Long non-coding RNA Databases in Cardiovascular Research

An increase in a long noncoding RNA ANRIL in peripheral plasma is an indicator of stable angina

INTRODUCTION

Stable angina develops during physical activity or stress, and it is typically an aspect of Coronary Heart Disease (CHD) that can lead to arrhythmia, heart failure and even sudden death. ANRIL, an Antisense Noncoding RNA gene in the INK4 Locus, is associated with multiple disorders including CHD; however, expressional levels of ANRIL in between patients with stable angina and myocardial infarction, one of the acute coronary syndrome, have not been clarified yet.

METHODS

The authors enrolled 62 patients with myocardial infarction and 59 with stable angina before primary percutaneous coronary intervention, as well as 48 healthy volunteers. Their peripheral blood was collected for analysis of ANRIL and cardiac troponin I, a traditional diagnostic index of CHD by real-time PCR.

RESULTS

The data showed that ANRIL is a better diagnostic indicator than cardiac troponin I in patients with stable angina and that the levels of ANRIL are higher in patients with stable angina than those with the myocardial infarction.

DISCUSSION

The levels of ANRIL in peripheral plasma could be used as a good biomarker for stable angina.

Sparse Independence Component Analysis for Competitive Endogenous RNA Co-Module Identification in Liver Hepatocellular Carcinoma

OBJECTIVE

Long non-coding RNAs (lncRNAs) have been shown to be associated with the pathogenesis of different kinds of diseases and play important roles in various biological processes. Although numerous lncRNAs have been found, the functions of most lncRNAs and physiological/pathological significance are still in its infancy. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood.

METHODS

In order to reveal functional lncRNAs and identify the key lncRNAs, we develop a new sparse independence component analysis (ICA) method to identify lncRNA-mRNA-miRNA expression co-modules based on the competitive endogenous RNA (ceRNA) theory using the sample-matched lncRNA, mRNA and miRNA expression profiles. The expression data of the three RNA combined together is approximated sparsely to obtain the corresponding sparsity coefficient, and then it is decomposed by using ICA constraint optimization to obtain the common basis and modules. Subsequently, affine propagation clustering is used to perform cluster analysis on the common basis under multiple running conditions to obtain the co-modules for the selection of different RNA elements.

RESULTS

We applied sparse ICA to Liver Hepatocellular Carcinoma (LIHC) dataset and the experiment results demonstrate that the proposed sparse ICA method can effectively discover biologically functional expression common modules.

CONCLUSION

It may provide insights into the function of lncRNAs and molecular mechanism of LIHC. Clinical and Translational Impact Statement-The results on LIHC dataset demonstrate that the proposed sparse ICA method can effectively discover biologically functional expression common modules, which may provide insights into the function of IncRNAs and molecular mechanism of LIHC.

Effect Of XBP1 Deficiency In Cartilage On The Regulatory Network Of LncRNA/circRNA-miRNA-mRNA

X-box binding protein 1(XBP1) is a critical component for unfolded protein response (UPR) in ER stress. According to previous studies performed with different XBP1-deficient mice, the XBP1 gene affects mouse cartilage development and causes other related diseases. However, how the complete transcriptome, including mRNA and ncRNAs, affects the function of cartilage and other tissues when XBP1 is deficient in chondrocytes is unclear. In this study, we aimed to screen the differentially expressed (DE) mRNAs, circRNAs, lncRNAs and miRNAs in XBP1 cartilage-specific knockout (CKO) mice using high throughput sequencing and construct the circRNA-miRNA-mRNA and lncRNA-miRNA-mRNA regulatory networks. DE LncRNAs (DE-LncRNAs), circRNAs (DE-circRNAs), miRNAs (DE-miRNAs), and mRNAs [differentially expressed genes (DEGs)] between the cartilage tissue of XBP1 CKO mice and controls were identified, including 441 DE-LncRNAs, 15 DE-circRNAs, 6 DE-miRNAs, and 477 DEGs. Further, 253,235 lncRNA-miRNA-mRNA networks and 1,822 circRNA-miRNA-mRNA networks were constructed based on the correlation between lncRNAs/circRNAs, miRNAs, mRNAs. The whole transcriptome analysis revealed that XBP1 deficiency in cartilage affects the function of cartilage and other different tissues, as well as associated diseases. Overall, our findings may provide potential biomarkers and mechanisms for the diagnosis and treatment of cartilage and other related diseases.

