Long noncoding RNA: a new player of heart failure?

ANRIL rs4977574 Gene Polymorphism in Women with Recurrent Pregnancy Loss

BACKGROUND

ANRIL rs4977574 gene polymorphism has been associated with arterial thrombosis and cardiovascular disease development. ANRIL rs4977574 gene polymorphism could also be associated with recurrent pregnancy loss (RPL) since there is increasing evidence in favor of a potential shared pathophysiological mechanism with cardiovascular disease, potentially through arterial thrombosis. This study's goal is to investigate the differences in ANRIL rs4977574 gene polymorphism between women with and without RPL, if any, as well as a potential association with the number of pregnancy losses.

METHODS

DNA was isolated from peripheral blood samples, and the sequence containing the polymorphism of interest was amplified with PCR. Results were visualized under UV light following electrophoresis in 3% agarose gel with ethidium bromide. ANRIL rs4977574 (A>G) prevalence was compared between 56 women with and 69 without RPL. Results were adjusted for women's age and BMI, while a stratified analysis was performed according to number of pregnancy losses.

RESULTS

Allele A was significantly more prevalent in the control group compared to RPL women [31 (44.9%) vs. 14 (25%), p = 0.021]. Although not reaching statistical significance, a gradually decreasing prevalence of allele A with an increasing number of pregnancy losses was observed [31 (44.9%) in control, eight (30.7%) with two, six (23.1%) with three, and 0 (0.0%) with four pregnancy losses, p = 0.078]. Results were also similar following adjustment.

CONCLUSIONS

This is the first study that demonstrates an association between RPL presence and ANRIL rs4977574 gene polymorphism (lower prevalence of allele A), while a difference according to the number of pregnancy losses cannot be excluded.

LINC00707 inhibits myocardial fibrosis and immune disorder in rheumatic heart disease by regulating miR-145-5p/S1PR1

LINC00707 is a lncRNA that can regulate a variety of diseases. This study mainly investigated that the expression of LINC00707 in rheumatic heart disease (RHD) and LINC00707 regulates S1PR1 by targeting miR-145-5p to inhibit myocardial fibrosis and immune disorder in RHD. A rat model of RHD induced by inactivated group A β-hemolytic streptococcus (GSA) was established. Sixty female Lewis rats (8 weeks of age) were randomly divided into six groups, including control (Con), RHD, RHD+NC, RHD+LINC00707, RHD+miR-145-5p and RHD+LINC00707+miR-145-5p. The mRNA expression was detected by Quantitative Real-time polymerase chain reaction (qRT-PCR). Protein expression of S1PR1 was detected by western blot. The levels of myocardial damage markers (CK-MB, cTnl) and inflammatory immune markers (IL-6, IL-17 and IL-21) were measured by enzyme linked immunosorbent assay (ELISA). The Collagen III/I(COLIII/I) ratio, mRNA expression of COLIIIα1 and FSP1 of rat heart valve tissue in the RHD group was observably higher by comparison with the CON group. The expression of LINC00707 was observably lower in the RHD group. LINC00707 inhibited myocardial fibrosis and immune disorder in RHD. MiR-145-5p was the target gene of LINC00707 via Targetscan prediction. Luciferase reporter experiment confirmed that miR-145-5p was directly regulated by LINC00707. The expression of miR-145-5p in the RHD group was observably higher by comparison with the CON group and LINC00707 observably decreased the expression of miR-145-5p. miR-145-5p mimic reversed the inhibiting effect of LINC00707 on myocardial fibrosis and immune disorder. Furthermore, S1PR1 was confirmed to be downstream gene of miR-145-5p and low expressed in the RHD model. LINC00707 could inhibit myocardial fibrosis and immune disorder in RHD by regulating miR-145-5p/S1PR1.

Epigenetic Mechanisms of Aging and Aging-Associated Diseases

Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.

Non-Coding RNAs in Cell-to-Cell Communication: Exploiting Physiological Mechanisms as Therapeutic Targets in Cardiovascular Pathologies

Cardiovascular disease, the leading cause of death worldwide, has been characterized at the molecular level by alterations in gene expression that contribute to the etiology of the disease. Such alterations have been shown to play a critical role in the development of atherosclerosis, cardiac remodeling, and age-related heart failure. Although much is now known about the cellular and molecular mechanisms in this context, the role of epigenetics in the onset of cardiovascular disease remains unclear. Epigenetics, a complex network of mechanisms that regulate gene expression independently of changes to the DNA sequence, has been highly implicated in the loss of homeostasis and the aberrant activation of a myriad of cellular pathways. More specifically, non-coding RNAs have been gaining much attention as epigenetic regulators of various pathologies. In this review, we will provide an overview of the ncRNAs involved in cell-to-cell communication in cardiovascular disease, namely atherosclerosis, cardiac remodeling, and cardiac ageing, and the potential use of epigenetic drugs as novel therapeutic targets.

Change of Heart: the Epitranscriptome of Small Non-coding RNAs in Heart Failure

Purpose of Review

Small non-coding RNAs regulate gene expression and are highly implicated in heart failure. Recently, an additional level of post-transcriptional regulation has been identified, referred to as the epitranscriptome, which encompasses the body of post-transcriptional modifications that are placed on RNA molecules. In this review, we summarize the current knowledge on the small non-coding RNA epitranscriptome in heart failure.

Recent Findings

With the rise of new methods to study RNA modifications, epitranscriptome research has begun to take flight. Over the past 3 years, the number of publications on the epitranscriptome in heart failure has significantly increased, and we expect many more highly relevant publications to come out over the next few years.

Summary

Currently, at least six modifications on small non-coding RNAs have been investigated in heart failure-relevant studies, namely N6-adenosine, N5-cytosine and N7-guanosine methylation, 2’-O-ribose-methylation, adenosine-to-inosine editing, and isomiRs. Their potential role in heart failure is discussed.

LncRNA-miRNA-mRNA regulatory axes in endometrial cancer: a comprehensive overview

INTRODUCTION

Recent research on tumorigenesis and progression has opened up an array of novel molecular mechanisms in the form of interactions between cellular non-coding RNAs (long non-coding RNA[lncRNA]/microRNA [miRNA]) and coding transcripts that regulate health and disease. Endometrial cancer (EC) is a prominent gynecological malignancy with a high incidence rate and poorly known etiology and prognostic factors that hinder the success of disease management. The emerging role of lncRNA-miRNA-mRNA interactions and their dysregulation in the pathophysiology of EC has been elucidated in many recent studies.

METHODS

A thorough literature review was conducted to explore information about lncRNA-miRNA-mRNA axes in EC.

RESULTS

Several lncRNAs act as molecular sponges that sequester various tumor suppressor miRNAs to inhibit their function, leading to the dysregulation of their target mRNA transcripts that contribute to the EC regulation.

CONCLUSIONS

This review summarizes these networks of molecular mechanisms and their contribution to different aspects of endometrial carcinogenesis, leading to a better conceptualization of the molecular pathways that underlie the disease and helping establish novel diagnostic biomarkers and therapeutic intervention points to aid the curative intent of EC.

