Epigenomes in Cardiovascular Disease.

If unifying principles could be revealed for how the same genome encodes different eukaryotic cells and for how genetic variability and environmental input are integrated to impact cardiovascular health, grand challenges in basic cell biology and translational medicine may succumb to experimental dissection. A rich body of work in model systems has implicated chromatin-modifying enzymes, DNA methylation, noncoding RNAs, and other transcriptome-shaping factors in adult health and in the development, progression, and mitigation of cardiovascular disease. Meanwhile, deployment of epigenomic tools, powered by next-generation sequencing technologies in cardiovascular models and human populations, has enabled description of epigenomic landscapes underpinning cellular function in the cardiovascular system. This essay aims to unpack the conceptual framework in which epigenomes are studied and to stimulate discussion on how principles of chromatin function may inform investigations of cardiovascular disease and the development of new therapies

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

The ever-evolving concept of the gene: The use of RNA/Protein experimental techniques to understand genome functions

The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as "junk" DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years

Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease

Cardiogenesis in mammals requires exquisite control of gene expression and faulty regulation of transcriptional programs underpins congenital heart disease (CHD), the most common defect among live births. Similarly, many adult cardiac diseases involve transcriptional changes and sometimes have a developmental basis. Long non‐coding RNAs (lncRNAs) are a novel class of transcripts that regulate cellular processes by controlling gene expression; however, detailed insights into their biological and mechanistic functions are only beginning to emerge. Here, we discuss recent findings suggesting that lncRNAs are important factors in regulation of mammalian cardiogenesis and in the pathogenesis of CHD as well as adult cardiac disease. We also outline potential methodological and conceptual considerations for future studies of lncRNAs in the heart and other contexts.National Heart, Lung, and Blood Institute (Bench to Bassinet Program U01HL098179)National Heart, Lung, and Blood Institute (Bench to Bassinet Program U01HL098188

Into the Wild: GWAS Exploration of Non-coding RNAs

Genome-wide association studies (GWAS) have proven a fundamental tool to identify common variants associated to complex traits, thus contributing to unveil the genetic components of human disease. Besides, the advent of GWAS contributed to expose unexpected findings that urged to redefine the framework of population genetics. First, loci identified by GWAS had small effect sizes and could only explain a fraction of the predicted heritability of the traits under study. Second, the majority of GWAS hits mapped within non-coding regions (such as intergenic or intronic regions) where new functional RNA species (such as lncRNAs or circRNAs) have started to emerge. Bigger cohorts, meta-analysis and technical improvements in genotyping allowed identification of an increased number of genetic variants associated to coronary artery disease (CAD) and cardiometabolic traits. The challenge remains to infer causal mechanisms by which these variants influence cardiovascular disease development. A tendency to assign potential causal variants preferentially to coding genes close to lead variants contributed to disregard the role of non-coding elements. In recent years, in parallel to an increased knowledge of the non-coding genome, new studies started to characterize disease-associated variants located within non-coding RNA regions. The upcoming of databases integrating single-nucleotide polymorphisms (SNPs) and non-coding RNAs together with novel technologies will hopefully facilitate the discovery of causal non-coding variants associated to disease. This review attempts to summarize the current knowledge of genetic variation within non-coding regions with a focus on long non-coding RNAs that have widespread impact in cardiometabolic diseases

Long non-coding RNA structure and function: Is there a link?

RNA has emerged as the prime target for diagnostics, therapeutics and the development of personalized medicine. In particular, the non-coding RNAs (ncRNAs) that do not encode proteins, display remarkable biochemical versatility. They can fold into complex structures and interact with proteins, DNA and other RNAs, modulating the activity, DNA targets or partners of multiprotein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of epigenetic control that is dysregulated in disease. Intriguingly, for long non-coding RNAs (lncRNAs, >200 nucleotides length) structural conservation rather than nucleotide sequence conservation seems to be crucial for maintaining their function. LncRNAs tend to acquire complex secondary and tertiary structures and their functions only impose very subtle sequence constraints. In the present review we will discuss the biochemical assays that can be employed to determine the lncRNA structural configurations. The implications and challenges of linking function and lncRNA structure to design novel RNA therapeutic approaches will also be analyzed

Non-coding RNA-based therapeutics and biomarkers for treatment and detection of vascular disease

