Epigenetic Regulation of Cardiac Regeneration




© Springer International Publishing Switzerland 2016
Rosalinda Madonna (ed.)Stem Cells and Cardiac RegenerationStem Cell Biology and Regenerative Medicine10.1007/978-3-319-25427-2_7


7. Epigenetic Regulation of Cardiac Regeneration



Silvia Agostini1, Marco Matteucci1, Valentina Casieri1, Gaia Papini1 and Vincenzo Lionetti 


(1)
Laboratory of Medical Science, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via G. Moruzzi, 1, Pisa, Italy

 



 

Vincenzo Lionetti



Keywords
MethylationUbiquitinationSumoylationLong non-coding RNAsExosomes



7.1 Self-Regeneration of the Adult Human Heart


A small percentage of cardiomyocyte’s proliferation occurs in adult human heart (Bergmann et al. 2009). This extraordinary phenomenon was demonstrated through the measurement of the amount of 14C incorporated into the DNA of cardiomyocytes of individuals born before and after the nuclear bomb tests and the comparison with the levels of atmospheric 14C. Interestingly, the detectable pool of new cardiomyocytes ranged from 1 % per year in young adults to 0.45 % in the elderly. While these renewal rates cannot support the endogenous myocardial self-regeneration in response to injury, they have nonetheless encouraged the study of any regulatory mechanism able to enhance it. Heart failure is an heterogeneous disease and recent scientific reports have demonstrated that the improvement of intercellular cross-talk is essential to foster a more effective adaptive response to injury (Tirziu et al. 2010). Less than a third of the total cell number of the adult myocardium consists of cardiomyocytes, which communicate with a broad pool of additional cell types, such as smooth muscle cells, endothelial cells, fibroblasts, mast cells, immune system-related cells and progenitor cells (Bu et al. 2009). The myocardial homeostasis implies different cell-to-cell and cell-to-matrix connections, which form a mature and self-regulated functional unit (Ausoni and Sartore 2009). These distinct cell pools also interact via a variety of soluble paracrine , autocrine and endocrine factors , which require a stable apparatus of gene expression (Lionetti et al. 2010a, b). Recent studies of developmental biology and integrative physiology have highlighted the role played by epigenetic modifications as common regulatory pathway of cell function and threshold of cell turnover in adult’s heart (Romano and Lionetti 2013). The epigenetic signals in fact activate, maintain, and change the cardiac transcriptional status underlying the tissue ability to tolerate the microenvironmental stress without losing functional coherence. All epigenetic pathways remodel chromatin and ensure the maintenance of cardiac homeostasis during several cell divisions and across generations without altering the DNA sequence. Lack of gene function and the cell death follow the failure of balancing epigenetic signals. Specific signaling pathways may drive the phenotype of cardiac resident cells at transcriptional and post-transcriptional levels in healthy and damaged hearts (Lionetti and Ventura 2013a, b). In particular, the following pathways play a key role in the self-regulation of the epigenetic state of adult cardiac cells: DNA methylation , histone modifications , and RNA-based modulation (Issa and Baylin 1996).


7.2 The Epigenetic Memory of Cardiac Cells: A Prelude to Myocardial Regeneration


The epigenetic memory relies on the ability of cardiac cells to translate environmental cues in adaptive response and it remains unchanged after several cell divisions. High levels of DNA methylation lead to maintenance of cell epigenetic memory (Sanchez-Freire et al. 2014). In addition, histone modifications support epigenetic inheritance mechanisms of adult cardiac cells during transient or persistent exposure to different microenvironments (Schlingman et al. 2014). Histone modifications, which determine the structure and function of the chromatin, transmit stable epigenetic information between proliferating cells. Finally, pool of regulatory small noncoding RNAs (ncRNAs) regulate the expression of factors leading to histone modifications, such as the Polycomb-group proteins (Mathiyalagan et al. 2014).


