Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure

Genome-wide association studies (GWASs) have identified numerous variants associated with polygenic traits and diseases. However, with few exceptions, a mechanistic understanding of which variants affect which genes in which tissues to modulate trait variation is lacking. Here, we present genomic analyses to explain trait heritability of blood pressure (BP) through the genetics of transcriptional regulation using GWASs, multiomics data from different tissues, and machine learning approaches. Approximately 500,000 predicted regulatory variants across four tissues explain 33.4% of variant heritability: 2.5%, 5.3%, 7.7%, and 11.8% for kidney-, adrenal-, heart-, and artery-specific variants, respectively. Variation in the enhancers involved shows greater tissue specificity than in the genes they regulate, suggesting that gene regulatory networks perturbed by enhancer variants in a tissue relevant to a phenotype are the major source of interindividual variation in BP. Thus, our study provides an approach to scan human tissue and cell types for their physiological contribution to any trait.

Extracellular Vesicle-Encapsulated Adeno-Associated Viruses for Therapeutic Gene Delivery to the Heart

BACKGROUND

Adeno-associated virus (AAV) has emerged as one of the best tools for cardiac gene delivery due to its cardiotropism, long-term expression, and safety. However, a significant challenge to its successful clinical use is preexisting neutralizing antibodies (NAbs), which bind to free AAVs, prevent efficient gene transduction, and reduce or negate therapeutic effects. Here we describe extracellular vesicle-encapsulated AAVs (EV-AAVs), secreted naturally by AAV-producing cells, as a superior cardiac gene delivery vector that delivers more genes and offers higher NAb resistance.

METHODS

We developed a 2-step density-gradient ultracentrifugation method to isolate highly purified EV-AAVs. We compared the gene delivery and therapeutic efficacy of EV-AAVs with an equal titer of free AAVs in the presence of NAbs, both in vitro and in vivo. In addition, we investigated the mechanism of EV-AAV uptake in human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and mouse models in vivo using a combination of biochemical techniques, flow cytometry, and immunofluorescence imaging.

RESULTS

Using cardiotropic AAV serotypes 6 and 9 and several reporter constructs, we demonstrated that EV-AAVs deliver significantly higher quantities of genes than AAVs in the presence of NAbs, both to human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and to mouse hearts in vivo. Intramyocardial delivery of EV-AAV9-sarcoplasmic reticulum calcium ATPase 2a to infarcted hearts in preimmunized mice significantly improved ejection fraction and fractional shortening compared with AAV9-sarcoplasmic reticulum calcium ATPase 2a delivery. These data validated NAb evasion by and therapeutic efficacy of EV-AAV9 vectors. Trafficking studies using human induced pluripotent stem cell-derived cells in vitro and mouse hearts in vivo showed significantly higher expression of EV-AAV6/9-delivered genes in cardiomyocytes compared with noncardiomyocytes, even with comparable cellular uptake. Using cellular subfraction analyses and pH-sensitive dyes, we discovered that EV-AAVs were internalized into acidic endosomal compartments of cardiomyocytes for releasing and acidifying AAVs for their nuclear uptake.

CONCLUSIONS

Together, using 5 different in vitro and in vivo model systems, we demonstrate significantly higher potency and therapeutic efficacy of EV-AAV vectors compared with free AAVs in the presence of NAbs. These results establish the potential of EV-AAV vectors as a gene delivery tool to treat heart failure.

Abstract P3097: Post-transcriptional Mechanisms Of FTO-regulated Cardiac Contractility

Background: N6-methyladenosine (m6A), the most abundant and functionally relevant mRNA modification, is reversibly demethylated by FTO, an m6A eraser and a primary regulator of m6A in the heart. In failing hearts, decreased FTO increases m6A, critically reducing cardiomyocyte contraction. FTO overexpression improved cardiac contraction and attenuated remodeling. Here, we investigate post-transcriptional and translational mechanisms of FTO-regulation of cardiomyocyte contraction in vitro and in vivo. We hypothesize that FTO directly binds to selective cardiac contractile mRNAs at their m6A site and affects their nuclear export, polysome binding, cytoplasmic availability, and protein expression.

