Current epigenetic aspects the clinical kidney researcher should embrace

Chronic kidney disease (CKD), affecting 10-12% of the world's adult population, is associated with a considerably elevated risk of serious comorbidities, in particular, premature vascular disease and death. Although a wide spectrum of causative factors has been identified and/or suggested, there is still a large gap of knowledge regarding the underlying mechanisms and the complexity of the CKD phenotype. Epigenetic factors, which calibrate the genetic code, are emerging as important players in the CKD-associated pathophysiology. In this article, we review some of the current knowledge on epigenetic modifications and aspects on their role in the perturbed uraemic milieu, as well as the prospect of applying epigenotype-based diagnostics and preventive and therapeutic tools of clinical relevance to CKD patients. The practical realization of such a paradigm will require that researchers apply a holistic approach, including the full spectrum of the epigenetic landscape as well as the variability between and within tissues in the uraemic milieu

Amelioration of Mitochondrial Bioenergetic Dysfunction in Diabetes Mellitus: Delving into Specialized and Non-specific Therapeutics for the Ailing Heart

Morbidity and mortality of the diabetic population is influenced by many confounding factors, but cardiovascular disease (CVD), remains the leading cause of death. Mitochondrial dysfunction is central in the development of cardiac contractile dysfunction, with decreased mitochondrial bioenergetic function, increased dependence on free fatty acid utilization, and a decrease in glucose utilization having been shown to contribute to contractile dysfunction. Strategies targeting the amelioration of mitochondrial bioenergetic function are attractive for limiting diabetes-induced heart failure, and preserving health-span. The goals of this dissertation were to assess two mitochondrial-centric approaches for the amelioration of mitochondrial and cardiac contractile dysfunction in diabetes mellitus. Our laboratory previously identified microRNA-378a (miR-378a) as a regulator of mitochondrially encoded ATP synthase membrane subunit 6 (mt-ATP6) mRNA, a component of the ATP synthase F0 complex. More recently, a second class of non-coding RNAs, long non-coding RNAs (lncRNA), have been proposed to regulate microRNA activity. LncRNA potassium voltage-gated channel subfamily Q member 1 overlapping transcript 1 (Kcnq1ot1), is predicted to bind miR-378a. Chapter 2 aimed to determine if inhibition of miR-378a could ameliorate cardiac contractile dysfunction in type 2 diabetes mellitus (T2DM), and to ascertain whether Kcnq1ot1 interacts with miR-378a to impact ATP synthase functionality by preserving mt-ATP6 levels. MiR-378a genomic loss, and inhibition by Kcnq1ot1, improved ATP synthase functionality, and preserved cardiac contractile function. Together, Kcnq1ot1 and miR-378a may act as constituents in an axis that regulates mt-ATP6 content. By acting as therapeutic targets, their manipulation may provide benefit to ATP synthase functionality in the heart during T2DM. A second method of ameliorating mitochondrial dysfunction is mitochondrial transplantation. Current literature suggests that mitochondrial transplantation may be of benefit to the diabetic heart. Chapter 3 aimed to assess mitochondrial transplantation as a prophylactic method of treating mitochondrial dysfunction in the diabetic heart. Following mitochondrial transplantation in vivo using ultrasound-guided echocardiography, mitochondrial signal was detectable in at least 30% of the left ventricle myocardium, primarily within and near injection sites. Poor mitochondrial distribution indicated a need for a more focused injection strategy aimed at targeting a cardiac region or segment of interest. Speckle tracking echocardiography has been utilized to evaluate spatial and progressive alterations in the diabetic heart independently, but the spatial and temporal manifestation of cardiac dysfunction remain elusive. Therefore, the objectives of Chapter 4 were to elucidate if cardiac dysfunction associated with T2DM occurs spatially, and if patterns of regional or segmental dysfunction manifest in a temporal fashion. Non-invasive echocardiography datasets were utilized to segregate mice into two pre-determined groups, wild-type and Db/Db, at 5, 12, 20, and 25 weeks. Machine learning was used to identify and rank cardiac regions, segments, and features by their ability to identify cardiac dysfunction. Overall, the Septal region, and the AntSeptum segment, best represented cardiac dysfunction associated with the diabetic state at 5, 20, and 25 weeks, with the AntSeptum also containing the greatest number of features which differed between diabetic and non-diabetic mice. These results suggested that cardiac dysfunction manifests in a spatial and temporal fashion, and is defined by patterns of regional and segmental dysfunction in the diabetic heart. Further, the Septal region, and AntSeptum segment, may provide a locale of interest for therapeutic interventions aimed at ameliorating cardiac dysfunction in T2DM

Unveiling ncRNA regulatory axes in atherosclerosis progression

Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks

Implications of long non-coding RNAs in the pathogenesis of diabetic retinopathy: a novel epigenetic paradigm.

