A Deep Sequencing Approach to Uncover the miRNOME in the Human Heart

MicroRNAs (miRNAs) are a class of non-coding RNAs of ∼22 nucleotides in length, and constitute a novel class of gene regulators by imperfect base-pairing to the 3′UTR of protein encoding messenger RNAs. Growing evidence indicates that miRNAs are implicated in several pathological processes in myocardial disease. The past years, we have witnessed several profiling attempts using high-density oligonucleotide array-based approaches to identify the complete miRNA content (miRNOME) in the healthy and diseased mammalian heart. These efforts have demonstrated that the failing heart displays differential expression of several dozens of miRNAs. While the total number of experimentally validated human miRNAs is roughly two thousand, the number of expressed miRNAs in the human myocardium remains elusive. Our objective was to perform an unbiased assay to identify the miRNOME of the human heart, both under physiological and pathophysiological conditions. We used deep sequencing and bioinformatics to annotate and quantify microRNA expression in healthy and diseased human heart (heart failure secondary to hypertrophic or dilated cardiomyopathy). Our results indicate that the human heart expresses >800 miRNAs, the majority of which not being annotated nor described so far and some of which being unique to primate species. Furthermore, >250 miRNAs show differential and etiology-dependent expression in human dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM). The human cardiac miRNOME still possesses a large number of miRNAs that remain virtually unexplored. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in regulating human heart disease.     

microRNA在常见致死性心脏病中的改变

微小RNA(micro RNA,mi RNA)是一类真核生物内源性非编码单链的小RNA分子,长度大约为19-23个核苷酸,拥有高度的保守性,不编码蛋白质,也是近年来研究最热门的一个新领域,通过与靶m RNA特异性结合来调节基因表达,且表达都具有组织特异性。最近,许多研究表明mi RNA在心血管系统疾病和肿瘤疾病方面的相关研究都取得了突破性的进展,mi RNA在肿瘤疾病中是通过调节癌基因及抑癌基因而调控肿瘤的生物学过程,在心血管系统疾病中与心肌肥厚及心肌再生等过程有密切的关系,包括冠状动脉疾病、心肌肥大、心肌梗死、心律失常、高血压和心力衰竭等疾病,且在心脏病学中扮演着及其重要的角色。Mi RNA的表达量增加或者减少对心血管疾病都有影响,该文对新近有关的mi RNA在心血管系统疾病中的研究进展、诊断、治疗以及预后予以综述。     

miRNAs got rhythm

Despite significant advances in treatments, cardiovascular disease (CVD) remains the leading cause of human morbidity and mortality in developed countries. The development of novel and efficient treatment strategies requires an understanding of the basic molecular mechanisms underlying cardiac function. MicroRNAs (miRNAs) are a family of small nonprotein-coding RNAs that have emerged as important regulators in cardiac and vascular developmental and pathological processes, including cardiac arrhythmia, fibrosis, hypertrophy and ischemia, heart failure and vascular atherosclerosis. The miRNA acts as an adaptor for the miRNA-induced silencing complex (miRISC) to specifically recognize and regulate particular mRNAs. Mature miRNAs recognize their target mRNAs by base-pairing interactions between nucleotides 2 and 8 of the miRNA (the seed region) and complementary nucleotides in the 3'-untranslated region (3'-UTR) of mRNAs and miRISCs subsequently inhibit gene expression by targeting mRNAs for translational repression or cleavage. In this review we summarize the basic mechanisms of action of miRNAs as they are related to cardiac arrhythmia and address the potential for miRNAs to be therapeutically manipulated in the treatment of arrhythmias.     

微核糖核酸在相关疾病发生发展中的调节作用

微核糖核酸（miRNA）是一类长度为18～25个核苷酸的内源性非编码小RNA,在转录后基因调控中发挥功能。miRNA通过降解mRNA或抑制蛋白翻译的方式调节特异基因表达。miRNA在多种生物进程包括发育、代谢、增殖、分化和凋亡中起到关键作用。miRNA的表达变化与相应的多种人类疾病及其发生发展密切相关。阐明miRNA对疾病基因的调节作用及其分子机制,将为人类某些疾病的基因治疗提供新的思路。     

Expression of NTPDase1 and caveolins in human cardiovascular disease

Pathological circumstances like inflammation or ischemic insult facilitate the release of adenine nucleotides from several types of cells. These extracellular nucleotides are rapidly converted to adenosine by ectonucleotidases, mainly ectonucleoside triphosphate diphosphohydrolase1 (NTPDase1/CD39) and CD73. NTPDase1/CD39 can interact with caveolins, structural proteins of signal-transducing microdomains termed caveolae. Caveolins are thought to have physiological roles in heart ageing and cardiac diseases. The aim of this study was to investigate the expression of NTPDase1 together with caveolins in chronic human cardiovascular diseases and elucidate their role in human heart. The HPLC analysis showed significant increase in ATPase activity in pathological samples from patients with ischemic heart disease. Immunostaining also showed alterations in the expression and distribution of NTPDase1. Caveolin-1 and caveolin-2 expression was much alike in control and pathological cases, while expression of caveolin-3 was lower in pathological samples. Changes in the expression of NTPDase1 and caveolins seem to be independent of human cardiovascular disease.     

