulates TET1 enzyme. In addition, TET1 activates PARP-1/ARTD1 independently of DNA breaks. Collectively, our results highlight a complex interplay between PARylation and TET1 which may be helpful in coordinating the multiple biological roles played by 5-hydroxymethylcytosine and TET proteins.


Subject(s)
Cytosine/analogs & derivatives , Gene Expression Regulation, Neoplastic , Mixed Function Oxygenases/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Proto-Oncogene Proteins/metabolism , 5-Methylcytosine/analogs & derivatives , Amino Acid Sequence , Catalytic Domain , Cytosine/metabolism , DNA Damage , DNA Methylation , Enzyme-Linked Immunosorbent Assay , Epigenesis, Genetic , Glutathione Transferase/metabolism , HEK293 Cells , Humans , Immunoprecipitation , Molecular Sequence Data , Poly (ADP-Ribose) Polymerase-1 , Protein Processing, Post-Translational , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid
14.
Oncotarget ; 6(17): 15008-21, 2015 Jun 20.
Article in English | MEDLINE | ID: mdl-25938539

ABSTRACT

To overcome cancer cells resistance to pharmacological therapy, the development of new therapeutic approaches becomes urgent. For this purpose, the use of poly(ADP-ribose) polymerase (PARP) inhibitors in combination with other cytotoxic agents could represent an efficacious strategy. Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification that plays a well characterized role in the cellular decisions of life and death. Recent findings indicate that PARP-1 may control the expression of Snail, the master gene of epithelial-mesenchymal transition (EMT). Snail is highly represented in different resistant tumors, functioning as a factor regulating anti-apoptotic programmes. MDA-MB-231 is a Snail-expressing metastatic breast cancer cell line, which exhibits chemoresistance properties when treated with damaging agents. In this study, we show that the PARP inhibitor ABT-888 was capable to modulate the MDA-MB-231 cell response to doxorubicin, leading to an increase in the rate of apoptosis. Our further results indicate that PARP-1 controlled Snail expression at transcriptional level in cells exposed to doxorubicin. Given the increasing interest in the employment of PARP inhibitors as chemotherapeutic adjuvants, our in vitro results suggest that one of the mechanisms through which PARP inhibition can chemosensitize cancer cells in vivo, is targeting Snail expression thus promoting apoptosis.


Subject(s)
Benzimidazoles/pharmacology , Doxorubicin/pharmacology , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly(ADP-ribose) Polymerases/metabolism , Transcription Factors/metabolism , Antibiotics, Antineoplastic/pharmacology , Apoptosis/drug effects , Apoptosis/genetics , Blotting, Western , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Inositol 1,4,5-Trisphosphate Receptors/genetics , MCF-7 Cells , Poly (ADP-Ribose) Polymerase-1 , Poly(ADP-ribose) Polymerases/genetics , Promoter Regions, Genetic/genetics , Protein Binding , Reverse Transcriptase Polymerase Chain Reaction , Snail Family Transcription Factors , Transcription Factors/genetics
15.
Mech Ageing Dev ; 151: 2-12, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25818235

ABSTRACT

Many candidate biomarkers of human ageing have been proposed in the scientific literature but in all cases their variability in cross-sectional studies is considerable, and therefore no single measurement has proven to serve a useful marker to determine, on its own, biological age. A plausible reason for this is the intrinsic multi-causal and multi-system nature of the ageing process. The recently completed MARK-AGE study was a large-scale integrated project supported by the European Commission. The major aim of this project was to conduct a population study comprising about 3200 subjects in order to identify a set of biomarkers of ageing which, as a combination of parameters with appropriate weighting, would measure biological age better than any marker in isolation.


Subject(s)
Aging/metabolism , Biomarkers/metabolism , European Union , Female , Humans , Male
16.
Mech Ageing Dev ; 151: 60-70, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25708826

ABSTRACT

A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.