The Yin and Yang of epigenetics in the field of nanoparticles

Nanoparticles (NPs) have become a very exciting research avenue, with multitudinous applications in various fields, including the biomedical one, whereby they have been gaining considerable interest as drug carriers able to increase bioavailability, therapeutic efficiency and specificity of drugs. Epigenetics, a complex network of molecular mechanisms involved in gene expression regulation, play a key role in mediating the effect of environmental factors on organisms and in the etiology of several diseases (e.g., cancers, neurological disorders and cardiovascular diseases). For many of these diseases, epigenetic therapies have been proposed, whose application is however limited by the toxicity of epigenetic drugs. In this review, we will analyze two aspects of epigenetics in the field of NPs: the first is the role that epigenetics play in mediating nanotoxicity, and the second is the possibility of using NPs for delivery of "epi-drugs" to overcome their limitations. We aim to stimulate discussion among specialists, specifically on the potential contribution of epigenetics to the field of NPs, and to inspire newcomers to this exciting technology.

The Role of ANRIL in Atherosclerosis

There is a huge number of noncoding RNA (ncRNA) transcripts in the cell with important roles in modulation of different mechanisms. ANRIL is a long ncRNA with 3.8 kb length that is transcribed in the opposite direction of the INK4/ARF locus in chromosome 9p21. It was shown that polymorphisms within this locus are associated with vascular disorders, notably coronary artery disease (CAD), which is considered as a risk factor for life-threatening events like myocardial infarction and stroke. ANRIL is subjected to a variety of splicing patterns producing multiple isoforms. Linear isoforms could be further transformed into circular ones by back-splicing. ANRIL regulates genes in atherogenic network in a positive or negative manner. This regulation is implemented both locally and remotely. While CAD is known as a proliferative disorder and cell proliferation plays a crucial role in the progression of atherosclerosis, the functions of ANRIL and CAD development are intertwined remarkably. This makes ANRIL a suitable target for diagnostic, prognostic, and even therapeutic aims. In this review, we tried to present a comprehensive appraisal on different aspects of ANRIL including its location, structure, isoforms, expression, and functions. In each step, the contribution of ANRIL to atherosclerosis is discussed.

Radiation-induced cardiovascular disease: an overlooked role for DNA methylation?

Radiotherapy in cancer treatment involves the use of ionizing radiation for cancer cell killing. Although radiotherapy has shown significant improvements on cancer recurrence and mortality, several radiation-induced adverse effects have been documented. Of these adverse effects, radiation-induced cardiovascular disease (CVD) is particularly prominent among patients receiving mediastinal radiotherapy, such as breast cancer and Hodgkin's lymphoma patients. A number of mechanisms of radiation-induced CVD pathogenesis have been proposed such as endothelial inflammatory activation, premature endothelial senescence, increased ROS and mitochondrial dysfunction. However, current research seems to point to a so-far unexamined and potentially novel involvement of epigenetics in radiation-induced CVD pathogenesis. Firstly, epigenetic mechanisms have been implicated in CVD pathophysiology. In addition, several studies have shown that ionizing radiation can cause epigenetic modifications, especially DNA methylation alterations. As a result, this review aims to provide a summary of the current literature linking DNA methylation to radiation-induced CVD and thereby explore DNA methylation as a possible contributor to radiation-induced CVD pathogenesis.

Role of Non-Coding RNA of Human Platelet in Cardiovascular Disease

Cardiovascular diseases (CVD) are the major cause of death in the world. Numerous genetic studies involving transcriptomic approaches aimed at the detailed understanding of the disease and the development of new therapeutic strategies have been conducted over recent years. There has been an increase in research on platelets, which are implicated in CVD due to their capacity to release regulatory molecules that affect various pathways. Platelets secrete over 500 various kinds of molecules to plasma including large amounts of non-coding (nc) RNA (miRNA, lncRNA or circRNA). These ncRNA correspond to 98% of transcripts that are not translated into proteins as they are important regulators in physiology and disease. Thus, miRNAs can direct protein complexes to mRNAs through base-pairing interactions, thus causing translation blockage or/and transcript degradation. The lncRNAs act via different mechanisms by binding to transcription factors. Finally, circRNAs act as regulators of miRNAs, interfering with their action. Alteration in the repertoire and/or the amount of the platelet-secreted ncRNA can trigger CVD as well as other diseases. NcRNAs can serve as effective biomarkers for the disease or as therapeutic targets due to their disease involvement. In this review, we will focus on the most important ncRNAs that are secreted by platelets (9 miRNA, 9 lncRNA and 5 circRNA), their association with CVD, and the contribution of these ncRNA to CVD risk to better understand the relation between ncRNA of human platelet and CVD.

Regulation of Mitochondrial Function by Noncoding RNAs in Heart Failure and Its Application in Diagnosis and Treatment

ABSTRACT

Heart failure (HF) is the terminal stage of multiple cardiovascular diseases. However, the pathogenesis of HF remains unclear and prompt; appropriate diagnosis and treatment of HF are crucial. Cardiomyocytes isolated from HF subjects frequently present mitochondrial impairment and dysfunction. Many studies have suggested that the regulation by noncoding RNAs (ncRNAs) of mitochondria can affect the occurrence and progression of HF. The regulation by ncRNAs of myocardial mitochondria during HF and the recent applications of ncRNAs in the diagnosis and treatment of HF are summarized in this review that is intended to gain keen insights into the mechanisms of HF and more effective treatments.

The Emerging Role of Epigenetics in Therapeutic Targeting of Cardiomyopathies

Cardiomyopathies (CMPs) are a heterogeneous group of myocardial diseases accountable for the majority of cases of heart failure (HF) and/or sudden cardiac death (SCD) worldwide. With the recent advances in genomics, the original classification of CMPs on the basis of morphological and functional criteria (dilated (DCM), hypertrophic (HCM), restrictive (RCM), and arrhythmogenic ventricular cardiomyopathy (AVC)) was further refined into genetic (inherited or familial) and acquired (non-inherited or secondary) forms. Despite substantial progress in the identification of novel CMP-associated genetic variations, as well as improved clinical recognition diagnoses, the functional consequences of these mutations and the exact details of the signaling pathways leading to hypertrophy, dilation, and/or contractile impairment remain elusive. To date, global research has mainly focused on the genetic factors underlying CMP pathogenesis. However, growing evidence shows that alterations in molecular mediators associated with the diagnosis of CMPs are not always correlated with genetic mutations, suggesting that additional mechanisms, such as epigenetics, may play a role in the onset or progression of CMPs. This review summarizes published findings of inherited CMPs with a specific focus on the potential role of epigenetic mechanisms in regulating these cardiac disorders.

Analysis of lncRNA-miRNA-mRNA expression pattern in heart tissue after total body radiation in a mouse model

Background

Radiation therapy is integral to effective thoracic cancer treatments, but its application is limited by sensitivity of critical organs such as the heart. The impacts of acute radiation-induced damage and its chronic effects on normal heart cells are highly relevant in radiotherapy with increasing lifespans of patients. Biomarkers for normal tissue damage after radiation exposure, whether accidental or therapeutic, are being studied as indicators of both acute and delayed effects. Recent research has highlighted the potential importance of RNAs, including messenger RNAs (mRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as biomarkers to assess radiation damage. Understanding changes in mRNA and non-coding RNA expression will elucidate biological pathway changes after radiation.

Methods

To identify significant expression changes in mRNAs, lncRNAs, and miRNAs, we performed whole transcriptome microarray analysis of mouse heart tissue at 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray (Gy). We also validated changes in specific lncRNAs through RT-qPCR. Ingenuity Pathway Analysis (IPA) was used to identify pathways associated with gene expression changes.