Cardiac expression of urocortin (Ucn) in diseased heart; preliminary results on possible involvement of Ucn in pathophysiology of cardiac diseases

Recently, several studies reported that urocortin (Ucn) had beneficial effects on cardiovascular system and was expressed both in the normal heart and in the heart of dilated cardiomyopathy (DCM), yet the relationship between high expression of Ucn and pathophysiology of Ucn in diseased heart has been discussed. Thus, the present study was designed to elucidate the expression of Ucn in the diseased heart by immunohistochemical approach using endomyocardial biopsy specimens. The involvement of immunoreactive Ucn in pathophysiology of cardiac disease was evaluated using endomyocardial biopsy specimens obtained from the patients with some heart diseases, including DCM and hypertrophic cardiomyopathy (HCM). Ucn was detected in all endomyocardial biopsy specimens of ventricular tissue obtained from the patients with such cardiac diseases, a specimens of atrial tissue, and normal heart specimens obtained from autopsy cases. In DCM patients, left ventricular end-diastolic pressure significantly elevated in severely stained group. On the contrary, in HCM patients, left ventricular ejection fraction was higher in the severely stained group. Ucn was expressed more abundantly in the diseased heart, especially in HCM and DCM, than in the normal heart. In conclusion, such close relationship between Ucn expression in the heart and cardiac function indicated that clinical features of Ucn resembled those of norepinephrine and Ucn could play a certain pathophysiological roles in the cardiac diseases.     

Expression profiling of microRNA using oligo DNA arrays

After 12 years from its first application, microarray technology has become the reference technique to monitor gene expression of thousands of genes in the same experiment. In the past few years an increasing amount of evidence showed the importance of non-coding RNA (ncRNA) in different human diseases. The microRNAs (miRNAs) are one of the groups of ncRNA. They are small RNA fragments, 19-25 nucleotides long, with a main regulatory function on both protein coding genes and non-coding RNAs. The application of microarray platforms applied to miRNA profiling determined their deregulation in virtually all human diseases that have been studied. We previously developed a custom miRNA microarray platform, and here we describe the protocol we used to work with it including the oligo design strategy, the microarray printing protocol, the target-probe hybridization and the signal detection.     

Purification of high-quality micro RNA from the heart tissue

Micro RNAs (miRNA) are an abundant class of small RNAs that regulate the stability and translation of cognate mRNAs. MiRNAs are potential diagnostic markers, moreover, they play an essential role in the development of various heart disesases. In case of limited tissue material, such as, e.g. human biopsies, purification of miRNAs with sufficient yield is critical. Reproducible expression analysis of miRNAs is highly dependent on the quality of the RNA, which is often difficult to achieve from fibrous tissue such as the heart. Several companies developed general purification kits for miRNAs, however, none of them are specialized to fibrotic tissues. Here we describe an optimized miRNA purification protocol that results in high miRNA yield as compared to other methods including trizol-based and column-based protocols. By using our improved protocol, miRNA obtained from heart tissue gave more reproducible results in QRT-PCR analysis and obtained more significant calls (172 vs. 118) during DNA microarray analysis when compared to the commercially available kit. In addition to the heart tissue, the present protocol can be applied to other fibrotic tissues, such as lung or skeletal muscle to isolate high-purity miRNA.     

Identifying miRNA-disease association based on integrating miRNA topological similarity and functional similarity