7.2.1 DNA Methylation


In cardiac cells the magnitude of DNA methylation at the C5 position of CpG islands is a balance of two biological processes : (1) de novo methylation or (2) maintenance of methylation during cellular DNA replication. Based on recent findings, the maintenance of methylation assumes a relevant biological role as DNA replication occurs in cardiomyocytes during adulthood (Bergmann et al. 2009). Cardiac DNA demethylation is specifically regulated by Ten-eleven translocation methylcytosine dioxygenase enzymes (TET) that oxidizes the methyl group of specific methylcytosines (Kinney et al. 2011).

The balance between DNA methylation or demethylation affects the expression and function of genes which regulate cardiac function. For example, low levels of circulating methylated Long Interspersed Nucleotide Elements-1 (LINE-1 ) gene, a biomarker of systemic DNA methylation (Yang et al. 2004), predicts intolerance to myocardial ischemia in elderly individuals (Baccarelli et al. 2010). Moreover, DNA hypermethylation even limits contractile function of rodent cardiomyocytes chronically exposed to norepinephrine-induced hypertrophy (Xiao et al. 2014). Different levels of DNA methylation in normal and failing hearts suggest that changes of epigenomic patterns affect the ability to predict the development of heart failure in humans (Movassagh et al. 2011). It is conceivable that high levels of DNA methylation represent an adaptive mechanism underlying the response to injury by adult cardiomyocytes.

Despite this fascinating hypothesis, DNA methylation does not affect tyrosine kinase-type cell surface receptor HER3 and Homeobox B13 genes, which play a key role in the expression of adaptive cardiac features in response to sustained contractile dysfunction (Haas et al. 2013).


7.2.2 Histone Modifications


Histones are basic proteins of the chromatin (H1, H2A and B, H3 and H4) that form the nucleosome after binding DNA. Histone modifications include the following enzymatic processes: acetylation (Taylor and Liew 1976), phosphorylation (Akhtar and Itzhaki 1977; Liew and Sole 1978), methylation (Kaneda et al. 2009), ADP-ribosylation (Martinez-Zamudio and Ha 2012), biotinylation (Kuroishi et al. 2011), ubiquitination (Zhang 2003) and sumoylation (Wang and Dasso 2009).

The balance between histone acetyltransferases (HATs ) or deacetylases (HDACs ) modulates DNA transcription in adult cardiac cells of animal models and humans (Miyamoto et al. 2006; Lee et al. 2007; Hariharan et al. 2010). In particular, nuclear HATs play a key role in cardiac hypertrophy (Qiao et al. 2014) and dilation (Miyamoto et al. 2006). However, loss of HATs activity causes the death of embryos due to serious cardiac congenital defects in p300 knock-in mice, where embryonal stem cells do not respond to cardiomyogenic factors (i.e.: BMP-2) (Shikama et al. 2003).

In 2010, we were one of the first to show that the early pharmacological inhibition of cardiac class I HDACs by intramyocardial injection of low dose of hyaluronan mixed estersof butyric and retinoic acid (HBR) induces the expression of paracrine factors that enhance angiogenesis (i.e.: vascular endothelial growth factor, VEGF) and survival/proliferation (i.e.: hepatocyte growth factor, HGF) of adult rat cardiomyocytes bordering the infarct zone. All these changes have preserved the cardiac function in a rodent model of myocardial infarction (Lionetti et al. 2010a, b). Other investigators have confirmed our data in vivo (Zhang et al. 2012). Preliminary evidences provided by us have also shown that HBR hampers cell proliferation and migration of cardiac fibroblasts , attenuates the differentiation to myofibroblasts and inhibits collagen expression (Cavallini et al. 2011). These evidences support the hypothesis that the inhibition of class I HDAC ) differently affects the myocardial epigenetic memory depending on the cell type.

Histone H3 phosphorylation at serine-10, a different histone modification, is detectable in proliferating cardiomyocytes of heart exposed to unloading conditions (Canseco et al. 2015) or stimulated with growth factors (Illi et al. 2005). In addition, Histone H3 Ser-10 phosphorylation leads to transcription of Mef2, a transcription factor that induces cell growth (Awad et al. 2013).

