Patrizia D’Aquila

miR-29b induces SOCS-1 expression by promoter demethylation and negatively regulates migration of multiple myeloma and endothelial cells

Epigenetic silencing of tumor suppressor genes frequently occurs and may account for their inactivation in cancer cells. We previously demonstrated that miR-29b is a tumor suppressor microRNA (miRNA) that targets de novo DNA methyltransferases and reduces the global DNA methylation of multiple myeloma (MM) cells. Here, we provide evidence that epigenetic activity of miR-29b leads to promoter demethylation of suppressor of cytokine signaling-1 (SOCS-1), a hypermethylated tumor suppressor gene. Enforced expression of synthetic miR-29b mimics in MM cell lines resulted in SOCS-1 gene promoter demethylation, as assessed by Sequenom MassARRAY EpiTYPER analysis, and SOCS-1 protein upregulation. miR-29b-induced SOCS-1 demethylation was associated with reduced STAT3 phosphorylation and impaired NFκB activity. Downregulation of VEGF-A and IL-8 mRNAs could be detected in MM cells transfected with miR-29b mimics as well as in endothelial (HUVEC) or stromal (HS-5) cells treated with conditioned medium from miR-29b-transfected MM cells. Notably, enforced expression of miR-29b mimics increased adhesion of MM cells to HS-5 and reduced migration of both MM and HUVEC cells. These findings suggest that miR-29b is a negative regulator of either MM or endothelial cell migration. Finally, the proteasome inhibitor bortezomib, which induces the expression of miR-29b, decreased global DNA methylation by a miR-29b-dependent mechanism and induced SOCS-1 promoter demethylation and protein upregulation. In conclusion, our data indicate that miR-29b is endowed with epigenetic activity and mediates previously unknown functions of bortezomib in MM cells.

Global DNA methylation in old subjects is correlated with frailty

Epigenetic variations have been widely described to occur during the aging process. To verify if these modifications are correlated with the inter-individual phenotypic variability of elderly people, we searched for a correlation between global DNA methylation levels and frailty. We found that the global DNA methylation levels were correlated to the frailty status in middle/advanced-aged subjects but not with age. A 7-year follow-up study also revealed that a worsening in the frailty status was associated to a significant decrease in the global DNA methylation levels. These results suggest that the relaxation of the epigenetic control in aging is specifically associated with the functional decline rather than with the chronological age of individuals. Thus, the modifications of DNA methylation, representing a drawbridge between the genetic and the environmental factors affecting the age-related decay of the organism, may play an important role in determining physiological changes over old age.

Mitochondria in health, aging and diseases: the epigenetic perspective

The rate/quality of human aging and the development/progression of diseases depend on a complex interplay among genetics, epigenetics and environment. In this scenario, mitochondrial function (or dysfunction) and mitochondrial DNA have emerged as major players. This is mainly due to their crucial role in energetic balance, in modulating epigenetic programs and in influencing cell stress response. Moreover, it is also emerging the existence of epigenetic changes in mitochondrial DNA and of non coding mitochondrial RNAs which, together with the nuclear ones, play regulatory roles in numerous human phenotypes. In this review we will provide an overview on “mitochondrial epigenetics” state of the art, by summarizing the involvement of mitochondrial function and of mitochondria–nucleus communication in regulating nuclear epigenome, as well as the key aspects of the epigenetic marks related to mitochondrial DNA. Despite the limited data available in the literature to date, mainly due to the novelty of the topic, the intriguing interplay of the mitochondrial epigenetic changes in both physiological and pathological conditions will also be presented.

Directed organization of DNA filaments in a soft matter template.

We have developed a noninvasive, all-optical, holographic technique for permanently aligning liquid crystalline DNA filaments in a microperiodic template realized in soft-composite (polymeric) materials. By combining optical intensity holography with a selective microfluidic etching process, a channelled microstructure has been realized which enables self-assembly of DNA. The striking chemicophysical properties of the structure immobilize the DNA filaments within the microchannels without the need of any kind of surface chemistry or functionalization. Polarized optical, confocal, and electronic microscopies have been used for characterizing the DNA geometry inside the microchannels in terms of birefringence, fluorescence, and nanoscale organization properties. In particular, observation of a far-field diffraction pattern confirms a periodic organization of the DNA filaments inside the polymeric template.