Background: MicroRNAs (miRNAs) are a significant type of non-coding RNAs, which usually were encoded by endogenous genes with about ~22 nt nucleotides. Accumulating biological experiments have shown that miRNAs have close associations with various human diseases. Although traditional experimental methods achieve great successes in miRNA-disease interaction identification, these methods also have some limitations. Therefore, it is necessary to develop computational method to predict miRNA-disease interactions. Methods: Here, we propose a computational framework (MDVSI) to predict interactions between miRNAs and diseases by integrating miRNA topological similarity and functional similarity. Firstly, the CosRA index is utilized to measure miRNA similarity based on network topological feature. Then, in order to enhance the reliability of miRNA similarity, the functional similarity and CosRA similarity are integrated based on linear weight method. Further, the potential miRNA-disease associations are predicted by using recommendation method. In addition, in order to overcome limitation of recommendation method, for new disease, a new strategy is proposed to predict potential interactions between miRNAs and new disease based on disease functional similarity. Results: To evaluate the performance of different methods, we conduct ten-fold cross validation and de novo test in experiment and compare MDVSI with two the-state-of-art methods. The experimental result shows that MDVSI achieves an AUC of 0.91, which is at least 0.012 higher than other compared methods. Conclusions: In summary, we propose a computational framework (MDSVI) for miRNA-disease interaction prediction. The experiment results demonstrate that it outperforms other the-state-of-the-art methods. Case study shows that it can effectively identify potential miRNA-disease interactions.     

微小RNAs在心力衰竭炎症机制中作用的研究进展

微小RNA是一组高度保守的长度约22个核苷酸非编码RNA,通过靶定相应的互补序列导致信使RNA的沉默,下调或者抑制翻译以调节基因和蛋白的表达。心力衰竭进程中存在慢性炎症激活和microRNA的异常表达,其中TLR4通路和NF-κB通路被广泛研究和认同,炎症因子如IL-1、IL-6、TNF-α参与心力衰竭的炎症激活过程,并且可以通过多种通路导致心肌细胞肥大,纤维化及凋亡,炎症因子激活、炎症通路中间因子及疾病进展形成复杂的病理网络,最终导致心肌功能紊乱和减退;microRNA可通过部分结合mRNA靶定部分在转录水平上抑制蛋白合成,参与心力衰竭炎症通路的整个过程,这一调节机制在心肌肥大、心力衰竭等多种心脏疾病中的作用逐渐被阐明。本文旨在总结微小RNAs在心力衰竭炎症机制中作用的研究进展,寻找微小RNA与心力衰竭中炎症激活过程的联系。     

心肌细胞过表达miR-27b导致小鼠发生心肌纤维化和线粒体损伤

以往的miRNA芯片研究结果显示, miR-27b在人类心脏疾病标本和压力负荷引起的小鼠心肌肥厚模型中表达水平明显升高, 提示其在心脏疾病发生过程中发挥了重要功能。为研究miR-27b在心脏组织中的功能, 文章建立了在心肌细胞特异性 a-肌球蛋白重链(a-MHC)启动子(5.5 kb)控制下过表达miR-27b的转基因小鼠。通过Real-time PCR检测, 发现miR-27b前体和成熟体表达水平在转基因小鼠心脏组织中明显升高。miR-27b转基因小鼠不仅出现心肌肥厚, 还表现出明显的心肌纤维化。进一步研究表明心肌纤维化的关键调节分子金属基质蛋白酶13(MMP13)是miR-27b的靶分子, 在miR-27b转基因小鼠中MMP13显著下调, 胶原分子I和 III则显著上调。此外, 还发现miR-27b转基因小鼠会出现心脏超微结构的损伤。以上研究结果表明, miR-27b可能通过抑制MMP13促进心肌纤维化。     

Stress response factors as hub‐regulators of microRNA biogenesis: implication to the diseased heart

MicroRNAs (miRNAs) are important regulators of heart function and then an intriguing therapeutic target for plenty of diseases. The problem raised is that many data in this area are contradictory, thus limiting the use of miRNA‐based therapy. The goal of this review is to describe the hub‐mechanisms regulating the biogenesis and function of miRNAs, which could help in clarifying some contradictions in the miRNA world. With this scope, we analyse an array of factors, including several known agents of stress response, mediators of epigenetic changes, regulators of alternative splicing, RNA editing, protein synthesis and folding and proteolytic systems. All these factors are important in cardiovascular function and most of them regulate miRNA biogenesis, but their influence on miRNAs was shown for non‐cardiac cells or some specific cardiac pathologies. Finally, we consider that studying the stress response factors, which are upstream regulators of miRNA biogenesis, in the diseased heart could help in (1) explaining some contradictions concerning miRNAs in heart pathology, (2) making the role of miRNAs in pathogenesis of cardiovascular disease more clear, and therefore, (3) getting powerful targets for its molecular therapy. Copyright © 2015 John Wiley & Sons, Ltd.     