Expression of lncRNA-ANRIL before and after Treatment and Its Predictive Value for Short-Term Survival in Patients with Coronary Heart Disease

This study aimed at observing the expression of lncRNA-ANRIL (ANRIL) before and after treatment and its predictive value for short-term survival in patients with coronary heart disease (CHD). Altogether, 112 patients with CHD admitted to the hospital were enrolled as a study group (SG), which was divided into a pretreatment study group (preSG) and a posttreatment study group (postSG). Further 72 healthy people undergoing physical examinations during the same period were enrolled as a control group (CG). Peripheral blood was collected from the subjects in the three groups, to detect the expression level of serum ANRIL using quantitative reverse transcription PCR (qRT-PCR). A receiver operating characteristic (ROC) curve was plotted to evaluate the diagnostic value of ANRIL for CHD. Kaplan-Meier survival curves were plotted to analyze 3-year survival rates in high- and low-ANRIL expression groups. Cox regression was conducted to analyze independent risk factors affecting the patients. The expression level of serum ANRIL in preSG was significantly lower than those in CG and postSG (P < 0.05). According to the ROC curve, the area under the curve (AUC) of serum ANRIL for diagnosing CHD in CG was 0.894 and the optimal cutoff value was 0.639, with the sensitivity of 86.61% and the specificity of 93.67%. According to the survival curves, the 3-year overall survival rate in the high-ANRIL expression group was significantly lower than that in the low-expression group (P < 0.05). History of smoking, high total cholesterol (TC), high triglyceride (TG), high homocysteine (Hcy), and ANRIL expression were independent prognostic factors affecting the overall survival time of the patients (P < 0.05). ANRIL is poorly expressed in the peripheral blood of patients with CHD. Its detection has good sensitivity and specificity for diagnosing the disease, and its expression may be related to the poor prognosis of the patients.

LncRNA-Cox2 regulates macrophage polarization and inflammatory response through the CREB-C/EBPβ signaling pathway in septic mice

LncRNA-Cox2 has been reported to regulate macrophage polarization, and the activation of macrophages is a major participant in the pathogenesis of sepsis. Therefore, we explored whether lncRNA-Cox2 was involved in the progression of sepsis. In this study, we established a cecal ligation and puncture (CLP) mouse model and found that silencing lncRNA-Cox2 in CLP mice improved the 7-day survival rate, and alleviated the increase of blood bacterial burdens, systemic inflammatory response, and pulmonary dysfunction induced by CLP. Besides, interference with lncRNA-Cox2 declined the percentage of M1 macrophages and increased the percentage of M2 macrophages in the spleens of CLP mice. In vitro, the knockdown of lncRNA-Cox2 suppressed LPS-induced inflammation and M1 macrophage marker expression, and promoted M2 macrophage marker expression in primary peritoneal macrophages and RAW264.7 cells. Moreover, lncRNA-Cox2 induced CREB phosphorylation by binding to CREB, and increased phosphorylated-CREB enrichment in the C/EBPβ promoter region, so as to promote C/EBPβ transcription, thereby activating the CREB-C/EBPβ cascade. In addition, overexpressing lncRNA-Cox2 enhanced the effect of LPS on inflammation and macrophage polarization, which was reversed by treatment with 666-15 (an inhibitor of CREB). In conclusion, silencing lncRNA-Cox2 restrained the progression of sepsis in mice by modulating macrophage polarization and inflammatory response through suppressing CREB-C/EBPβ pathway.