Methods and Results: We performed immunostaining to examine the intracellular location and expression of FTO under different pathological stimuli in human ventricular cardiomyocyte cell line (AC16 cells), rat primary cardiomyocytes and mouse and human hearts. FTO was detected in both cytoplasmic and nuclear compartments, and was significantly reduced in pathological hearts compared to healthy controls. MeRIP (immunoprecipitation of m6A-RNA) sequencing analysis uncovered that FTO targets different sets of cardiac mRNAs in the cytoplasm and nucleus of cardiomyocytes. Knocking down FTO increased nuclear retention of cardiac mRNAs, which was reversed with FTO overexpression. Immunoprecipitation experiments demonstrated that FTO directly binds to cardiac mRNAs. To determine the effect of FTO on translation of select cardiac mRNAs, we isolated the polysome fraction from the cytoplasm of AC16 cells. Interestingly, our stable isotope labeling with amino acids in cell culture (SILAC) and mass spectrometry analyses suggested increased expression of cardiac contractile proteins with FTO overexpression.

Conclusion: We demonstrate that FTO positively regulates post-transcriptional nuclear export, polysome binding of cardiac contractile mRNAs, and regulates their translation under pathological stimuli. By combining experimental and predictive models in human and mice, we have characterized the transcriptome-proteome molecular interplay regulating cardiac function.

Regulation of the Methylation and Expression Levels of the BMPR2 Gene by SIN3a as a Novel Therapeutic Mechanism in Pulmonary Arterial Hypertension

BACKGROUND

Epigenetic mechanisms are critical in the pathogenesis of pulmonary arterial hypertension (PAH). Previous studies have suggested that hypermethylation of the BMPR2 (bone morphogenetic protein receptor type 2) promoter is associated with BMPR2 downregulation and progression of PAH. Here, we investigated for the first time the role of SIN3a (switch-independent 3a), a transcriptional regulator, in the epigenetic mechanisms underlying hypermethylation of BMPR2 in the pathogenesis of PAH.

METHODS

We used lung samples from PAH patients and non-PAH controls, preclinical mouse and rat PAH models, and human pulmonary arterial smooth muscle cells. Expression of SIN3a was modulated using a lentiviral vector or a siRNA in vitro and a specific adeno-associated virus serotype 1 or a lentivirus encoding for human SIN3a in vivo.

RESULTS

SIN3a is a known transcriptional regulator; however, its role in cardiovascular diseases, especially PAH, is unknown. It is interesting that we detected a dysregulation of SIN3 expression in patients and in rodent models, which is strongly associated with decreased BMPR2 expression. SIN3a is known to regulate epigenetic changes. Therefore, we tested its role in the regulation of BMPR2 and found that BMPR2 is regulated by SIN3a. It is interesting that SIN3a overexpression inhibited human pulmonary arterial smooth muscle cells proliferation and upregulated BMPR2 expression by preventing the methylation of the BMPR2 promoter region. RNA-sequencing analysis suggested that SIN3a downregulated the expression of DNA and histone methyltransferases such as DNMT1 (DNA methyltransferase 1) and EZH2 (enhancer of zeste 2 polycomb repressive complex 2) while promoting the expression of the DNA demethylase TET1 (ten-eleven translocation methylcytosine dioxygenase 1). Mechanistically, SIN3a promoted BMPR2 expression by decreasing CTCF (CCCTC-binding factor) binding to the BMPR2 promoter. Last, we identified intratracheal delivery of adeno-associated virus serotype human SIN3a to be a beneficial therapeutic approach in PAH by attenuating pulmonary vascular and right ventricle remodeling, decreasing right ventricle systolic pressure and mean pulmonary arterial pressure, and restoring BMPR2 expression in rodent models of PAH.

CONCLUSIONS

All together, our study unveiled the protective and beneficial role of SIN3a in pulmonary hypertension. We also identified a novel and distinct molecular mechanism by which SIN3a regulates BMPR2 in human pulmonary arterial smooth muscle cells. Our study also identified lung-targeted SIN3a gene therapy using adeno-associated virus serotype 1 as a new promising therapeutic strategy for treating patients with PAH.

Therapeutic and Diagnostic Translation of Extracellular Vesicles in Cardiovascular Diseases: Roadmap to the Clinic

Exosomes are small membrane-bound vesicles of endocytic origin that are actively secreted. The potential of exosomes as effective communicators of biological signaling in myocardial function has previously been investigated, and a recent explosion in exosome research not only underscores their significance in cardiac physiology and pathology, but also draws attention to methodological limitations of studying these extracellular vesicles. In this review, we discuss recent advances and challenges in exosome research with an emphasis on scientific innovations in isolation, identification, and characterization methodologies, and we provide a comprehensive summary of web-based resources available in the field. Importantly, we focus on the biology and function of exosomes, highlighting their fundamental role in cardiovascular pathophysiology to further support potential applications of exosomes as biomarkers and therapeutics for cardiovascular diseases.