Results

We observed sustained increases in lncRNAs and mRNAs, across all doses of radiation. Alas2, Aplnr, and Cxc3r1 were the most significantly downregulated mRNAs across all doses. Among the significantly upregulated mRNAs were cell-cycle arrest biomarkers Gdf15, Cdkn1a, and Ckap2. Additionally, IPA identified significant changes in gene expression relevant to senescence, apoptosis, hemoglobin synthesis, inflammation, and metabolism. LncRNAs Abhd11os, Pvt1, Trp53cor1, and Dino showed increased expression with increasing doses of radiation. We did not observe any miRNAs with sustained up- or downregulation across all doses, but miR-149-3p, miR-6538, miR-8101, miR-7118-5p, miR-211-3p, and miR-3960 were significantly upregulated after 12 Gy.

Conclusions

Radiation-induced RNA expression changes may be predictive of normal tissue toxicities and may indicate targetable pathways for radiation countermeasure development and improved radiotherapy treatment plans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02998-w.

Clinical Value of Circulating ZFAS1 and miR-590-3p in the Diagnosis and Prognosis of Chronic Heart Failure

Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of various cardiovascular diseases, including chronic heart failure (CHF). In this study, we aimed to investigate the role of ZFAS1/miR-590-3p axis in the diagnosis and prognosis of CHF. The expression of ZFAS1 and miR-590-3p in the serum samples of CHF was measured using quantitative real-time polymerase chain reaction. Pearson correlation coefficient was applied to analyze the correlation between ZFAS1 and miR-590-3p. The receiver operating characteristic (ROC) curve was used to examine the diagnostic accuracy of ZFAS1, miR-590-3p, and brain natriuretic peptide (BNP). The Kaplan-Meier curve and Cox regression analysis were used to assess the prognostic value of ZFAS1 and miR-590-3p in CHF. This study found that the serum levels of ZFAS1 were significantly higher, while miR-590-3p levels were significantly lower in CHF. ROC results indicated that the combined diagnostic accuracy of ZFAS1 + miR-590-3p + BNP was significantly higher than that of these indicators used alone. Kaplan- Meier results showed that patients with low expression of miR-590-3p or high expression of ZFAS1 had poor prognosis. In conclusion, CHF patients had increased ZFAS1 and decreased miR-590-3p expression. ZFAS1 and miR-590-3p might serve as novel non-invasive diagnostic and prognostic markers for patients with CHF.

Novel Biomarkers in Heart Failure: New Insight in Pathophysiology and Clinical Perspective

Heart failure (HF) is a complex clinical syndrome with a huge social burden in terms of cost, morbidity, and mortality. Brain natriuretic peptide (BNP) appears to be the gold standard in supporting the daily clinical management of patients with HF. Novel biomarkers may supplement BNP to improve the understanding of this complex disease process and, possibly, to personalize care for the different phenotypes, in order to ameliorate prognosis. In this review, we will examine some of the most promising novel biomarkers in HF. Inflammation plays a pivotal role in the genesis and progression of HF and, therefore, several candidate molecules have been investigated in recent years for diagnosis, prognosis, and therapy monitoring. Noncoding RNAs are attractive as biomarkers and their potential clinical applications may be feasible in the era of personalized medicine. Given the complex pathophysiology of HF, it is reasonable to expect that the future of biomarkers lies in the application of precision medicine, through wider testing panels and “omics” technologies, to further improve HF care delivery.

Epigenetics of aging and disease: a brief overview

Aging is an important risk factor for several human diseases such as cancer, cardiovascular disease and neurodegenerative disorders, resulting from a combination of genetic and environmental factors (e.g., diet, smoking, obesity and stress), which, at molecular level, cause changes in gene expression underlying the decline of physiological function. Epigenetics, which include mechanisms regulating gene expression independently of changes to DNA sequence, regulate gene expression by modulating the structure of chromatin or by regulating the binding of transcriptional machinery to DNA. Several studies showed that an impairment of epigenetic mechanisms promotes alteration of gene expression underlying several aging-related diseases. Alteration of these mechanisms is also linked with changes of gene expression that occurs during aging processes of different tissues. In this review, we will outline the potential role of epigenetics in the onset of two age-related pathologies, cancer and cardiovascular diseases.

Dysregulation of lncRNA-CCRR contributes to brain metastasis of breast cancer by intercellular coupling via regulating connexin 43 expression

Cardiac conduction regulatory RNA (CCRR) is down‐regulated in the pathogenesis of heart failure (HF), which accordingly suppresses cardiac conduction while promoting arrhythmogenicity. Meanwhile, CX43 was reported to play a role in the pathogenesis of metastatic breast cancer and melanoma brain colonization. In this study, we studied the role of long non‐coding RNA CCRR and its interaction with CX43 in brain metastasis of breast cancer. Breast cancer patients were grouped according to the metastasis status. Real‐time PCR and IHC assay were used to measure the expression of lncRNA‐CCRR and CX43 in patients. Western blot was conducted to observe the effect of lncRNA‐CCRR on the expression of CX43 in MDA‐MB‐231BR and BT‐474BR cells. Compared with the non‐metastasis group, the mRNA expression of tissue lncRNA‐CCRR, cerebrospinal fluid (CSF) lncRNA‐CCRR, tissue CX43 and tissue protein expression of CX43 were both evidently up‐regulated in metastasis patients, especially in patients with brain metastasis. The expression of lncRNA‐CCRR was positively correlated with the up‐regulated expression of CX43. Moreover, CX43 expression was significantly lower in MDA‐MB‐231WT cells compared with that in MDA‐MB‐231BR cells. Also, the overexpression of lncRNA‐CCRR evidently increased dye transfer rate from astrocytes to MDA‐MB‐231BR/BT‐474BR cells but reduced lncRNA‐CCRR expression and suppressed the transmigration of MDA‐MB‐231BR/BT‐474BR cells in a blood‐brain barrier (BBB) model. In this study, we demonstrated that the presence of lncRNA‐CCRR could up‐regulate the expression of CX43, which promoted gap junction formation in brain metastasis of breast cancer. Accordingly, the communication between breast cancer cells and astrocytes was also promoted.

Matrine regulates H2O2-induced oxidative stress through long non-coding RNA HOTAIR/miR-106b-5p axis via AKT and STAT3 pathways

Matrine is a main active constituent of Chinese herb Sophora flavescens Ait (Kushen), which has shown various pharmacological effects, and has been reported to exhibit protective effects in heart failure. In the present study, the underlying mechanism of matrine was explored in H₂O₂-induced H9c2 cell line. It was confirmed that matrine could alleviate H₂O₂-induced injury in H9c2 cells. And the down-regulation of long non-coding RNA HOTAIR induced by H₂O₂ could be reversed by treating with matrine. Moreover, overexpression of HOTAIR promoted cell viability and superoxide dismutase (SOD) level, but inhibited cell apoptosis and lactate dehydrogenase (LDH) level. We found that miR-106b-5p was a target of HOTAIR and negatively regulated by HOTAIR. Moreover, up-regulation of miR-106b-5p restored the effects of HOTAIR overexpression on cell viability, apoptosis, and the levels of LDH and SOD. In addition, matrine protected H9c2 cells from H₂O₂-induced injury through HOTAIR/miR-106b-5p axis. Furthermore, we discovered that matrine exerted protective effects on H₂O₂-induced H9c2 cells through activating STAT3 and AKT pathway. In brief, matrine modulated H₂O₂-induced myocardial oxidative stress repair through HOTAIR/miR-106b-5p axis via AKT and STAT3 signaling pathway. Our study may provide a therapeutic target for the therapy of oxidative stress heart diseases.