Long noncoding RNA LINC01291 promotes the aggressive properties of melanoma by functioning as a competing endogenous RNA for microRNA-625-5p and subsequently increasing IGF-1R expression

Studies have confirmed the relationship between dysregulated long noncoding RNAs and melanoma pathogenesis. However, the regulatory functions of long intergenic non-protein coding RNA 1291 (LINC01291) in melanoma remain unknown. Therefore, we evaluated LINC01291 expression in melanoma and explored its roles in regulating tumor behaviors. Further, the molecular events via which LINC01291 affects melanoma cells were investigated. LINC01291 expression in melanoma cells was analyzed using The Cancer Genome Atlas database and quantitative real-time polymerase chain reaction. Functional assays, including the Cell Counting Kit-8 assay, colony formation assay, flow cytometry, cell migration and invasion assays, and tumor xenograft models, were used to examine LINC01291’s role in melanoma cells. Additionally, bioinformatics analysis, RNA immunoprecipitation, luciferase reporter assay, and western blotting were conducted to determine the tumor-promoting mechanism of LINC01291. LINC01291 was upregulated in melanoma tissues and cell lines. Following LINC01291 knockdown, cell proliferation, colony formation, migration, and invasion were diminished, whereas apoptosis was enhanced and the cell cycle was arrested at G0/G1. In addition, loss of LINC01291 decreased the chemoresistance of melanoma cells to cisplatin. Furthermore, LINC01291 interference inhibited melanoma tumor growth in vivo. Mechanistically, LINC01291 functions as a competing endogenous RNA by sponging microRNA-625-5p (miR-625-5p) in melanoma cells and maintaining insulin-like growth factor 1 receptor (IGF-1R) expression. Rescue experiments revealed that the roles induced by LINC01291 depletion in melanoma cells could be reversed by suppressing miR-625-5p or overexpressing IGF-1R. Our study identified the LINC01291/miR-625-5p/IGF-1R competing endogenous RNA pathway in melanoma cells, which may represent a novel diagnostic biomarker and an effective therapeutic target for melanoma.

LncRNA MHRT Promotes Cardiac Fibrosis via miR-3185 Pathway Following Myocardial Infarction

Long-chain noncoding RNA (lncRNA) is a new class of molecular regulators in heart development and disease. However, the role of specific lncRNA in cardiac fibrosis remains to be fully explored. This study aimed to investigate the role and potential mechanism of lncRNA MHRT in myocardial fibrosis after myocardial infarction (MI).Cardiac fibroblasts (CFs) were isolated from a mouse model of MI. The expression levels of MHRT and miR-3185 in the hearts of MI and CFs mice treated with transforming growth factor beta 1 (TGF-β1) were analyzed by qRT-PCR. The collagen expression was assessed using qRT-PCR and Western blot. Cell proliferation was assessed by performing MTT and EdU assays. The direct interaction between lncRNA and miRNA was analyzed by luciferase assay, RNA-binding protein immunoprecipitation (RIP) assay, and RNA pull-down assay.The expression levels of MHRT were raised in MI and CFs mice treated with TGF-β1. Overexpression of MHRT promoted collagen production and CF proliferation, while silencing of MHRT showed the opposite effect. MiR-3185 was a target gene of MHRT. In addition, overexpression of MHRT reduced the expression levels of miR-3185, and siMHRT reversed the inhibitory effect of TGF-β1 on the expression of miR-3185. Overexpression of miR-3185 inhibited the upregulation of Col I and Col III induced by TGF-β1.MHRT promoted cardiac fibrosis after MI through miR-3185 and increased myocardial collagen deposition and promoted myocardial fibrosis.