Mono-, di- or tri-methylation of arginine or lysine residues of histone H3 and H4 leads to active or repressed states of chromatin in murine adult cardiac cells (Chaturvedi et al. 2014). Loss of methylation at lysine K4 of histone H3 (H3K4) increases intracellular calcium levels resulting in improved contractile function (Stein et al. 2011). The role of histone biotinylation , ADP-ribosylation and sumoylation in myocardial adaptive response to stressors is still unknown.


7.2.3 RNA-Based Epigenetic Modulators


MicroRNAs (miR) are small non-coding RNAs , long about 22 nucleotides, that degrade the complementary mRNA after binding the RNA-induced silencing complex (RISC ) (Brennecke et al. 2005). To date, miRNAs play a role as pathophysiological hallmark of cardiac disease/repair at post-trascriptional level. For example, high circulating levels of miR-1, 21, 133a, 208 and 499 are detectable after myocardial injury (Zile et al. 2011).

In addition, plasma levels of cardiac muscle-enriched miR (i.e.: miR-133a and 208a) increase in patients with coronary artery disease (Fichtlscherer et al. 2010). The profile of circulating miRNAs may be helpful to identify cardiovascular patients even at earlier and later stages of disease. They are also helpful to track the short- and long-term effects of different regenerative approach. In fact, high levels of miR-323-3p and -652 are detected in untreated patients affected by acute coronary syndrome compared to healthy controls up to 4 months post-hospitalization (Pilbrow et al. 2014) and significantly improve the risk stratification in combination with established biomarkers of cardiac dysfunction, such as high levels of N-terminal of the prohormone brain natriuretic peptide (NT-proBNP ) and low left ventricular ejection fraction (Pilbrow et al. 2014). Recent studies even highlighted the role of miRNAs as epigenetic paracrine mediators of cell-to-cell/cell-to-matrix interactions in adult heart. Cardioprotective and proangiogenic miRNAs are released into exosomes , nanosized extracellular vesicles, which are detectable in myocardial interstitium and have a strong therapeutic potential (Cervio et al. 2015).

Long non-coding RNAs (LncRNAs ), long about 200 nucleotides, play a role in regulating cardiac physiological traits at both transcriptional and post-transcriptional levels, even if they lack significant protein-coding potential (Guttman et al. 2009). Despite LncRNAs expression being affected by cardiovascular disorders (Ounzain et al. 2015), their epigenetic role in mediating myocardial regeneration is still not well defined. Emerging evidences suggest that LncRNAs modulate the expression of miRNAs during hypertrophic response of adult cardiomyocytes to stressors, as angiotensin II (Wang et al. 2014).

Deregulated epigenetic patterns through LncRNAs expression underlies the lack of angiogenic ability of coronary endothelial cells in response to hypoxia. For example, lower levels of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a lncRNA highly expressed in hypoxic adult endothelial cells , inhibit endothelial cell proliferation and VEGF-dependent vessel growth (Michalik et al. 2014). A recent study demonstrated that lncRNAs have a differential abundance in exosomes, indicating a selective loading by producing cells (Gezer et al. 2014).


7.3 Epigenetic Modifications in Regenerating Myocardium


Epigenetic modifications are emerging as endogenous mechanisms sustaining cardiac self-renewing properties and are therapeutic candidates for regeneration of heart failure.


7.3.1 DNA Methylation


Leferovich et al. (2001) have observed a high cardiac regenerative potential in MRL/MpJ mice, which show cells arrested in the G2/M phase and high activity of matrix metalloproteinases. In particular, the heart of adult MRL/MpJ mice shows high levels of DNA methylation and retains embryonic features (Górnikiewicz et al. 2013). However, the heart of these mice does not heal after myocardial infarction (Cimini et al. 2008) and I/R injury (Abdullah et al. 2005). This observation suggests that the microenvironment promotes the switch on DNA methylation peak from embryonic to adult profile therefore limiting the regenerative potential of the myocardium. This model may be helpful to detect the genes responsible of the low regenerative capacity of adult heart. Recent studies have demonstrated that Notch-responsive promoters, which support cardiomyocytes proliferation in zebrafish heart (Zhao et al. 2014), show higher levels of permanent CpG DNA methylation in adult murine cardiomyocytes of infarcted hearts compared to healthy ones (Felician et al. 2014). Notch-responsive promoters are permanently silenced by DNA methylation.