LncRNA FENDRR Inhibits ox-LDL Induced Mitochondrial Energy Metabolism Disorder in Aortic Endothelial Cells via miR-18a-5p/PGC-1α Signaling Pathway

Atherosclerosis (AS) is the main cause of morbidity and mortality in the world. Mitochondrial dysfunction is closely related to AS. At present, several signaling pathways related to mitochondrial dysfunction have been found, one of which is around PGC-1α. PGC-1α is a transcription activator, which is related to mitochondrial biogenesis and antioxidant defense. In this study, we explored the effect of miR-18a-5p/PGC-1α signaling pathway on mitochondrial energy metabolism in HAECs with ox-LDL treatment. The results showed that the mitochondrial energy metabolism disorder in HAECs treated by ox-LDL was related to the downregulation of LncRNA FENDRR and PGC-1α. FENDRR could reverse ox-LDL induced mitochondrial energy metabolism disorder and upregulate the PGC-1α expression. FENDRR could be used as ceRNA to inhibit the miR-18a-5p expression and reduce the negative regulation of miR-18a-5p on PGC-1α. Downregulation of miR-18a-5p expression or upregulation of PGC-1α in ox-LDL treated HAECs could reverse mitochondrial energy metabolism disorder. In conclusion, these findings suggested that FENDRR/miR-18a-5p/PGC-1α signaling pathway regulated mitochondrial energy metabolism in HAECs; ox-LDL downregulated the expression of PGC-1α and cause mitochondrial energy metabolism disorder by inhibiting this signal pathway.

Role of the Epigenome in Heart Failure

Gene expression is needed for the maintenance of heart function under normal conditions and in response to stress. Each cell type of the heart has a specific program controlling transcription. Different types of stress induce modifications of these programs and, if prolonged, can lead to altered cardiac phenotype and, eventually, to heart failure. The transcriptional status of a gene is regulated by the epigenome, a complex network of DNA and histone modifications. Until a few years ago, our understanding of the role of the epigenome in heart disease was limited to that played by histone deacetylation. But over the last decade, the consequences for the maintenance of homeostasis in the heart and for the development of cardiac hypertrophy of a number of other modifications, including DNA methylation and hydroxymethylation, histone methylation and acetylation, and changes in chromatin architecture, have become better understood. Indeed, it is now clear that many levels of regulation contribute to defining the epigenetic landscape required for correct cardiomyocyte function, and that their perturbation is responsible for cardiac hypertrophy and fibrosis. Here, we review these aspects and draw a picture of what epigenetic modification may imply at the therapeutic level for heart failure.

The functions of LncRNA in the heart

Cardiovascular disease is a major cause of death and disability worldwide. Recently, increasing evidence has demonstrated that various lncRNAs play critical roles in the pathogenesis of cardiovascular diseases, including myocardial ischemia and reperfusion (I/R) injury. LncRNAs are transcripts longer than 200 nucleotides. They are considered a class of dynamic noncoding RNAs known to be involved in physiological and pathological conditions with regulatory and structural roles in numerous biological processes, including genomic imprinting, epigenetic regulation, cell proliferation, development, aging and apoptosis. They are emerging as potential key regulators of a variety of cardiovascular diseases. However, the roles of lncRNAs in the heart function remain largely unknown. The purpose of this review was to summarize the functions of lncRNAs in the heart and discuss the challenges and possible strategies of lncRNA research for cardiovascular disease.

Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5—a gene specifying a master cardiomyogenic lineage transcription factor (TF)—which we call Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs). The IRENEs are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5: IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription.

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Two eRNAs (IRENE-SS, IRENE-div) with opposing functions are found upstream of Nkx2-5

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IRENE-SS works as a classical eRNA, acting as a transcriptional activator

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IRENE-div acts unconventionally, functioning as a transcriptional repressor

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IRENEs epigenetically control enhancer status and, subsequently, locus architecture

Circulating Non-coding RNAs and Cardiovascular Diseases

The discovery of noncoding RNAs (ncRNAs) including short microRNAs, long ncRNAs and circular RNAs has broaden our knowledge about mammalian genomes and transcriptomes. A growing number of evidence on aberrantly regulated ncRNAs in cardiovascular diseases has indicated that ncRNAs are critical contributors to cardiovascular pathophysiology. Moreover, multiple recent studies have reported that ncRNAs can be detected in the bloodstream that differs between health subjects and diseased patients and some of them are remarkably stable. Although our knowledge about the origin and function of the circulating ncRNAs is still limited, these molecules have been regarded as promising noninvasive biomarker for risk stratification, diagnosis and prognosis of various cardiovascular diseases. In this chapter, we have described biological characteristics of circulating ncRNAs and discussed current trends and future prospects for the usage of circulating ncRNAs as biomarkers for common cardiovascular diseases.

An Overview of Non-coding RNAs and Cardiovascular System

Cardiovascular disease management and timely diagnosis remain a major dilemma. Delineating molecular mechanisms of cardiovascular diseases is opening horizon in the field of molecular medicines and in the development of early diagnostic markers. Non-coding RNAs are the highly functional and vibrant nucleic acids and are known to be involved in the regulation of endothelial cells, vascular and smooth muscles cells, cardiac metabolism, ischemia, inflammation and many processes in cardiovascular system. This chapter is comprehensively focusing on the overview of the non-coding RNAs including their discovery, generation, classification and functional regulation. In addition, overview regarding different non-coding RNAs as long non-coding, siRNAs and miRNAs involvement in the cardiovascular diseases is also addressed. Detailed functional analysis of this vast group of highly regulatory molecules will be promising for shaping future drug discoveries.

An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure

Accumulating evidence suggests that long noncoding RNAs (lncRNAs) are emerging as important regulators involved in diseases, including heart failure (HF). In this study, we used microarray profiles to examine the transcriptome of lncRNAs in left ventricle samples derived from HF patients. We designed a custom pipeline to reannotate lncRNAs from microarray data and identified a set of consistently dysregulated lncRNAs in HF across the three independent cohorts. In total, 84 lncRNAs were found to be consistently dysregulated in at least two cohorts. By using a rank aggregation method, we integrated correlated protein-coding genes of the consistently dysregulated lncRNAs derived from HF samples and characterized their biological functions based on the correlated genes. The transcriptional regulation relationships of these lncRNAs ranged from 104 to 261, suggesting their important regulatory functions. Among the conserved lncRNAs, AC018647.1 and AC009113.1 showed significant dysregulation across all three cohorts. Our results showed that the two lncRNAs were involved in development-associated and cardiac cycle-associated functions.