Subject(s)
Aging/metabolism , CpG Islands/physiology , DNA Methylation/physiology , Epigenesis, Genetic/physiology , Genome, Human/physiology , Aging/genetics , Animals , Humans
17.
Biochim Biophys Acta ; 1839(9): 813-25, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24984200

ABSTRACT

Aberrant upregulation of NOTCH3 gene plays a critical role in cancer pathogenesis. However, the underlying mechanisms are still unknown. We tested here the hypothesis that aberrant epigenetic modifications in the NOTCH3 promoter region might account for its upregulation in cancer cells. We compared DNA and histone methylation status of NOTCH3 promoter region in human normal blood cells and T cell acute lymphoblastic leukemia (T-ALL) cell lines, differentially expressing NOTCH3. We found that histone methylation, rather than DNA hypomethylation, contributes towards establishing an active chromatin status of NOTCH3 promoter in NOTCH3 overexpressing cancer cells. We discovered that the chromatin regulator protein BORIS/CTCFL plays an important role in regulating NOTCH3 gene expression. We observed that BORIS is present in T-ALL cell lines as well as in cell lines derived from several solid tumors overexpressing NOTCH3. Moreover, BORIS targets NOTCH3 promoter in cancer cells and it is able to induce and to maintain a permissive/active chromatin conformation. Importantly, the association between NOTCH3 overexpression and BORIS presence was confirmed in primary T-ALL samples from patients at the onset of the disease. Overall, our results provide novel insights into the determinants of NOTCH3 overexpression in cancer cells, by revealing a key role for BORIS as the main mediator of transcriptional deregulation of NOTCH3.


Subject(s)
DNA-Binding Proteins/physiology , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Receptors, Notch/genetics , Cells, Cultured , DNA Methylation , Humans , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Promoter Regions, Genetic , Receptor, Notch3
18.
Oncotarget ; 5(21): 10356-67, 2014 Nov 15.
Article in English | MEDLINE | ID: mdl-24939750

ABSTRACT

TET enzymes are the epigenetic factors involved in the formation of the sixth DNA base 5-hydroxymethylcytosine, whose deregulation has been associated with tumorigenesis. In particular, TET1 acts as tumor suppressor preventing cell proliferation and tumor metastasis and it has frequently been found down-regulated in cancer. Thus, considering the importance of a tight control of TET1 expression, the epigenetic mechanisms involved in the transcriptional regulation of TET1 gene are here investigated. The involvement of poly(ADP-ribosyl)ation in the control of DNA and histone methylation on TET1 gene was examined. PARP activity is able to positively regulate TET1 expression maintaining a permissive chromatin state characterized by DNA hypomethylation of TET1 CpG island as well as high levels of H3K4 trimethylation. These epigenetic modifications were affected by PAR depletion causing TET1 down-regulation and in turn reduced recruitment of TET1 protein on HOXA9 target gene. In conclusion, this work shows that PARP activity is a transcriptional regulator of TET1 gene through the control of epigenetic events and it suggests that deregulation of these mechanisms could account for TET1 repression in cancer.


Subject(s)
Breast Neoplasms/genetics , DNA-Binding Proteins/metabolism , Epigenesis, Genetic , Poly(ADP-ribose) Polymerases/metabolism , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Proto-Oncogene Proteins/metabolism , Adenosine Diphosphate/metabolism , DNA Methylation/genetics , DNA-Binding Proteins/genetics , Female , Gene Expression Regulation, Neoplastic , Histones/genetics , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Humans , Jurkat Cells , MCF-7 Cells , Mixed Function Oxygenases , Poly(ADP-ribose) Polymerases/genetics , Proto-Oncogene Proteins/genetics , Transcription, Genetic/genetics
19.
BMC Cancer ; 14: 151, 2014 Mar 05.
Article in English | MEDLINE | ID: mdl-24593254

ABSTRACT

BACKGROUND: Chemoresistance of glioblastoma multiforme (GBM) has been attributed to the presence within the tumor of cancer stem cells (GSCs). The standard therapy for GBM consists of surgery followed by radiotherapy and the chemotherapeutic agent temozolomide (TMZ). However, TMZ efficacy is limited by O6-methylguanine-DNA-methyltransferase (MGMT) and Mismatch Repair (MMR) functions. Strategies to counteract TMZ resistance include its combination with poly(ADP-ribose) polymerase inhibitors (PARPi), which hamper the repair of N-methylpurines. PARPi are also investigated as monotherapy for tumors with deficiency of homologous recombination (HR). We have investigated whether PARPi may restore GSC sensitivity to TMZ or may be effective as monotherapy. METHODS: Ten human GSC lines were assayed for MMR proteins, MGMT and PARP-1 expression/activity, MGMT promoter methylation and sensitivity to TMZ or PARPi, alone and in combination. Since PTEN defects are frequently detected in GBM and may cause HR dysfunction, PTEN expression was also analyzed. The statistical analysis of the differences in drug sensitivity among the cell lines was performed using the ANOVA and Bonferroni's post-test or the non-parametric Kruskal-Wallis analysis and Dunn's post-test for multiple comparisons. Synergism between TMZ and PARPi was analyzed by the median-effect method of Chou and Talalay. Correlation analyses were done using the Spearman's rank test. RESULTS: All GSCs were MMR-proficient and resistance to TMZ was mainly associated with high MGMT activity or low proliferation rate. MGMT promoter hypermethylation of GSCs correlated both with low MGMT activity/expression (Spearman's test, P = 0.004 and P = 0.01) and with longer overall survival of GBM patients (P = 0.02). Sensitivity of each GSC line to PARPi as single agent did not correlate with PARP-1 or PTEN expression. Notably, PARPi and TMZ combination exerted synergistic antitumor effects in eight out of ten GSC lines and the TMZ dose reduction achieved significantly correlated with the sensitivity of each cell line to PARPi as single agent (P = 0.01). CONCLUSIONS: The combination of TMZ with PARPi may represent a valuable strategy to reverse GSC chemoresistance.