Conversely, another study has shown that the pharmacological inhibition of DNA methylation in rodent stem cells induces protein expression of homeobox protein Nkx2.5 , transcription factor GATA binding protein 4 (GATA4) and cardiac troponin T which trigger the differentiation to cardiac lineage (Naeem et al. 2013). Therefore, the modulators of levels of DNA methylation are therapeutic candidate to enhance myocardial regeneration.


7.3.2 Histone Modifications


HATs activation increases acetylation of lysine K9 and K14 of histone H3 at physiological level, reduces levels of DNA CpG methylation, and recovers the ability of mesenchymal stem cells to proliferate and differentiate to cardiac lineage in the presence of oxidative stress (Vecellio et al. 2014).

Conversely, the inhibition of HDACs induces the proliferation of adult rodent cardiomyocytes both in vitro and in vivo (Majumdar et al. 2012). In small and large animal models of heart failure, myocardial histone acetylation increase the expression and release of paracrine factors, such as the hepatocyte growth factor (HGF) (Iwasaki et al. 2005) or the vascular endothelial growth factor (VEGF) (Tao et al. 2011).

Some growth factors may in turn activate HDACs. For example, VEGF play an epigenetic role by inducing the degradation of HDAC7 via phospholipase C gamma-inositol-1,4,5-trisphosphate kinase signal pathway, which prevents the HDAC7-mediated inhibition of cell proliferation, as observed in mature endothelial cells (Margariti et al. 2010).

Recent studies have highlighted the epigenetic role of other important paracrine factors involved in myocardial angiogenesis . Li et al. (2014) have demonstrated that carbon monoxide enhances the levels of histone acetylation, which in turn improves endothelial cell migration , and increases the angiogenic ability of human endothelial cells (Lionetti et al. 2010a, b; Agostini et al. 2015) following the treatment with inhibitors of class I HDACs. These data refute previous in vitro studies demonstrating that the maintenance of HDAC activity induces angiogenesis (Kim et al. 2001; Mottet et al. 2007).

Furthermore, Mezentseva et al. (2013) have demonstrated in vitro that low levels of methylation at lysine9 of histone H3 leads to reprogramming of bone marrow stem cells towards a cardiac lineage.

These studies encourage the development of novel and safer histone modulators also to optimize the cardiac differentiation of circulating bone marrow -derived stem cells engrafted in the failing heart.


7.3.3 RNA-Based Epigenetic Modulators


The cardiac delivery of miR-590 and -199 promoted cell cycle re-entry of adult cardiomyocytes and enhanced cardiomyocyte proliferation in infarcted murine heart (Eulalio et al. 2012). These data are in accord with previous studies suggesting that endogenous miRNAs act as endogenous regulators of cell reprogramming and as therapeutic targets in the setting of novel avenue in cell-free cardiac regeneration. However, miRNAs even may exert negative effect on cell function.

Bonauer et al. (2009) have shown that high levels of miR-92a inhibits the formation of new blood vessels, which play a relevant role in the functional recovery of murine infarcted heart . In light of this evidence, the synthesis of miRNA antagonists may be a helpful tool to promote myocardial regeneration . In fact, treatment with selective LNA-modified anti-miR-15 prevented loss of hypoxic cardiomyocytes, reduced infarct scar size and preserved cardiac function in murine infarcted heart (Hullinger et al. 2012). Interestingly, stable myocardial down-regulation of miR-24 enhances angiogenesis and blood perfusion in the myocardium surrounding the infarct area and improves cardiac function despite promoting apoptosis of fibroblasts and cardiomyocytes (Meloni et al. 2013).