FTO-Dependent N6-Methyladenosine Regulates Cardiac Function During Remodeling and Repair

BACKGROUND

Despite its functional importance in various fundamental bioprocesses, studies of N⁶-methyladenosine (m6A) in the heart are lacking. Here, we show that the FTO (fat mass and obesity-associated protein), an m6A demethylase, plays a critical role in cardiac contractile function during homeostasis, remodeling, and regeneration.

METHODS

We used clinical human samples, preclinical pig and mouse models, and primary cardiomyocyte cell cultures to study the functional role of m6A and FTO in the heart and in cardiomyocytes. We modulated expression of FTO by using adeno-associated virus serotype 9 (in vivo), adenovirus (both in vivo and in vitro), and small interfering RNAs (in vitro) to study its function in regulating cardiomyocyte m6A, calcium dynamics and contractility, and cardiac function postischemia. We performed methylated (m6A) RNA immunoprecipitation sequencing to map transcriptome-wide m6A, and methylated (m6A) RNA immunoprecipitation quantitative polymerase chain reaction assays to map and validate m6A in individual transcripts, in healthy and failing hearts, and in myocytes.

RESULTS

We discovered that FTO has decreased expression in failing mammalian hearts and hypoxic cardiomyocytes, thereby increasing m6A in RNA and decreasing cardiomyocyte contractile function. Improving expression of FTO in failing mouse hearts attenuated the ischemia-induced increase in m6A and decrease in cardiac contractile function. This is performed by the demethylation activity of FTO, which selectively demethylates cardiac contractile transcripts, thus preventing their degradation and improving their protein expression under ischemia. In addition, we demonstrate that FTO overexpression in mouse models of myocardial infarction decreased fibrosis and enhanced angiogenesis.

CONCLUSIONS

Collectively, our study demonstrates the functional importance of the FTO-dependent cardiac m6A methylome in cardiac contraction during heart failure and provides a novel mechanistic insight into the therapeutic mechanisms of FTO.

Abstract 326: FTO-mediated mRNA Demethylation Regulates Cardiac Contractile Protein Expression and Function

Background: Exciting new discoveries in RNA biology underscore the importance of post-transcriptional chemical modifications to mRNAs (epitranscriptome) in regulating RNA stability, nuclear export, cellular compartmentalization, splicing, translation and degradation. The most abundant and functionally relevant modification in RNA, N6-methyladenosine (m6A) is reversibly demethylated by one of the m6A demethylases, fat mass and obesity-associated protein (FTO) whose function in the mammalian heart remains incompletely understood.

Materials and Methods: We used clinical human samples, preclinical pig and mouse models and primary cardiomyocytes to study m6A and FTO in the heart and in cardiomyocytes. We modulated FTO expression using AAV9 (in vivo), adenovirus (in vivo and in vitro) and siRNAs (in vitro). We investigated m6A-induced changes to contractile protein expression using m6A RNA immunoprecipitation sequencing (MeRIP-seq) and stable isotope labeling of amino acids in cell culture (SILAC).

Results: We discovered in human heart failure that reduced FTO expression is associated with aberrant increase in m6A mRNA methylation, which is conserved in swine and mouse models of myocardial ischemia (MI). AAV9-mediated FTO gene delivery in mouse MI attenuated m6A increase and improved cardiac function with enhanced contractility, angiogenesis and reduced fibrosis. At the molecular level, FTO-mediated mRNA demethylation serves to increase contractile protein expression in mouse hearts as well as in isolated primary cardiomyocytes. By comparing human and mouse transcriptome-wide m6A maps with SILAC proteomic profiling from cardiomyocytes, we identified FTO-mediated m6A demethylation is transcript-specific and leads to altered protein expression of several key contractile, angiogenic and regenerative proteins.

Conclusion: Using new RNA-based investigations, we uncovered a novel regulatory layer beyond the genome working at the level of epitranscriptome governing cardiac function. Our findings on the dynamic nature of the cardiac m6A-epitranscriptome will lead to deeper understanding of the mechanism of cardiac remodeling on one hand and innovative therapeutic interventions on the other.