Construction and analysis for differentially expressed long non-coding RNAs and mRNAs in acute myocardial infarction

Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides. Some lncRNAs are related to acute myocardial infarction (AMI) and can serve as blood-based biomarkers for AMI detection. To identify whether new lncRNAs participate in AMI, the expression of lncRNAs and mRNAs was analysed by microarray analysis (Agilent human array) with the limma package in R in two series: five paired peripheral blood mononuclear cell (PBMC) samples and four paired plasma samples from different AMI patients. In PBMCs, a total of 2677 upregulated and 458 downregulated lncRNAs were significantly differentially expressed; additionally, 1168 mRNAs were upregulated and 1334 mRNAs were downregulated between the AMI patients and controls. In plasma, we found 41 upregulated and 51 downregulated lncRNAs that were differentially expressed, as well as 9 mRNAs that were upregulated and 9 mRNAs that were downregulated among the two groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the clusterProfiler package in R, and differentially expressed mRNAs were functionally annotated. The top differentially expressed mRNAs were associated with circadian rhythm, the NF-kB pathway, the p53 pathway and the metabolism pathway. We further performed target gene prediction and coexpression analysis and revealed the interrelationships among the significantly differentially expressed lncRNAs and mRNAs. The expression of four lncRNAs (uc002ddj.1, NR_047662, ENST00000581794.1 and ENST00000509938.1) was validated in the newly diagnosed AMI and control groups by quantitative real-time PCR (qRT-PCR). Our study demonstrated that the clustered expression of lncRNAs between PBMCs and plasma showed tremendous differences. The newly screened lncRNAs may play indispensable roles in the development of AMI, although their biological functions need to be further validated.

RETRACTED: Down-regulated microRNA-195-5p and up-regulated CXCR4 attenuates the heart function injury of heart failure mice via inactivating JAK/STAT pathway

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. Concern was raised about the integrity of the images in Figure 6, which appear to contain suspected image duplications, as detailed here: https://pubpeer.com/publications/A31DE9EEF13ED6B88BCC86A9CAC8D9 and here: https://docs.google.com/spreadsheets/d/1r0MyIYpagBc58BRF9c3luWNlCX8VUvUuPyYYXzxWvgY/edit#gid=262337249. Most of these image duplications involve either pasting portions of one image into another, or rotating/flipping the image. Numerous additional suspected image duplications were detected within Figures 2A and 7A. The journal requested the corresponding author comment on these concerns and provide the raw data. The authors did not respond to this request and therefore the Editor-in-Chief decided to retract the article.

Transcriptomic Analyses for Identification and Prioritization of Genes Associated With Alzheimer's Disease in Humans

Long non-coding RNAs (lncRNAs), as important ncRNA regulators, play crucial roles in the regulation of various biological processes, and their aberrant expression is related to the occurrence and development of diseases, which is gradually validated by more and more studies. Alzheimer’s disease (AD) is a chronic neurodegenerative disease that often develops slowly and gradually deteriorates over time. However, which functions the lncRNAs perform in AD are almost unknown. In this study, we performed transcriptome analysis in AD, containing 12,892 known lncRNAs and 19,053 protein-coding genes (PCGs). Further, 14 down-regulated and 39 up-regulated lncRNAs were identified, compared with normal brain samples, which indicated that these lncRNAs might play critical roles in the pathogenesis of AD. In addition, 19 down-regulated and 28 up-regulated PCGs were also detected. Using the differentially expressed lncRNAs and PCGs through the WGCNA method, an lncRNA–mRNA co-expressed network was constructed. The results showed that lncRNAs RP3-522J7, MIR3180-2, and MIR3180-3 were frequently co-expressed with known AD risk PCGs. Interestingly, PCGs in the network are significantly enriched in brain- or AD-related biological functions, including the brain renin–angiotensin system, cell adhesion, neuroprotective role of THOP1 in AD, and so on. Furthermore, it was shown that 18 lncRNAs and 7 PCGs were highly expressed in normal brain tissue relative to other normal tissue types, suggesting their potential as diagnostic markers of AD, especially RP3-522J7, MIR3180-2, MIR3180-3, and CTA-929C8. In total, our study identified a compendium of AD-related dysregulated lncRNAs and characterized the corresponding biological functions of these lncRNAs in AD, which will be helpful to understand the molecular basis and pathogenesis of AD.

Interactions Among Regulatory Non-coding RNAs Involved in Cardiovascular Diseases

Non-coding RNAs (ncRNAs) are important regulatory players in human cells that have been shown to modulate different cellular processes and biological functions through controlling gene expression, being also involved in pathological conditions such as cardiovascular diseases. Among them, long non-coding RNAs (lncRNAs) and circular (circRNAs) could act as competing endogenous RNAs (ceRNAs) sequestering other ncRNAs. This entangled network of interactions has been reported to trigger the decay of the targeted ncRNAs having important roles in gene regulation. Growing evidences have been demonstrated that the regulatory mechanism underlying the crosstalk between different ncRNA species, namely lncRNAs, circRNAs and miRNAs has also an important role in the pathophysiological processes of cardiovascular diseases. In this chapter, the main regulatory relationship among lncRNAs, circRNAs and miRNAs were summarized and their role in the control and development of cardiovascular diseases was highlighted.

ANRIL and atherosclerosis

WHAT IS KNOWN AND OBJECTIVE

The 3.8-kb-long antisense non-coding RNA at the INK4 locus (ANRIL) is transcribed from the short arm of human chromosome 9 on P21 and is associated with malfunction of the vascular endothelium, vascular smooth muscle cell (VSMC) proliferation/migration/senescence/apoptosis, mononuclear cell adhesion and proliferation, glycolipid metabolism disorder and DNA damage. Hence, ANRIL plays an important role in atherogenesis. Moreover, genome-wide association studies (GWAS) have identified ANRIL as a biomarker that is closely related to coronary heart disease (CHD). The objective of this review was to discuss the pathological mechanism of ANRIL in atherosclerotic development and its significance as a predictor of cardiovascular disease.

METHODS

Review of the PubMed, EMBASE and Cochrane databases for articles demonstrating the roles of ANRIL in the development of atherosclerotic diseases.

RESULTS AND DISCUSSION

The abnormal expression of ANRIL is linked to vascular endothelium injury; the proliferation, migration, senescence and apoptosis of VSMCs; mononuclear cell adhesion and proliferation; glycolipid metabolism disorder; DNA damage; and competing endogenous RNAs. Moreover, ANRIL accelerates the progression of CHD by regulating its single nucleotide polymorphisms (SNPs).

WHAT IS NEW AND CONCLUSION

Considering that ANRIL accelerates atherosclerosis (AS) development and is a risk factor for CHD, it is reasonable for us to explore an efficacious ANRIL-based therapy for AS in CHD.

Long non-coding RNA cardiac hypertrophy-associated regulator governs cardiac hypertrophy via regulating miR-20b and the downstream PTEN/AKT pathway

Pathological cardiac hypertrophy (CH) is a key factor leading to heart failure and ultimately sudden death. Long non‐coding RNAs (lncRNAs) are emerging as a new player in gene regulation relevant to a wide spectrum of human disease including cardiac disorders. Here, we characterize the role of a specific lncRNA named cardiac hypertrophy‐associated regulator (CHAR) in CH and delineate the underlying signalling pathway. CHAR was found markedly down‐regulated in both in vivo mouse model of cardiac hypertrophy induced by pressure overload and in vitro cellular model of cardiomyocyte hypertrophy induced by angiotensin II (AngII) insult. CHAR down‐regulation alone was sufficient to induce hypertrophic phenotypes in healthy mice and neonatal rat ventricular cells (NRVCs). Overexpression of CHAR reduced the hypertrophic responses. CHAR was found to act as a competitive endogenous RNA (ceRNA) to down‐regulate miR‐20b that we established as a pro‐hypertrophic miRNA. We experimentally established phosphatase and tensin homolog (PTEN), an anti‐hypertrophic signalling molecule, as a target gene for miR‐20b. We found that miR‐20b induced CH by directly repressing PTEN expression and indirectly increasing AKT activity. Moreover, CHAR overexpression mitigated the repression of PTEN and activation of AKT by miR‐20b, and as such, it abrogated the deleterious effects of miR‐20b on CH. Collectively, this study characterized a new lncRNA CHAR and unravelled a new pro‐hypertrophic signalling pathway: lncRNA‐CHAR/miR‐20b/PTEN/AKT. The findings therefore should improve our understanding of the cellular functionality and pathophysiological role of lncRNAs in the heart.