Subject(s)
Antineoplastic Agents, Alkylating/pharmacology , Dacarbazine/analogs & derivatives , Drug Resistance, Neoplasm , Glioblastoma/metabolism , Neoplastic Stem Cells/drug effects , Neoplastic Stem Cells/metabolism , Poly(ADP-ribose) Polymerase Inhibitors , Cell Line, Tumor , CpG Islands , DNA Methylation , Dacarbazine/pharmacology , Glioblastoma/genetics , Glioblastoma/mortality , Humans , O(6)-Methylguanine-DNA Methyltransferase/genetics , O(6)-Methylguanine-DNA Methyltransferase/metabolism , Poly (ADP-Ribose) Polymerase-1 , Poly(ADP-ribose) Polymerases/metabolism , Promoter Regions, Genetic , Temozolomide
20.
Proc Natl Acad Sci U S A ; 111(5): 2005-10, 2014 Feb 04.
Article in English | MEDLINE | ID: mdl-24449909

ABSTRACT

Many of the long-term effects of cocaine on the brain's reward circuitry have been shown to be mediated by alterations in gene expression. Several chromatin modifications, including histone acetylation and methylation, have been implicated in this regulation, but the effect of other histone modifications remains poorly understood. Poly(ADP-ribose) polymerase-1 (PARP-1), a ubiquitous and abundant nuclear protein, catalyzes the synthesis of a negatively charged polymer called poly(ADP-ribose) or PAR on histones and other substrate proteins and forms transcriptional regulatory complexes with several other chromatin proteins. Here, we identify an essential role for PARP-1 in cocaine-induced molecular, neural, and behavioral plasticity. Repeated cocaine administration, including self-administration, increased global levels of PARP-1 and its mark PAR in mouse nucleus accumbens (NAc), a key brain reward region. Using PARP-1 inhibitors and viral-mediated gene transfer, we established that PARP-1 induction in NAc mediates enhanced behavioral responses to cocaine, including increased self-administration of the drug. Using chromatin immunoprecipitation sequencing, we demonstrated a global, genome-wide enrichment of PARP-1 in NAc of cocaine-exposed mice and identified several PARP-1 target genes that could contribute to the lasting effects of cocaine. Specifically, we identified sidekick-1--important for synaptic connections during development--as a critical PARP-1 target gene involved in cocaine's behavioral effects as well as in its ability to induce dendritic spines on NAc neurons. These findings establish the involvement of PARP-1 and PARylation in the long-term actions of cocaine.


Subject(s)
Cocaine/pharmacology , Poly Adenosine Diphosphate Ribose/metabolism , Animals , Behavior, Animal/drug effects , Chromatin Immunoprecipitation , Cocaine/administration & dosage , Dendritic Spines/drug effects , Dendritic Spines/metabolism , Gene Expression Regulation, Enzymologic/drug effects , Genome/genetics , Immunoglobulin G/metabolism , Male , Membrane Proteins/metabolism , Mice , Mice, Inbred C57BL , Nucleus Accumbens/drug effects , Nucleus Accumbens/enzymology , Poly(ADP-ribose) Polymerases/genetics , Poly(ADP-ribose) Polymerases/metabolism , Protein Binding/drug effects , RNA, Messenger/genetics , RNA, Messenger/metabolism , Rats , Substrate Specificity/drug effects , Transcription, Genetic/drug effects
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