Abstract 170: Exosomal AAV-mediated SERCA2a Gene Transfer Improves Cardiac Function in a Mouse Model of Heart Failure

Adeno-associated viruses (AAVs) are promising therapeutic tools for gene delivery to the heart. However, pre-existing antibodies (NAbs) to many cardiotropic AAV serotypes naturally present in humans pose a critical challenge for the translation of gene therapies to clinical applications. Here, we describe the use of exosomal AAVs (eAAV) as a robust heart gene delivery system that improves transduction efficiency while protecting from pre-existing immunity to the viral capsid. To obtain eAAV specimens from conditioned medium from AAV-producing HEK-293T cells, we have developed a state-of-the-art multi-step ultracentrifugation strategy. We demonstrated through electron microscopy-based visualization, size distribution measurements and distribution of AAV genomes in post-centrifugation iodixanol gradients, that our purification process enables isolation of eAAVs with high purity and minimal contamination with standard AAVs. Efficiency of heart targeting was then evaluated for eAAV9 or eAAV6 and standard AAV9 or AAV6 in human cardiomyocytes (hCMs) in vitro and in passive immunity nude mouse model in vivo . Regardless of the presence or absence of NAbs, we demonstrated that eAAVs are more efficient in transduction of cells in the same titer ranges as standard AAVs. To test the therapeutic efficacy, eAAV9-SERCA2a or AAV9-SERCA2a were injected intramyocardially in post-myocardial infarction (MI) mice preinjected with NAbs. Remarkably, eAAV9-SERCA2a outperformed standard AAVs 6 weeks post-MI, significantly improving cardiac function in the presence of NAbs (%EF 55.14 ± 3.50 vs. 27.31 ± 1.63, respectively). Additionally, we demonstrated in vivo that eAAV9-mediated gene delivery is more specific to CMs than to other cell types present in the heart, which suggests that eAAVs preserve cardiotropic properties of AAV9 serotype. With examination of colocalization of eAAVs and markers specific for endosomes (Rab5 and Rab7) in hCMs in vitro , our preliminary data indicated that eAAV infectious entry potentially involves trafficking via endocytic compartments. In conclusion, these results underline the therapeutic potential of eAAVs to evade NAbs, and to facilitate the clinical translation of AAV-based gene therapies to a larger human population.

Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart

In the heart, primary microRNA-208b (pri-miR-208b) and Myheart (Mhrt) are long non-coding RNAs (lncRNAs) encoded by the cardiac myosin heavy chain genes. Although preclinical studies have shown that lncRNAs regulate gene expression and are protective for pathological hypertrophy, the mechanism underlying sex-based differences remains poorly understood. In this study, we examined DNA- and RNA-methylation-dependent regulation of pri-miR-208b and Mhrt. Expression of pri-miR-208b is elevated in the left ventricle of the female heart. Despite indistinguishable DNA methylation between sexes, the interaction of MeCP2 on chromatin is subject to RNase digestion, highlighting that affinity of the methyl-CG reader is broader than previously thought. A specialized procedure to isolate RNA from soluble cardiac chromatin emphasizes sex-based affinity of an MeCP2 co-repressor complex with Rest and Hdac2. Sex-specific Mhrt methylation chromatinizes MeCP2 at the pri-miR-208b promoter and extends the functional relevance of default transcriptional suppression in the heart.

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Mechanisms underlying sex-based gene expression are poorly understood

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Expression of primary miR-208b is independent of DNA methylation in the heart

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Sex-specific methylation of the long non-coding RNA Mhrt distinguishes MeCP2

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Procedures assessing soluble chromatin emphasize RNA-dependent affinities

Abstract 584: FTO-Dependent m6A Regulates Cardiomyocyte and Cardiac Function During Remodeling and Repair

Background: Despite its functional importance in various fundamental bioprocesses, the studies of N6-methyladenosine (m6A) in the heart are lacking. In this study, we investigated the role of fat mass and obesity-associated (FTO), an m6A demethylase, in cardiac contractile function during homeostasis and remodeling.

Methods: We used clinical human samples, preclinical pig and mouse models and primary cardiomyocyte cell cultures to study the functional role of m6A and FTO in the heart and in cardiomyocytes. We modulated expression of FTO using AAV9 (in vivo), adenovirus (both in vivo and in vitro) and siRNAs (in vitro). We performed methylated (m6A) RNA immunoprecipitation sequencing (MeRIP-seq) to map transcriptome-wide m6A, and MeRIP qPCR assays to map and validate m6A in individual transcripts, in healthy and failing hearts and myocytes. We performed proteomics analysis using stable isotope labeling with amino acids in cell culture to study m6A role in mRNA to protein translation.

Results: We discovered that FTO has decreased expression in failing mammalian hearts and hypoxic cardiomyocytes, thereby increasing m6A in RNA and decreasing cardiomyocyte contractile function. Improving expression of FTO in failing mouse hearts attenuated the ischemia-induced increase in m6A and decrease in cardiac contractile function. This is carried out by the demethylation activity of FTO, which selectively demethylates cardiac contractile transcripts, thus preventing their degradation and improving their protein expression under ischemia.