Inhibition of prostaglandin E2 receptor 4 by lnc000908 to promote the endothelial-mesenchymal transition participation in cardiac remodelling

Long non‐coding RNAs (lncRNAs) have emerged as potent regulators of cardiac disease; however, the role of lncRNA in cardiac fibrosis remains partially understood. In this study, we identified a cardiac endothelial‐enriched lncRNA‐lnc000908, which was markedly up‐regulated in rats with cardiac fibrosis. In addition, the expression of prostaglandin E2 receptor 4 (EP4) was decreased in cardiac fibrosis. In vivo lnc000908 silencing by lentivirus increased the EP4 level, decreased endothelial‐mesenchymal transition (EndMT) and improved cardiac fibrosis and cardiac function. Consistently, the lnc000908 knockdown also up‐regulated EP4 and suppressed transforming growth factor‐beta (TGF‐β)‐induced EndMT in cardiac microvascular endothelial cells. In contrast, the lnc000908 overexpression by lentivirus decreased the EP4 level and induced EndMT. Of note, these pro‐ or anti‐EndMT effects were reversed by the EP4 overexpression or the EP4 antagonist AH‐23848, respectively. This study demonstrates that lnc000908 is a novel regulator of cardiac fibrosis by modulating the EP4 expression and EndMT.

LncRNA GASL1 is downregulated in chronic heart failure and regulates cardiomyocyte apoptosis

Background

TGF-β1 contributes to chronic heart failure. It is known that lncRNA GASL1 can inactivate TGF-β1 in cancer biology.

Methods

All the participants were enrolled in the First People’s Hospital of Zhaoqing during the period June 2012 to June 2013. ELISA, RT-qPCR, vectors, transient transfections and western blot were carried out during the research.

Results

We found that plasma levels of TGF-β1 were significantly higher, while levels of GASL1 in plasma were significantly lower in chronic heart failure (CHF) patients compared to the control group. TGF-β1 and GASL1 were inversely correlated in CHF patients. Low pretreatment plasma levels of GASL1 were closely associated with poor survival of CHF patients. GASL1 expression was not significantly affected by TGF-β1 overexpression in cardiomyocytes, while cardiomyocytes with GASL1 overexpression showed downregulated TGF-β1. Overexpression of GASL1 led to a decreased, while TGF-β1 overexpression led to an increased apoptotic rate of cardiomyocytes under H₂O₂ treatment. In addition, TGF-β1 overexpression attenuated the effect of GASL1 overexpression.

Conclusion

In conclusion, GASL1 was downregulated in CHF. GASL1 overexpression may improve CHF by inhibiting cardiomyocyte apoptosis through the inactivation of TGF-β1.

A therapeutic approach towards microRNA29 family in vascular diabetic complications: A boon or curse?

Diabetes Mellitus (DM) is one of the major metabolic disorders and its severity leads to death. Enhancement in hyperglycaemic conditions of DM gives rise to endothelial impairment in small and large blood vessels contributing towards microvascular and macrovascular complications respectively. The pathogenesis of diabetic complications is associated with interruption of various signal transduction pathways due to epigenetic modifications such as aberrant histone modifications, DNA methylation and expression of miRNAs along with the long non-coding RNAs (lncRNAs). Amongst these epigenetic alterations, modulated expressions of miRNAs confer to apoptosis and endothelial dysfunction of organs that gives rise to vascular complications. In this review, we principally focussed on physiological role of miR29 family in DM and have discussed crosstalk between miR29 family and numerous genes involved in signal transduction pathways of Diabetic vascular complications. Incidences of diabetic retinopathy exploiting the role of miR29 in regulation of EMT process, differential expression patterns of miR29 and promising therapeutic role of miR29 have been discussed. We have summarised the therapeutic role of miR29 in podocyte impairment and how miR29 regulates the expressions of profibrotic, inflammatory and ECM encoding genes in renal fibrosis under diabetic conditions. We have also highlighted impact of miR29 expression patterns in cardiac angiopathy, cardiomyocyte's apoptosis and cardiac fibrosis. Additionally, we have also presented the contradictory actions of miR29 family in amelioration as well as in enhancement of diabetic complications.

Decreased FENDRR and LincRNA-p21 expression in atherosclerotic plaque

Objective:

Cardiovascular diseases are the most important cause of mortality worldwide, particularly atherosclerosis. Recently, lncRNAs affecting atherosclerotic progression have been reported in vascular smooth muscle cells, endothelial cells, and monocytes, suggesting that lncRNAs play an important role in atherosclerosis.

Methods:

In recent clinical studies, nowadays, it was determined that internal mammary bypass grafts are closest to ideal grafts in coronary artery bypass surgery. In this study, we used tissue samples taken from atherosclerotic coronary arteries and the internal mammary artery (IMA) during coronary artery bypass surgery. Using RT-PCR, we investigated the role of two lncRNAs, FENDRR and LincRNA-p21, by comparing their expression levels in coronary artery plaques and normal mammary arteries of 20 atherosclerotic patients.

Results:

We found that the FENDRR and LincRNA-p21 expressions decreased by approximately 2 and 7 fold in coronary artery plaques, respectively, compared with those in IMA, which is known to have no plaque development.

Conclusion:

This study was the first to use mammary artery tissues of the same patients as a control and to study FENDRR expression. Our data may provide helpful insights regarding the association of lncRNAs and atherosclerosis.

Sub-pathway based approach to systematically track candidate sub-pathway biomarkers for heart failure

Identification of potential novel biomarkers for heart failure was undertaken using a sub-pathway based method. To realize this goal, heart failure-relevant dataset, reference pathways, and lncRNA-miRNA-mRNA interactions were firstly recruited. Secondly, the informative pathways were extracted relying on KEGG pathways and the mRNAs in the PCC-weighted lncRNA-mRNA interactions. Thirdly, lncRNA-regulated sub-pathways were dissected after construction of condition-specific lncRNA competitively regulated pathways (LCRP). To detect crucial heart failure-relevant lncRNAs, degree analysis was conducted for all nodes within the LCRP. Ultimately, the significance of candidate sub-pathways were assessed to further identify the significant sub-pathways. There were 44 lncRNAs, 165 mRNAs and 224 co-expressed interactions. After putting the 165 mRNAs into the reference pathways, 56 informative pathways were obtained which were then embedded into undirected graphs, and 44 lncRNAs were inserted into the pathway graphs to further construct the condition-specific LCRP. According to degree distribution, 4 hub lncRNAs were selected, including ERVK13-1, YLPM1, PDXDC2P, and LINC00482. Based on the LCRP information, a total of 36 sub-pathways mediated by lncRNAs participated in 40 complete pathways. Among these 40 pathways, we mainly concentrated on the top three sub-pathways, including a sub-part of MAPK signaling pathway, an important sub-part in ErbB signaling pathway, and a part of chemokine signaling pathway. In the top 3 significant sub-pathways, gene AKT3 was simultaneously regulated by ERVK13-1, YLPM1, and PDXDC2P. Sub-pathways including MAPK signaling pathway and hub lncRNAs (ERVK13-1, YLPM1, and PDXDC2P) may play an important role in heart failure.