Changes in extra cellular matrix remodelling and re-expression of fibronectin and tenascin-C splicing variants in human myocardial tissue of the right atrial auricle: implications for a targeted therapy of cardiovascular diseases using human SIP format antibodies

Cardiovascular diseases are accompanied by changes in the extracellular matrix (ECM) including the re-expression of fibronectin and tenascin-C splicing variants. Using human recombinant small immunoprotein (SIP) format antibodies, a molecular targeting of these proteins is of therapeutic interest. Tissue samples of the right atrial auricle from patients with coronary artery disease and valvular heart disease were analysed by PCR based ECM gene expression profiling. Moreover, the re-expression of fibronectin and tenascin-C splicing variants was investigated by immunofluoerescence labelling. We demonstrated changes in ECM gene expression depending on histological damage or underlying cardiac disease. An increased expression of fibronectin and tenascin-C mRNA in association to histological damage and in valvular heart disease compared to coronary artery disease could be shown. There was a distinct re-expression of ED-A containing fibronectin and A1 domain containing tenascin-C detectable with human recombinant SIP format antibodies in diseased myocardium. ED-A containing fibronectin showed a clear vessel positivity. For A1 domain containing tenascin-C, there was a particular positivity in areas of interstitial and perivascular fibrosis. Right atrial myocardial tissue is a valuable model to investigate cardiac ECM remodelling. Human recombinant SIP format antibodies usable for an antibody-mediated targeted delivery of drugs might offer completely new therapeutic options in cardiac diseases.     

Strategies for profiling microRNA expression

MicroRNAs (miRNAs) are a class of small RNAs ( approximately 22-nt) that play an important role in the control of different cell processes by negative regulation of protein-coding genes. In the last several years, a number of miRNA profiling strategies have been used to document the miRNA expression changes during physiological and pathological processes. Aberrant expression of miRNAs has been linked to developmental defects, cancer, neurological disorders, and heart diseases. Over 540 human miRNAs have been validated to date; however, computer models suggest there may be thousands more. As bench work continue to verify in silico predictions, miRNA profiling will remain a prominent tool for identification of differential expression miRNAs in normal cellular courses and human disorders. This review focuses on current strategies for miRNA expression profiling and discusses their sensitivity and specificity, as well as advantage and disadvantage.     

An optimized isolation and labeling platform for accurate microRNA expression profiling

MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression in both plants and animals. miRNA genes have been implicated in a variety of important biological processes, including development, differentiation, apoptosis, fat metabolism, viral infection, and cancer. Similar to protein-coding messenger RNAs, miRNA expression varies between tissues and developmental states. To acquire a better understanding of global miRNA expression in tissues and cells, we have developed isolation, labeling, and array procedures to measure the relative abundance of all of the known human mature miRNAs. The method relies on rapid isolation of RNA species smaller than ~40 nucleotides (nt), direct and homogenous enzymatic labeling of the mature miRNAs with amine modified ribonucleotides, and hybridization to antisense DNA oligonucleotide probes. A thorough performance study showed that this miRNA microarray system can detect subfemtomole amounts of individual miRNAs from <1 mug of total RNA, with 98% correlation between independent replicates. The system has been applied to compare the global miRNA expression profiles in 26 different normal human tissues. This comprehensive analysis identified miRNAs that are preferentially expressed in one or a few related tissues and revealed that human adult tissues have unique miRNA profiles. This implicates miRNAs as important components of tissue development and differentiation. Taken together, these results emphasize the immense potential of microarrays for sensitive and high-throughput analysis of miRNA expression in normal and disease states.     

Isolation of single atrial and ventricular cells from the human heart.

The single isolated heart cell has recently emerged as a model for the study of the structure and function of cardiac cells. Heart muscle cells of adult animals of various species have been successfully isolated by enzymatic digestion of intact cardiac tissue. In this paper a dissociation method that yields living cells from atrial and ventricular tissue of young and adult humans is detailed. The cells retain the morphologic features of cells in intact cardiac tissue, and they generate action potentials and contractions in response to electrical stimulation. The study of isolated human heart cells should make a valuable contribution to knowledge of the normal and diseased heart.     

Identification of miRNAs in C. roseus and their potential targets

MicroRNAs are small (20-22 nucleotides) none coding, regulatory RNAs, whose pivotal role in gene expression has been associated in number of diseases, therefore prediction of miRNA is an essential yet challenging field. In this study miRNAs of C. roseus are predicted along with their possible target genes. A total of 19,899 ESTs were downloaded from dbEST database and processed and trimmed through SeqClean. Nine sequences were trashed and 31 sequences were trimmed by the program and the resulting sequences were submitted to Repeatmasker and TGICL for clustering and assembly. This contig database was now used to find the putative miRNAs by performing a local BLAST with the miRNAs of B. rapa retrieved from miRBase. The targets were scanned by hybridizing screened ESTs with the UTRs of human using miRanda software. Finally, 7 putative miRNAs were found to hybridize with the various targets of signal transduction and apoptosis that may play significant role in preventing diseases like Leukemia, Arthritis and Alzheimer.