To date, it remains unclear whether the modulation of single miR-dependent pathway is sufficient to trigger cardiomyocyte’s proliferation in regenerating the adult infarcted heart. The selective inhibition of miRNA-15 even increases the rate of proliferation of adult cardiomyocytes and significantly improves the cardiac function of infarcted murine heart (Porrello et al. 2013). Conversely, other investigators found that an effective proliferation of adult cardiomyocytes require the combined action of several miRNAs, such as miR17-92 cluster (Chen et al. 2013). Jayawardena et al. (Jayawardena et al. 2012) have demonstrated in mice that a cocktail of miR-1, -133, -208 and -499 restores the post-ischemic loss of cardiomyocyte’s pool with a population of fibroblast-derived cardiomyocytes due to gene reprogramming. All these findings suggest that mir-crine mechanisms hold great promise as therapeutic candidates for the development of personalized myocardial regeneration.

Regulatory miRNAs are naturally released by cardiomyocytes , endothelial cells , fibroblasts or cardiac/endothelial progenitor cells , as demonstrated in adult mice (Brás-Rosário et al. 2013). Exosomes containing miRNAs are released into the extracellular microenvironment by adult cardiomyocytes (Wang et al. 2014), cardiac fibroblasts (Bang et al. 2014), endothelial cells (Ong et al. 2014) and cardiac progenitor cells (Vrijsen et al. 2010).

Exosomes secreted by human cardiac progenitor cells (CPCs ) contain higher amounts of miRNA210, 132 and 146a-3p compared with human cardiac fibroblasts (Barile et al. 2014). Each miRNA acts on specific pathways; miRNA210 inhibits cardiomyocyte’s apoptosis through the down regulation of ephrin A3 and protein-tyrosine phosphatase 1B (PTP1B) expression, while miRNA132 increases the angiogenic ability of mature endothelial cells through the down regulation of RasGAP-p120 expression . The single intramyocardial injection of CPCs-derived exosomes hampers cardiac remodeling and preserves left ventricular ejection fraction of infarcted rat heart in a dose-dependent manner. Conversely, fibroblasts-derived exosomes did not exert any cardioprotective effects. Other investigators have found similar findings in a murine model of heart failure (Ibrahim et al. 2014).

Some investigators are developing new methods to increase the endogenous release of cardioprotective exosomes containing miRNAs. Original study found that high levels of hypoxia-inducible factor-1 (HIF-1), a transcription factor that protects against ischemia and highly expressed in human failing heart (Lionetti et al. 2014), increase the release of exosomes containing miRNA126 and 210 (Ong et al. 2014). Therefore, the exosomes have the potential to circumvent many limitations of stem cells transplantation for therapeutic applications in cardiac regenerative medicine.

Recently, it has been shown that exosomes deliver LncRNAs (Gezer et al. 2014). To date, a few studies have characterized the regenerative potential of LncRNAs in the adult heart. For example, the LncRNA steroid receptor RNA activator 1 (SRA1 ) regulates the expression of myogenic differentiation 1 (MyoD1) (Caretti et al. 2006) and is essential for myocardial function. Further investigations should be encouraged to better address the therapeutic potential of exosomes containing LncRNAs.


7.4 Conclusions and Perspectives


Studies conducted so far have provided convincing experimental evidences that different epigenetic mechanisms underlie the changes of the cardiac physiological traits during myocardial regeneration. The pleiotropic non-invasive modulation of the epigenetic threshold of resident cardiac cells by drugs or diet is a frontier of investigation that should be encouraged in order to overcome the limitations that hinder an efficient structural and functional recovery of the adult heart in an epigenetic manner. In fact, emerging scientific evidences have shown that it is possible to modulate the cardiac epigenome and to induce cardiac benefits by the regular intake of lower doses of active plant compounds, such as barley beta-glucan (Agostini et al. 2015), or by the administration of selected exosomes (Barile et al. 2014). To best of our knowledge, the cardiac repair following the administration of the potential epigenetic modulators will be more effective at lower doses and mainly focused to histone or RNA-based modifications. Further translational investigations should be conducted in large animal models of heart failure and humans to better address dose, timing and route of administration.

Jul 13, 2016 | Posted by in CARDIOLOGY | Comments Off on Epigenetic Regulation of Cardiac Regeneration

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