Reactive Oxygen Species Related Noncoding RNAs as Regulators of Cardiovascular Diseases

Reactive oxygen species (ROS) are a class of reactive molecules that have been implicated in a variety of cardiovascular diseases, accompanied by disorder of multiple signaling events. As cardiomyocytes maintain abundant of mitochondria, which supply the major source of endogenous ROS, oxidative damage to mitochondria often drives apoptotic cell death and initiates cardiac pathology. In recent years, non-coding RNAs (ncRNAs) have received much attention to uncover their roles in regulating gene expression during those pathological events in the heart, such as myocardial infarction, cardiac hypertrophy, and heart failure. Emerging evidences have highlighted that different ROS levels in response to diverse cardiac stresses result in differential expression of ncRNAs, subsequently altering the expression of pathogenetic genes. However, the knowledge about the ncRNA-linked ROS regulatory mechanisms in cardiac pathologies is still largely unexplored. In this review, we summarize the connections that exist among ROS, ncRNAs, and cardiac diseases to understand the interactions among the molecular entities underlying cardiac pathological events in the hopes of guiding novel therapies for heart diseases in the future.

A long noncoding RNA NR_045363 controls cardiomyocyte proliferation and cardiac repair

Long noncoding RNAs (lncRNAs) play important roles in the regulation of genes involved in cell proliferation. We have previously sought to more globally understand the differences of lncRNA expression between human fetal heart and adult heart to identify some functional lncRNAs which involve in the process of heart repair. We found that a highly conserved long noncoding RNA NR_045363 was mainly expressed in cardiomyocytes and rarely in non-cardiomyocytes. NR_045363 overexpression in 7-day-old mice heart could improve cardiac function and stimulate cardiomyocyte proliferation after myocardial infarction. Furthermore, NR_045363 knockdown inhibited proliferation of primary embryonic cardiomyocytes, while NR_045363 overexpression enhanced DNA synthesis and cytokinesis in neonatal cardiomyocytes in vitro. Mechanistic analysis revealed that NR_045363 promoted cardiomyocyte proliferation through interaction with miR-216a, which regulated the JAK2-STAT3 pathway. Our results showed that NR_045363 is a potent lncRNA modulator essential for cardiomyocyte proliferation.

Long non-coding RNA CCRR controls cardiac conduction via regulating intercellular coupling

Long non-coding RNAs (lncRNAs) have emerged as a new class of gene expression regulators playing key roles in many biological and pathophysiological processes. Here, we identify cardiac conduction regulatory RNA (CCRR) as an antiarrhythmic lncRNA. CCRR is downregulated in a mouse model of heart failure (HF) and in patients with HF, and this downregulation slows cardiac conduction and enhances arrhythmogenicity. Moreover, CCRR silencing induces arrhythmias in healthy mice. CCRR overexpression eliminates these detrimental alterations. HF or CCRR knockdown causes destruction of intercalated discs and gap junctions to slow longitudinal cardiac conduction. CCRR overexpression improves cardiac conduction by blocking endocytic trafficking of connexin43 (Cx43) to prevent its degradation via binding to Cx43-interacting protein CIP85, whereas CCRR silence does the opposite. We identified the functional domain of CCRR, which can reproduce the functional roles and pertinent molecular events of full-length CCRR. Our study suggests CCRR replacement a potential therapeutic approach for pathological arrhythmias.

Regulation of IL-17 by lncRNA of IRF-2 in the pearl oyster

Long noncoding RNAs (lncRNAs), once thought to be nonfunctional, have recently been shown to participate in the multilevel regulation of transcriptional, posttranscriptional and epigenetic modifications and to play important roles in various biological processes, including immune responses. However, the expression and roles of lncRNAs in invertebrates, especially nonmodel organisms, remain poorly understood. In this study, by comparing a transcriptome to the PfIRF-2 genomic structure, we identified lncIRF-2 in the PfIRF-2 genomic intron. The results of the RNA interference (RNAi) and the nucleus grafting experiments indicated that PfIRF-2 might have a negative regulatory effect on lncIRF-2, and PfIRF-2 and lncIRF-2 may have a positive regulatory effect on PfIL-17. Additionally, lncIRF-2, PfIRF-2 and PfIL-17 were involved in responses to the nucleus graft. These results will enhance the knowledge of lncIRF-2, IRF-2, and IL-17 functions in both pearl oysters and other invertebrates.

Long noncoding RNA SRA1 attenuates hypoxia-induced injury in H9c2 cardiomyocytes through regulating PPARγ/NF-κB signaling pathway

This study aimed to investigate the effects and mechanisms of long noncoding RNA SRA1 on regulating hypoxia-induced injury in H9c2 cardiomyocytes. The H9c2 cardiomyocytes were cultured under hypoxic (3% O₂) conditions and whether hypoxia induced injury was assessed by detecting cell viability, apoptosis and autophagy. Then, SRA1 was overexpressed and suppressed in H9c2 cardiomyocytes by transfection with pc-SRA1 and sh-SRA1, and the effects of SRA1 dysregulation on cell viability, apoptosis, and autophagy of H9c2 cardiomyocytes under hypoxia condition were detected. Furthermore, the regulatory relationship between SRA1 and PPARγ was explored, as well as the association between SRA1 and NF-κB signaling. Hypoxia induced injury to H9c2 cardiomyocytes, such as inhibiting cell viability, and promoting cell apoptosis and autophagy. Moreover, hypoxia resulted in a decreased expression of SRA1 in H9c2 cardiomyocytes, and overexpression of SRA1 alleviated hypoxia-induced injury, while suppression of SRA1 indicated the contrary results. Further studies showed that SRA1 positively regulated PPARγ. Overexpression of SRA1 alleviated hypoxia injury by activating PPARγ. Besides, suppression of SRA1 activated NF-κB pathway in hypoxia-treated H9c2 cardiomyocytes, which were significantly reversed after suppression of SRA1 and overexpression of PPARγ at the same time. Our findings indicated that suppression of SRA1 may aggravate hypoxia-induced injury to H9c2 cardiomyocytes by positive regulation of PPARγ and activation of NF-κB pathway. SRA1 may serve as a promising perspective for the therapy of heart failure induced by hypoxia.