Cardiovascular disease (CVD), with atherosclerosis as its main underlying pathology, is the most prominent cause of death worldwide. Progression and rupture of atherosclerotic plaques lead to potential adverse pathological events such as myocardial infarction and stroke. Although largely successful, primary and secondary prevention strategies have thus far been insufficient in minimizing the vast consequences of atherosclerotic disease progression on global health. Abdominal aortic aneurysm (AAA) disease shares a similar risk profile with atherosclerosis. A consequence of undiagnosed AAAs can be their subsequent rupture, which up to 90% of patients will not survive. In both atherosclerosis and AAA, treatment and prevention are complicated by the fact that they progress silently and rarely lead to significant health impacts in their early stages. In addition, different pathological processes are known to be of importance as the diseases progress. These are also affected by patient-specific genetic and environmental risk factors. It would therefore be of benefit to find better ways of stratifying patient-specific disease risk and develop novel treatments. In the past decades, non-coding RNAs have emerged as powerful disease regulators in CVD and have been implicated as disease biomarkers in several research fields. In this thesis, we have sought to: (1) identify novel long non-coding RNAs (lncRNAs) involved in late-stage atherosclerotic disease and AAA, (2) establish techniques of their targeted delivery to affected vasculature, and (3) identify novel microRNA biomarkers of AAA with direct roles in disease development and progression. In study I, we have identified lncRNA MIAT as a novel regulator of vascular smooth muscle cell (VSMC) dynamics in carotid atherosclerotic disease, with positive effects on their survival – a beneficial trait in late-stage disease. Its effects on earlier disease stages were however detrimental through regulation of VSMC phenotypic switching into macrophage-like phenotypes and through regulation of macrophage-specific processes. In study II, we identified the lncRNA NUDT6, the natural antisense transcript of FGF2, to be up-regulated in fibrous caps of vulnerable vs stable plaques. NUDT6 was also up-regulated in AAA vs control aortic tissues. In experimental animal models of atherosclerosis and AAA, FGF2 de-repression by the way of NUDT6 inhibition had a beneficial effect on disease phenotypes and was successful in limiting the progression of these diseases. In studies II and III, we successfully used drug-eluting balloons to deliver therapeutics to the abdominal aorta of the translational mini-pig model of AAA. In addition, in study III, we observed beneficial effects of lenvatinib (VEGF-signaling inhibitor) on experimental AAA disease phenotype through positive effects on VSMC contractility and decreased diameter growth. Finally, in study IV, we identified miR-15a-5p as a novel disease biomarker of AAA. We showed miR-15a-5p to be relevant in AAA pathogenesis through its ability to modulate VSMCs into more inflammatory phenotypes, and its inhibition was able to limit experimental murine AAA diameter growth. In conclusion, our studies not only confirm that non-coding RNAs are promising targets for treatment of CVD, but also underline the translational feasibility of their use

LncRNAs: A new trend in molecular biology of diseases; A review

BACKGROUND: Non-coding ribonucleotide sequences, including short and long-term ribonucleic acid (RNA) molecules, are a major part of the gene expression products, which have recently been identified on a large genomic scale. The long non-coding RNAs (lncRNAs) have a length of greater than 200 nucleotides. Only a small fraction of the function of lncRNA molecules is known to date.METHODS: PubMed, Scopus, Embase, and Google Scholar were searched from January 2000 to May 2018. Based on the study inclusion and exclusion criteria and specific keywords, 92 original, relevant, experimental studies with moderate bias were selected. LncRNAs were evaluated as a new trend in molecular biology of diseases.RESULTS: Our analysis showed that the presently available evidence confirmed that lncRNAs can be a tool for the diagnosis and prognosis of many diseases and alternative therapies.CONCLUSION: LncRNAs are an emerging field of investigation as they are suggested to regulate key biological processes, including cellular proliferation and differentiation, and their aberrant expression is associated with many diseases. An improved understanding of the role of lncRNAs in disease would provide valuable information about key biological-promoting pathways and might be highly useful for diagnostic, prognostic, and alternative therapies assessments. This knowledge might also lead to advancement in the management of disease through the development of novel, personalized lncRNAs-based therapies

Long non-coding RNA structure and function: Is there a link?

RNA has emerged as the prime target for diagnostics, therapeutics and the development of personalized medicine. In particular, the non-coding RNAs (ncRNAs) that do not encode proteins, display remarkable biochemical versatility. They can fold into complex structures and interact with proteins, DNA and other RNAs, modulating the activity, DNA targets or partners of multiprotein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of epigenetic control that is dysregulated in disease. Intriguingly, for long non-coding RNAs (lncRNAs, >200 nucleotides length) structural conservation rather than nucleotide sequence conservation seems to be crucial for maintaining their function. LncRNAs tend to acquire complex secondary and tertiary structures and their functions only impose very subtle sequence constraints. In the present review we will discuss the biochemical assays that can be employed to determine the lncRNA structural configurations. The implications and challenges of linking function and lncRNA structure to design novel RNA therapeutic approaches will also be analyzed

Circulating microRNAs as novel biomarkers for diabetes mellitus.

Diabetes mellitus is characterized by insulin secretion from pancreatic β cells that is insufficient to maintain blood glucose homeostasis. Autoimmune destruction of β cells results in type 1 diabetes mellitus, whereas conditions that reduce insulin sensitivity and negatively affect β-cell activities result in type 2 diabetes mellitus. Without proper management, patients with diabetes mellitus develop serious complications that reduce their quality of life and life expectancy. Biomarkers for early detection of the disease and identification of individuals at risk of developing complications would greatly improve the care of these patients. Small non-coding RNAs called microRNAs (miRNAs) control gene expression and participate in many physiopathological processes. Hundreds of miRNAs are actively or passively released in the circulation and can be used to evaluate health status and disease progression. Both type 1 diabetes mellitus and type 2 diabetes mellitus are associated with distinct modifications in the profile of miRNAs in the blood, which are sometimes detectable several years before the disease manifests. Moreover, circulating levels of certain miRNAs seem to be predictive of long-term complications. Technical and scientific obstacles still exist that need to be overcome, but circulating miRNAs might soon become part of the diagnostic arsenal to identify individuals at risk of developing diabetes mellitus and its devastating complications