Conclusion: Collectively, our study demonstrates the functional importance of FTO-dependent cardiac m6A methylome in cardiac contraction during heart failure and provides a novel mechanistic insight into the therapeutic mechanisms of FTO.

Abstract 104: AAV-Exosomes: A Novel Platform for Myocardial Gene Delivery for Cardioprotection

Introduction: Adeno-associated viruses (AAVs) are viral vectors of choice for delivering genes for long-term expression due to their safety in clinics. However, pre-existing immunity to AAVs from naturally present neutralizing antibodies (NAbs, present in between 60% and 90% of population) poses a significant challenge for AAV-mediated gene delivery. NAbs prevent AAVs from infecting target cells, greatly reducing transduction efficiency and, therefore, the clinical efficacy. Thus, it is essential to develop novel AAV-based vectors that circumvent the effect of NAbs.

Objectives: We aimed to investigate the ability of exosome-encapsulated AAVs (AAVExo) to evade NAbs and serve as a highly efficient gene transfer tool for cardiovascular therapeutics.

Methods and Results: We developed a multi-step purification strategy using iodixanol density gradient to isolate AAVExo with minimal contamination from free AAVs (AAV1, 6 or 9). Biochemical assays, flow cytometry, IVIS Spectrum in vivo optical imaging and echocardiography were used to detect AAV-mediated gene delivery and evaluate cardiac function. AAV6Exo-mCherry and AAV9Exo-FLuc were resistant to NAbs and significantly improved expression of mCherry and firefly luciferase (FLuc) both in mouse and human (iPSC-derived) cardiomyocytes in vitro , and in murine hearts in vivo (in nude mice preinjected with NAbs), compared to free AAVs. To test the therapeutic efficacy of AAVExo-mediated gene delivery in the presence of NAbs, we injected AAV9-SERCA2a or AAV9Exo-SERCA2a into post-MI hearts of nude mice preinjected with IVIg (human intravenous immunoglobulin) preparation. Hearts treated with AAV9Exo-SERCA2a had significantly improved cardiac function compared to those treated with free AAV9-SERCA2a (%EF 62.6 ± 9.8 vs. 28.4 ± 5.3, respectively; 2 weeks after surgery).

Conclusion: Delivery of AAVs protected by carrier exosomes is a promising approach to circumvent the issue of NAbs in AAV-based gene therapy, which can be used in the entire population of patients and may result in higher gene delivery efficacy.

Abstract 301: An m6A Demethylase, FTO Mediates Post-transcriptional mRNA Modifications to Regulate Cardiac and Cardiomyocyte Function

Background: Post-transcriptional modifications in the form of m6A (N6-methyladenosine) regulate mRNA fate and translation, miRNA biogenesis, lncRNA function and several cellular processes. However, m6A mechanisms in the mature post-mitotic tissues such as the mammalian heart remain unexplored. Here, we investigated the role of transcriptome-wide m6A in cardiac protein expression as well as lncRNA function.

Methods: Using biochemical assays, we investigated the spatiotemporal gene expression patterns of m6A regulators in non-failing, failing (ischemic) human hearts, in mouse and pig MI models. In mouse heart, we mapped transcriptome-wide m6A by developing state-of-the-art MeRIP-seq coupled with novel bioinformatics analysis. To investigate the functional relevance of m6A to cardiac proteome, we used SILAC-LC-MS. By silencing (siRNA) m6A-reader proteins, we investigated the role of m6A in cardiomyocyte mRNA stability, decay and nuclear export. For in vivo myocardial gene delivery, we used AAV9 and adenovirus vectors. Finally, we performed immunohistology in cardiomyocytes and mouse heart tissues to study nuclei size, fibrosis and angiogenesis.

Results: We discovered that the expression of m6A demethylase, FTO is decreased in ischemic myocardium and cardiomyocytes, thus in vivo FTO gene delivery resulted in attenuation of ischemia-induced increase in m6A and decrease in cardiac contractile function post-MI. FTO overexpression in mouse heart and human cardiomyocytes revealed selective demethylation (MeRIP-seq) of cardiac contractile transcripts resulting in induced contractile protein expression (SILAC-LC-MS) thus rescuing heart function post-MI. Mechanistically, we demonstrate that the cardioprotective mechanism of FTO is mediated by selective demethylation of cardiac contractile transcripts under ischemia, which prevents mRNA degradation as well as enhanced nuclear compaction. Finally, we demonstrate that FTO overexpression in mouse models of MI resulted in decreased fibrosis and enhanced angiogenesis.