Epigenetic modifications in multiple myeloma: recent advances on the role of DNA and histone methylation

ABSTRACT Introduction: Multiple Myeloma (MM) is a clonal late B-cell disorder accounting for about 13% of hematological cancers and 1% of all neoplastic diseases. Recent studies on the molecular pathogenesis and biology of MM have highlighted a complex epigenomic landscape contributing to MM onset, prognosis and high individual variability. Areas covered: We describe here the current knowledge on epigenetic events characterizing MM initiation and progression, focusing on the role of DNA and histone methylation and on the most promising epi-therapeutic approaches targeting the methylation pathway. Expert opinion: Data published so far indicate that alterations of the epigenetic framework, which include aberrant global or gene/non-coding RNA specific methylation profiles, feature prominently in the pathobiology of MM. Indeed, the aberrant expression of components of the epigenetic machinery as well as the reversibility of the epigenetic marks make this pathway druggable, providing the basis for the design of epigenetic therapies against this still fatal malignancy.

Estradiol via estrogen receptor beta influences ROS levels through the transcriptional regulation of SIRT3 in human seminoma TCam-2 cells

Human testis, gonocytes, and adult germ cells mainly express estrogen receptor beta, and estrogen receptor beta loss is associated with advanced tumor stage; however, the molecular mechanisms of estrogen receptor beta–protective effects are still to be defined. Herein, we provide evidence that in human seminoma TCam-2 cells, E2 through estrogen receptor beta upregulates the mitochondrial deacetylase sirtuin-3 at protein and messenger RNA levels. Specifically, E2 increases sirtuin-3 expression through a transcriptional mechanism due to the occupancy of sirtuin-3 promoter by estrogen receptor beta, together with the transcription factor Sp1 as evidenced by Chip reChIp assay. This complex binds to a GC cluster located between −128 bp/+1 bp and is fundamental for E2 effects, as demonstrated by Sp1 small interfering RNA studies. Beside, after 24 h, E2 stimulus significantly increased activities of superoxide dismutase and catalase to scavenge reactive oxygen species produced by 30 min of E2 stimulus. In summary, this article indicates a novel functional interplay between estrogen receptor beta and sirtuin-3 counteracting reactive oxygen species production in TCam-2 cells. Our findings thus show that an important tumor-suppressive pathway through estrogen receptor beta is target of E2, actually proposing a distinctive protecting action against seminoma. Future studies may lead to additional strategies for the current therapy of seminoma.

The methylation of nuclear and mitochondrial DNA in ageing phenotypes and longevity

An increasing body of data is progressively indicating that the comprehension of the epigenetic landscape, actively integrated with the genetic elements, is crucial to delineate the molecular basis of the inter-individual complexity of ageing process. Indeed, it has emerged that DNA methylation changes occur during ageing, consisting mainly in a progressive process of genome demethylation, in a hypermethylation of gene-specific CpG dinucleotides, as well as in an inter-individual divergence of the epigenome due to stochastic events and environmental exposures throughout life, namely as epigenetic drift. Additionally, it has also come to light an implication of the mitochondrial genome in the regulation of the intracellular epigenetic landscape, as demonstrated by the being itself object of epigenetic modifications. An overview of DNA methylation changes occurring during ageing process at both nuclear and mitochondrial level will be described in this review, also taking into account the recent and promising data available on the 5-hydroxymethylcytosine.