LncRNA and mRNA interaction study based on transcriptome profiles reveals potential core genes in the pathogenesis of human thoracic aortic dissection

The aim of the present study was to determine the potential core genes in the pathogenesis of human thoracic aortic dissection (TAD) by analyzing microarray profiles of long non‑coding (lnc)‑RNAs between TAD and normal thoracic aorta (NTA). The differentially expressed lncRNA profiles of the aorta tissues between TAD patients (TAD group, n=6) and age‑matched donors with aortic diseases (NTA group, n=6) were analyzed by lncRNAs microarray. Gene ontology (GO), pathway and network analyses were used to further investigate candidate lncRNAs and mRNAs. Differentially expressed lncRNAs and mRNAs were validated by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). In total, the present study identified 765 lncRNAs and 619 mRNAs with differential expression between TAD and NTA (fold change >2.0, P<0.01). GO analysis demonstrated that the differentially upregulated lncRNAs are associated with cell differentiation, homeostasis, cell growth and angiogenesis. Kyoto Encyclopedia of Gene and Genomes pathway analysis demonstrated that the differentially downregulated lncRNAs are mainly associated with arrhythmogenic right ventricular cardiomyopathy, hypertrophic cardiomyopathy and dilated cardiomyopathy. To reduce the lncRNAs for further investigation and to enrich those potentially involved in TAD, a total of 16 candidate lncRNAs with a significant expression (fold change >4, P<0.01) were selected, that were associated with an annotated protein‑coding gene through the GO term and scientific literatures. Then a set of significantly expressed lncRNAs [purinergic receptor P2X7 (P2RX7), hypoxia inducing factor (HIF)‑1A‑AS2, AX746823, RP11‑69I8.3 and RP11‑536K7.5) and the corresponding mRNAs (P2RX7, cyclin dependent kinase inhibitor 2B, HIF‑1A, runt‑related transcription factor 1, connective tissue growth factor and interleukin 2 receptor a chain] were confirmed using RT‑qPCR. The present study revealed that the expression profiles of lncRNAs and mRNAs in aorta tissues from TAD were significantly altered. These results may provide important insights into the pathogenesis of TAD disease.

Recombinant human brain natriuretic peptide regulates PI3K/AKT/mTOR pathway through lncRNA EGOT to attenuate hypoxia-induced injury in H9c2 cardiomyocytes

This study aimed to investigate whether recombinant human brain natriuretic peptide (rhBNP) regulated hypoxia-induced injury in H9c2 cardiomyocytes through lncRNA EGOT. H9c2 cardiomyocytes were cultured under normoxia and hypoxia (21% and 3% O₂) conditions, and whether hypoxia induced injury by assessing cell viability, apoptosis and autophagy. H9c2 cells were then treated with different doses of exogenous rhBNP (200, 600 and 900 nmol/L, respectively) and the effects of rhBNP on hypoxia-induced injury in H9c2 cells as well as the expression of EGOT were studied. In addition, the regulatory relationships between rhBNP and EGOT as well as between rhBNP and PI3K/AKT/mTOR pathway in hypoxia-treated H9c2 cells were investigated. Hypoxia significantly induced injury in H9c2 cells (inhibited cell viability and promoted cell apoptosis and autophagy) and decreased the expression of EGOT. However, administration of rhBNP alleviated hypoxia-induced injury in H9c2 cells and elevated expression of EGOT. Suppression of EGOT significantly reversed the effects of rhBNP on hypoxia-induced injury in H9c2 cells. Further studies showed that the effects of EGOT on cell viability and apoptosis were by positively regulating the expression of Cyclin D1. Moreover, rhBNP alleviated hypoxia-induced cell injury by activating PI3K/AKT/mTOR pathway in H9c2 cells. Our results reveal that rhBNP may play a protective role in attenuating hypoxia-induced injury in H9c2 cardiomyocytes via regulating lncRNA EGOT/Cyclin D1/PI3K/AKT/mTOR pathway axis. The findings will provide a new strategy for the treatment of heart failure induced by hypoxia.

Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis

LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.

Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network

Long non-coding RNAs (lncRNAs) are involved in many biological processes, such as immune response, development, differentiation and gene imprinting and are associated with diseases and cancers. But the functions of the vast majority of lncRNAs are still unknown. Predicting the biological functions of lncRNAs is one of the key challenges in the post-genomic era. In our work, We first build a global network including a lncRNA similarity network, a lncRNA-protein association network and a protein-protein interaction network according to the expressions and interactions, then extract the topological feature vectors of the global network. Using these features, we present an SVM-based machine learning approach, PLNRGO, to annotate human lncRNAs. In PLNRGO, we construct a training data set according to the proteins with GO annotations and train a binary classifier for each GO term. We assess the performance of PLNRGO on our manually annotated lncRNA benchmark and a protein-coding gene benchmark with known functional annotations. As a result, the performance of our method is significantly better than that of other state-of-the-art methods in terms of maximum F-measure and coverage.

RETRACTED: LncRNA myocardial infarction-associated transcript (MIAT) contributed to cardiac hypertrophy by regulating TLR4 via miR-93

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief after concerns were raised about the article on PubPeer (https://pubpeer.com/publications/88E67BAC524E92069B2AA3474D2BB8?utm_source=Chrome&utm_medium=BrowserExtension&utm_campaign=Chrome). In addition the editor found more issues in some Western Blot figures. 1. Bands of figure 1C ANF 30min , 60min, 12h, 24h are identical to those in Fig 4C ANF control, AngII, AngII+si-NC and AngII+si-MAT 2. Beta-actin bands of Fig 1C are identical to those in Fig 4C, but blots represent different experimental conditions/samples. 3. Bands in Fig 6 D AngII and AngII+mir-NC show similarities with these of AngII+mir-93 and AngII+mir93+vector (band shapes and irregularities appear identical) After several attempts to reach out to the corresponding author, no response was provided. The manipulation of images casts doubts on all the data, and accordingly also the conclusions based on that data, in this publication. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Role of noncoding RNAs in regulation of cardiac cell death and cardiovascular diseases

Loss of functional cardiomyocytes is a major underlying mechanism for myocardial remodeling and heart diseases, due to the limited regenerative capacity of adult myocardium. Apoptosis, programmed necrosis, and autophagy contribute to loss of cardiac myocytes that control the balance of cardiac cell death and cell survival through multiple intricate signaling pathways. In recent years, non-coding RNAs (ncRNAs) have received much attention to uncover their roles in cell death of cardiovascular diseases, such as myocardial infarction, cardiac hypertrophy, and heart failure. In addition, based on the view that mitochondrial morphology is linked to three types of cell death, ncRNAs are able to regulate mitochondrial fission/fusion of cardiomyocytes by targeting genes involved in cell death pathways. This review focuses on recent progress regarding the complex relationship between apoptosis/necrosis/autophagy and ncRNAs in the context of myocardial cell death in response to stress. This review also provides insight into the treatment for heart diseases that will guide novel therapies in the future.

Long non-coding RNAs and complex diseases: from experimental results to computational models

LncRNAs have attracted lots of attentions from researchers worldwide in recent decades. With the rapid advances in both experimental technology and computational prediction algorithm, thousands of lncRNA have been identified in eukaryotic organisms ranging from nematodes to humans in the past few years. More and more research evidences have indicated that lncRNAs are involved in almost the whole life cycle of cells through different mechanisms and play important roles in many critical biological processes. Therefore, it is not surprising that the mutations and dysregulations of lncRNAs would contribute to the development of various human complex diseases. In this review, we first made a brief introduction about the functions of lncRNAs, five important lncRNA-related diseases, five critical disease-related lncRNAs and some important publicly available lncRNA-related databases about sequence, expression, function, etc. Nowadays, only a limited number of lncRNAs have been experimentally reported to be related to human diseases. Therefore, analyzing available lncRNA–disease associations and predicting potential human lncRNA–disease associations have become important tasks of bioinformatics, which would benefit human complex diseases mechanism understanding at lncRNA level, disease biomarker detection and disease diagnosis, treatment, prognosis and prevention. Furthermore, we introduced some state-of-the-art computational models, which could be effectively used to identify disease-related lncRNAs on a large scale and select the most promising disease-related lncRNAs for experimental validation. We also analyzed the limitations of these models and discussed the future directions of developing computational models for lncRNA research.