Conclusion: Our study provides the first description of a cardiac active m6A demethylase working at post-transcriptional level as a critical regulator of cardiac contractile function, fibrosis and angiogenesis.

Exosomal microRNA-21-5p Mediates Mesenchymal Stem Cell Paracrine Effects on Human Cardiac Tissue Contractility

RATIONALE

The promising clinical benefits of delivering human mesenchymal stem cells (hMSCs) for treating heart disease warrant a better understanding of underlying mechanisms of action. hMSC exosomes increase myocardial contractility; however, the exosomal cargo responsible for these effects remains unresolved.

OBJECTIVE

This study aims to identify lead cardioactive hMSC exosomal microRNAs to provide a mechanistic basis for optimizing future stem cell-based cardiotherapies.

METHODS AND RESULTS

Integrating systems biology and human engineered cardiac tissue (hECT) technologies, partial least squares regression analysis of exosomal microRNA profiling data predicted microRNA-21-5p (miR-21-5p) levels positively correlate with contractile force and calcium handling gene expression responses in hECTs treated with conditioned media from multiple cell types. Furthermore, miR-21-5p levels were significantly elevated in hECTs treated with the exosome-enriched fraction of the hMSC secretome (hMSC-exo) versus untreated controls. This motivated experimentally testing the human-specific role of miR-21-5p in hMSC-exo-mediated increases of cardiac tissue contractility. Treating hECTs with miR-21-5p alone was sufficient to recapitulate effects observed with hMSC-exo on hECT developed force and expression of associated calcium handling genes (eg, SERCA2a and L-type calcium channel). Conversely, knockdown of miR-21-5p in hMSCs significantly diminished exosomal procontractile and associated calcium handling gene expression effects on hECTs. Western blots supported miR-21-5p effects on calcium handling gene expression at the protein level, corresponding to significantly increased calcium transient amplitude and decreased decay time constant in comparison to miR-scramble control. Mechanistically, cotreating with miR-21-5p and LY294002, a PI3K inhibitor, suppressed these effects. Finally, mathematical simulations predicted the translational capacity for miR-21-5p treatment to restore calcium handling in mature ischemic adult human cardiomyocytes.

CONCLUSIONS

miR-21-5p plays a key role in hMSC-exo-mediated effects on cardiac contractility and calcium handling, likely via PI3K signaling. These findings may open new avenues of research to harness the role of miR-21-5p in optimizing future stem cell-based cardiotherapies.

Exosomes-Based Gene Therapy for MicroRNA Delivery

Despite recent advances in scientific knowledge and clinical practice, cardiovascular disease management and treatment remain a major burden. While several treatment strategies using drugs and surgeries are being developed for cardiovascular manifestations, gene-based therapies hold significant promise. Recent findings from our laboratory unveiled a novel mechanism that exosomes, secreted nanovesicles from stem cells, mediate cardiac repair via transferring their unique repertoire of microRNAs (miRNA) to recipient cells in the heart. Exosomes, unlike other vectors for gene delivery, present unique advantages such that exosomes are a cell-free natural system for ferrying RNA between cells, robust exosomal membrane can protect the RNA/gene of interest from digestion, and exosomes are rapidly taken up by target cells making them a more efficient vehicle for gene delivery. Here, we describe a stepwise protocol developed in our laboratory for generating exosomes from human CD34⁺ stem cells that carry exogenously applied Cy3 dye-labeled pre-miR miRNA precursors. We demonstrate that human CD34⁺ stem cell exosomes can rigorously enter into recipient cells and deliver Cy3 dye-labeled pre-miR miRNA precursors to regulate gene expression. Identification of key molecular targets to treat disease conditions is the foremost critical step and the novel approach presented here to generate exosomes carrying exogenous genetic information offers a valuable clinical tool for more effective treatment strategies.

Abstract 12: M6A Modification in RNA Regulates Cardiomyocyte and Cardiac Function in Heart Failure

Background: Adenosine in RNA is a substrate for addition or removal of methyl group. Reported five decades ago, methylated adenosine (m6A), the most abundant and functionally relevant chemical modification in RNA, whose transcriptome-wide mapping became possible only recently due to next generation sequencing (NGS). Coupled with NGS, m6A-methylated RNA capture (MeRIP-seq) identified widespread m6A distribution in ~8000 mRNA and ~1000 lncRNA transcripts in human and mouse transcriptome.