Aging and nutrition induce tissue-specific changes on global DNA methylation status in rats

A number of epigenetic studies have demonstrated that DNA methylation patterns exhibit a tissue specificity, but not much has been done to highlight the extent of this phenomenon. Moreover, it is unknown how external factors modulate the plasticity of the tissue specific epigenetic profile. We examined global DNA methylation profiles in tissues from rats of different age, fed with standard or low-calorie diet, and evaluated their association with aging and nutrition. Tissue-specific variations occur during aging with hyper-methylation taking place in all tissues except for liver. The expression of enzymes involved in methylation reactions (DNMTs and TETs) was consistent with the methylation patterns. Nutrition affects global DNA methylation status throughout lifespan. Interestingly, the differences among different tissues are magnified in 96 weeks old rats fed with low calorie diet. Moreover, the low-calorie diet appears to affect the offsprings epigenetic status more strongly if administered during the maternal pre-gestational period than the gestational and lactation time. Therefore, we propose that changes in the global DNA methylation status may represent an epigenetic mechanism by which age and nutrition intersect each other and, in turn, influence the aging plasticity.

Heterogeneity of Thyroid Function and Impact of Peripheral Thyroxine Deiodination in Centenarians and Semi-Supercentenarians: Association With Functional Status and Mortality

Thyroid hormones (FT3, FT4) and thyroid-stimulating hormone (TSH) were evaluated in a population of 672 well-characterized Italian subjects (age range: 52-113 years), including an unprecedented number of centenarians, semi-supercentenarians, as well as centenarians offspring and age-matched elderly (CENT, 105+, CENTOFF, and CTRL, respectively). The results show that FT3 level and FT3/FT4 ratio decrease while FT4 and TSH increase in an age-dependent manner. In CENT/105+, higher FT4 level, and lower FT3/FT4 ratio are associated with an impaired functional status and an increased mortality. A cluster analysis identified three clusters of CENT/105+ based on their FT3, FT4, and TSH levels. Cluster 3, characterized by lower FT3 and TSH and higher FT4, shows the worst health status and the shortest survival. Thus, the age-related changes of thyroid hormones extend to the most advanced age, and CENT/105+ are highly heterogeneous regarding thyroid function. This heterogeneity is related to different health, functional and cognitive status, as well as with survival/mortality in CENT/105+. Finally, we investigated a remarkable number of CENT/105+ showing a thyroid profile suggestive of non-thyroidal illness syndrome (NTIS) (excluded from the previous analysis). NTIS CENT/105+ are characterized by a worse functional and cognitive status and an increased mortality with respect to CENT/105+ without NTIS.

rRNA-gene methylation and biological aging

Epigenetic modifications, which are programmed across the individual’s lifespan by the genetic background but also modulated by environmental and lifestyle factors, are widely studied to identify biomarkers of human aging. Indeed, Garagnani et al. identified three genes whose methylation level strongly correlates with age [1]. Subsequently, Horvarth defined a high precise DNA methylation clock, able to predict age, with a low margin of error, based on methylation levels of a series of CpG sites scattered throughout the genome. These markers, and others which have consequently been identified, have proved to be reliable enough to be used for forensic purposes in order to define the age of human subjects by analysing these markers in different specimens (such as teeth, blood, semen) [2]. On the other hand, most of the scientists involved with research on aging are willing to identify epigenetic modifications correlated with biological rather than with chronological age. Such markers may be important firstly because the definition of biological age in the elderly may be much more useful than chronological age to identify the subjects needing (medical or social) care; secondly, because the identification of genes the methylation of which is correlated with biological aging may give important clues on the aging process and, possibly, on how to modulate it. Many hints suggest that these markers are likely to exist. For instance, global methylation showed to be correlated with biological and not with chronological age [3]. Ribosomal RNA (rRNA) genes consist of highly evolutionary conserved tandem and clusters of units within nucleolar organizer regions, distributed, in humans, on the short arms of acrocentric chromosomes. The expression of rRNA genes is regulated during different stages of lifetime by several factors, including nutrients, transcription factors and epigenetic marks as well [4, 5]. Previous studies have indicated that alterations of rRNA expression may be related to specific pathological conditions, such as different types of cancers and Alzheimer Disease [6]. In addition, the analysis of fibroblasts from patients with Werner Syndrome, and of hematopoietic cells from rats of different ages suggested a correlation with physiological and pathological aging. These data, coupled with the acknowledged importance of protein use and storage in the elderly, attracted our interest, suggesting that the expression of rRNA genes may be correlated to the functional status of old subjects Editorial