With the rising incidence of diabetic retinopathy (DR), there is an urgent need for novel therapies. Presently, several altered metabolic pathways have been implicated in the pathogenesis of DR. Recent advances in genomic technologies have identified considerable epigenetic alterations that also contribute to DR progression. Long non-coding RNAs (lncRNAs; \u3e200 nucleotides), critical regulators of gene expression, are aberrantly expressed in DR and have not been comprehensively characterized. Our microarray analyses using human retinal endothelial cells (HRECs) revealed thousands of differentially expressed lncRNAs following high glucose (HG) exposure, with profound increases in the lncRNAs MALAT1 and HOTAIR. Using multiple techniques, I sought to elucidate the roles of these two molecules in inflammation and angiogenesis during DR. My findings demonstrated that MALAT1 is upregulated in HG and in diabetic animals, and regulates inflammatory transcripts (IL-6 and TNF-α) through its association with polycomb repressive complex 2 (PRC2). Vitreous humors from diabetic patients revealed parallel findings. DNA methylation array analyses did not demonstrate significant alterations at CpG sites across the MALAT1 gene, but inhibition of DNA methyltransferases significantly increased MALAT1 and associated inflammatory transcripts. Furthermore, HG upregulated HOTAIR and angiogenic transcripts (VEGF-A and ET-1) in HRECs and promoted an association with RNA-binding proteins, P300 and EZH2. HOTAIR knockdown reduced the expressions of angiogenic cytokines, EZH2 and P300. HG did not induce significant hypomethylation in HOTAIR CpG regions, while inhibitors for histone methylation, DNA methylation and HOTAIR significantly impacted VEGF-A and ET-1 expressions. HOTAIR expressions were elevated in the vitreous of DR patients and in the retinas of diabetic rodents. HOTAIR knockdown reduced HG-induced oxidative DNA and mitochondrial damage. The studies were further extended to delineate how these epigenetic mechanisms influence the regulation of a specific vasoactive factor, ET-1, in DR. DNA methylation array demonstrated hypomethylation in the ET1 promoter in HG. Blocking DNA methylation or histone methylation significantly increased ET-1 mRNA expressions in control and HG-treated HRECs; while, knocking down pathogenetic lncRNAs (MALAT1 and HOTAIR) subsequently prevented glucose-induced ET-1 upregulation. Collectively, I uncovered a novel epigenetic paradigm that demonstrates a complex web of epigenetic mechanisms that regulate glucose-induced transcription of molecules in important pathological processes (inflammation and angiogenesis) during DR

RNA Interference

RNA interference (RNAi), a hallmark of all biological sciences of twenty-first century, is an evolutionarily conserved and double-stranded RNA-dependent eukaryotic cell defense process. Opportunity to utilize an organisms own gene and to systematically induce and trigger RNAi for any desired sequence made RNAi an efficient approach for functional genomics, providing a solution for conventional longstanding obstacles in life sciences. RNAi research and application have significantly advanced during past two decades. This book RNA interference provides an updated knowledge and progress on RNAi in various organisms, explaining basic principles, types, and property of inducers, structural modifications, delivery systems/methodologies, and various successful bench-to-field or clinic applications and disease therapies with some aspects of limitations, alternative tools, safety, and risk assessment

The Roles of H19 in Regulating Inflammation and Aging.

Accumulating evidence suggests that long non-coding RNA H19 correlates with several aging processes. However, the role of H19 in aging remains unclear. Many studies have elucidated a close connection between H19 and inflammatory genes. Chronic systemic inflammation is an established factor associated with various diseases during aging. Thus, H19 might participate in the development of age-related diseases by interplay with inflammation and therefore provide a protective function against age-related diseases. We investigated the inflammatory gene network of H19 to understand its regulatory mechanisms. H19 usually controls gene expression by acting as a microRNA sponge, or through mir-675, or by leading various protein complexes to genes at the chromosome level. The regulatory gene network has been intensively studied, whereas the biogenesis of H19 remains largely unknown. This literature review found that the epithelial-mesenchymal transition (EMT) and an imprinting gene network (IGN) might link H19 with inflammation. Evidence indicates that EMT and IGN are also tightly controlled by environmental stress. We propose that H19 is a stress-induced long non-coding RNA. Because environmental stress is a recognized age-related factor, inflammation and H19 might serve as a therapeutic axis to fight against age-related diseases

Role of miRNAs in Cancer

MicroRNAs are the best representatives of the non-coding part of the genome and their functions are mostly linked to their target genes. During the process of carcinogenesis, both dysregulation of microRNAs and their target genes can explain the development of the disease. However, most of the target genes of microRNAs have not yet been elucidated. In this book, we add new information related to the functions of microRNAs in various tumors and their associated targetome

Epi-Drugs in Heart Failure

Unveiling the secrets of genome's flexibility does not only foster new research in the field, but also gives rise to the exploration and development of novel epigenetic-based therapies as an approach to alleviate disease phenotypes. A better understanding of chromatin biology (DNA/histone complexes) and non-coding RNAs (ncRNAs) has enabled the development of epigenetic drugs able to modulate transcriptional programs implicated in cardiovascular diseases. This particularly applies to heart failure, where epigenetic networks have shown to underpin several pathological features, such as left ventricular hypertrophy, fibrosis, cardiomyocyte apoptosis and microvascular dysfunction. Targeting epigenetic signals might represent a promising approach, especially in patients with heart failure with preserved ejection fraction (HFpEF), where prognosis remains poor and breakthrough therapies have yet to be approved. In this setting, epigenetics can be employed for the development of customized therapeutic approaches thus paving the way for personalized medicine. Even though the beneficial effects of epi-drugs are gaining attention, the number of epigenetic compounds used in the clinical practice remains low suggesting that more selective epi-drugs are needed. From DNA-methylation changes to non-coding RNAs, we can establish brand-new regulations for drug targets with the aim of restoring healthy epigenomes and transcriptional programs in the failing heart. In the present review, we bring the timeline of epi-drug discovery and development, thus highlighting the emerging role of epigenetic therapies in heart failure