Methods and Results: In a first of its kind approach, we examined m6A RNA methylation in both failing and non-failing hearts. We discovered that global m6A RNA methylation is significantly higher in left ventricles (LV) of failing human, swine and mouse hearts as compared to non-failing controls. Increase in m6A was associated with significantly lower expression of one of the key m6A demethylases, FTO, in the ischemic heart. siRNA-mediated silencing of FTO resulted in significant arrhythmias, loss of Ca 2+ dynamics such as Ca 2+ transient decay (Tau) and cardiomyocyte relaxation time in isolated adult rat cardiomyocytes. Conversely, FTO gene transfer reduced m6A and improved Ca 2+ transients and contractile function in primary cardiomyocytes under hypoxia. In a mouse model of MI, AAV-mediated gene transfer of FTO significantly improved cardiac function post-MI. We identified transcriptome-wide m6A distribution signatures and conserved methylated sites of several mRNAs and lncRNAs using MeRIP-seq in both human and mouse failing and non-failing LV. Detailed MeRIP map of individual transcripts identified differentially methylated 3’-UTR, 5’-UTR and exon sites within several cardiac mRNAs that are important for cardiac function.

Conclusion: Our data provide first evidence that m6A modification in RNA is a regulator of cardiomyocyte Ca 2+ dynamics and cardiac function. Our findings on the dynamic nature of the cardiac m6A-epitranscriptome will add another portfolio to mRNA and lncRNA regulation of cardiac remodeling.

Angiogenic Mechanisms of Human CD34+ Stem Cell Exosomes in the Repair of Ischemic Hindlimb

RATIONALE

Paracrine secretions seem to mediate therapeutic effects of human CD34⁺ stem cells locally transplanted in patients with myocardial and critical limb ischemia and in animal models. Earlier, we had discovered that paracrine secretion from human CD34⁺ cells contains proangiogenic, membrane-bound nanovesicles called exosomes (CD34Exo).

OBJECTIVE

Here, we investigated the mechanisms of CD34Exo-mediated ischemic tissue repair and therapeutic angiogenesis by studying their miRNA content and uptake.

METHODS AND RESULTS

When injected into mouse ischemic hindlimb tissue, CD34Exo, but not the CD34Exo-depleted conditioned media, mimicked the beneficial activity of their parent cells by improving ischemic limb perfusion, capillary density, motor function, and their amputation. CD34Exo were found to be enriched with proangiogenic miRNAs such as miR-126-3p. Knocking down miR-126-3p from CD34Exo abolished their angiogenic activity and beneficial function both in vitro and in vivo. Interestingly, injection of CD34Exo increased miR-126-3p levels in mouse ischemic limb but did not affect the endogenous synthesis of miR-126-3p, suggesting a direct transfer of stable and functional exosomal miR-126-3p. miR-126-3p enhanced angiogenesis by suppressing the expression of its known target, SPRED1, simultaneously modulating the expression of genes involved in angiogenic pathways such as VEGF (vascular endothelial growth factor), ANG1 (angiopoietin 1), ANG2 (angiopoietin 2), MMP9 (matrix metallopeptidase 9), TSP1 (thrombospondin 1), etc. Interestingly, CD34Exo, when treated to ischemic hindlimbs, were most efficiently internalized by endothelial cells relative to smooth muscle cells and fibroblasts, demonstrating a direct role of stem cell-derived exosomes on mouse endothelium at the cellular level.

CONCLUSIONS

Collectively, our results have demonstrated a novel mechanism by which cell-free CD34Exo mediates ischemic tissue repair via beneficial angiogenesis. Exosome-shuttled proangiogenic miRNAs may signify amplification of stem cell function and may explain the angiogenic and therapeutic benefits associated with CD34⁺ stem cell therapy.

Epigenetic-mediated reprogramming of pancreatic endocrine cells

SIGNIFICANCE

Type 1 diabetes (T1D) results from cell-mediated autoimmune destruction of insulin-secreting pancreatic beta cells (β-cells). In the context of T1D, the scarcity of organ donors has driven research to alternate sources of functionally competent, insulin-secreting β-cells as substitute for donor islets to meet the clinical need for transplantation therapy.

RECENT ADVANCES

Experimental evidence of an inherent plasticity of pancreatic cells has fuelled interest in in vivo regeneration of β-cells. Transcriptional modulation and direct reprogramming of noninsulin secreting pancreatic α-cells to functionally mimic insulin-secreting β-cells is one of the promising avenues to the treatment of diabetes. Recent studies now show that adult progenitor and glucagon(+) α-cells can be converted into β-like cells in vivo, as a result of specific activation of the Pax4 gene in α-cells and curing diabetes in preclinical models.

CRITICAL ISSUES

The challenge now is to understand the precise developmental transitions mediated by endocrine transcription factors and co-regulatory determinants responsible for pancreatic function and repair.

FUTURE DIRECTIONS

Epigenetic-mediated regulation of transcription factor binding in pancreatic α-cells by specific drugs to direct reprogramming into functional insulin producing cells could be of potential innovative therapy for the treatment of T1D.

Chromatin modifications remodel cardiac gene expression

Signalling and transcriptional control involve precise programmes of gene activation and suppression necessary for cardiovascular physiology. Deep sequencing of DNA-bound transcription factors reveals a remarkable complexity of co-activators or co-repressors that serve to alter chromatin modification and regulate gene expression. The regulated complexes characterized by genome-wide mapping implicate the recruitment and exchange of proteins with specific enzymatic activities that include roles for histone acetylation and methylation in key developmental programmes of the heart. As for transcriptional changes in response to pathological stress, co-regulatory complexes are also differentially utilized to regulate genes in cardiac disease. Members of the histone deacetylase (HDAC) family catalyse the removal of acetyl groups from proteins whose pharmacological inhibition has profound effects preventing heart failure. HDACs interact with a complex co-regulatory network of transcription factors, chromatin-remodelling complexes, and specific histone modifiers to regulate gene expression in the heart. For example, the histone methyltransferase (HMT), enhancer of zeste homolog 2 (Ezh2), is regulated by HDAC inhibition and associated with pathological cardiac hypertrophy. The challenge now is to target the activity of enzymes involved in protein modification to prevent or reverse the expression of genes implicated with cardiac hypertrophy. In this review, we discuss the role of HDACs and HMTs with a focus on chromatin modification and gene function as well as the clinical treatment of heart failure.

The primary microRNA-208b interacts with Polycomb-group protein, Ezh2, to regulate gene expression in the heart

The Polycomb-group protein, Ezh2, is required for epigenetic gene silencing in the adult heart by unknown mechanism. We investigated the role of Ezh2 and non-coding RNAs in a mouse model of pressure overload using transverse aortic constriction (TAC) attenuated by the prototypical histone deacetylase inhibitor, trichostatin A (TSA). Chromatin immunoprecipitation of TAC and TAC+TSA hearts suggests interaction of Ezh2 and primary microRNA-208b (pri-miR-208b) in the regulation of hypertrophic gene expression. RNAi silencing of pri-miR-208b and Ezh2 validate pri-miR-208b-mediated transcriptional silencing of genes implicated in cardiac hypertrophy including the suppression of the bi-directional promoter (bdP) of the cardiac myosin heavy chain genes. In TAC mouse heart, TSA attenuated Ezh2 binding to bdP and restored antisense β-MHC and α-MHC gene expression. RNA-chromatin immunoprecipitation experiments in TAC hearts also show increased pri-miR-208b dependent-chromatin binding. These results are the first description by which primary miR interactions serve to integrate chromatin modifications and the transcriptional response to distinct signaling cues in the heart. These studies provide a framework for MHC expression and regulation of genes implicated in pathological remodeling of ventricular hypertrophy.

Interplay of chromatin modifications and non-coding RNAs in the heart

Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.

Cardiac ventricular chambers are epigenetically distinguishable

The left and right ventricles are muscular chambers of the heart that differ significantly in the extent of pressure work-load. The regional and differential distribution of gene expression patterns is critical not only for heart development, but, also in the establishment of cardiac hypertrophy phenotypes. the cells of the myocardium employ elaborate regulatory mechanisms to establish changes in chromatin structure and function, yet, the role of epigenetic modifications and specific gene expression patterns in cardiac ventricles remains poorly understood. We have examined gene expression changes and studied histone H3 and H4 acetylation as well as dimethylation of lysine 4 on histone H3 on promoters of alpha-Myosin heavy chain gene (alpha-MHC), beta-Myosin heavy chain gene (beta-MHC), Atrial natriuretic peptide gene (ANp), B-type natriuretic peptide gene (BNP) and Sarcoplasmic reticulum Ca(2+) ATPase gene (SERCA2a). The recruitment of histone acetyltransferase (HAT) enzyme p300, which is a transcriptional coactivator, was also studied on the hyperacetylated promoters using immunopurification of soluble chromatin in the left and right ventricles of the mouse. We present evidence for the first time that the pattern of gene expression is closely linked with histone modifications and propose the left and right chambers of the heart are epigenetically distinguishable.