Phenotype-genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs

The phenotype–genotype relationship is a key for personalized and precision medicine for complex diseases. To unravel the complexity of the clinical phenotype–genotype network, we used cardiovascular diseases (CVDs) and associated non-coding RNAs (ncRNAs) (i.e. miRNAs, long ncRNAs, etc.) as the case for the study of CVDs at a systems or network level. We first integrated a database of CVDs and ncRNAs (CVDncR, http://sysbio.org.cn/cvdncr/) to construct CVD–ncRNA networks and annotate their clinical associations. To characterize the networks, we then separated the miRNAs into two groups, i.e. universal miRNAs associated with at least two types of CVDs and specific miRNAs related only to one type of CVD. Our analyses indicated two interesting patterns in these CVD–ncRNA networks. First, scale-free features were present within both CVD–miRNA and CVD–lncRNA networks; second, universal miRNAs were more likely to be CVDs biomarkers. These results were confirmed by computational functional analyses. The findings offer theoretical guidance for decoding CVD–ncRNA associations and will facilitate the screening of CVD ncRNA biomarkers.

Database URL: http://sysbio.org.cn/cvdncr/

An enhanced machine learning tool for cis-eQTL mapping with regularization and confounder adjustments

Many expression quantitative trait loci (eQTL) studies have been conducted to investigate the biological effects of variants in gene regulation. However, these eQTL studies may suffer from low or moderate statistical power and overly conservative false-discovery rate. In practice, most algorithms for eQTL identification do not model the joint effects of multiple genetic variants with weak or moderate influence. Here we present a novel machine-learning algorithm, lasso least-squares kernel machine (LSKM-LASSO) that model the association between multiple genetic variants and phenotypic traits simultaneously with the existence of nongenetic and genetic confounding. With a more general and flexible framework for the estimation of genetic confounding, LSKM-LASSO is able to provide a more accurate evaluation of the joint effects of multiple genetic variants. Our simulations demonstrate that our approach outperforms three state-of-the-art alternatives in terms of eQTL identification and phenotype prediction. We then apply our method to genotype and gene expression data of 11 tissues obtained from the Genotype-Tissue Expression project. Our algorithm was able to identify more genes with eQTL than other algorithms. By incorporating a regularization term and combining it with least-squares kernel machine, LSKM-LASSO provides a powerful tool for eQTL mapping and phenotype prediction.

The interaction mechanism between autophagy and apoptosis in colon cancer

Autophagy and apoptosis play crucial roles in tumorigenesis. Recent studies have shown that autophagy and apoptosis have a cross-talk relationship in anti-tumor therapy. It is well established that apoptosis is one of the main pathways of tumor cell death. While autophagy can occurs in tumors with opposite function: protective autophagy and lethal autophagy. Protective autophagy can inhibit tumor apoptosis induced by anticancer drugs, while lethal autophagy can induce tumor cell apoptosis in cooperation with anticancer drugs. Hence, autophagy and apoptosis have synergistic and antagonistic effects in tumor. Colorectal cancer is a common malignant tumor with high morbidity and mortality. In recent years, colorectal carcinoma has achieved improved clinical efficacy with drug treatment. Nonetheless, increasing drug-resistance limit the treatment efficacy, highlighting the urgency of exploring the molecular events that drive drug resistance. Researchers have found that autophagy is one of the major factors leading to drug resistance in colon cancer. Therefore, elucidating the interaction between autophagy and apoptosis is helpful to improve the efficacy of anticancer drugs in clinical treatment of colorectal cancer. This review attaches great importance to the relationship between autophagy and apoptosis and related factors in colorectal cancer.

Non-Coding RNA Databases in Cardiovascular Research

Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research.

Transcriptome Analyses of lncRNAs in A2E-Stressed Retinal Epithelial Cells Unveil Advanced Links between Metabolic Impairments Related to Oxidative Stress and Retinitis Pigmentosa

: Long non-coding RNAs (lncRNAs) are untranslated transcripts which regulate many biological processes. Changes in lncRNA expression pattern are well-known related to various human disorders, such as ocular diseases. Among them, retinitis pigmentosa, one of the most heterogeneous inherited disorder, is strictly related to oxidative stress. However, little is known about regulative aspects able to link oxidative stress to etiopathogenesis of retinitis. Thus, we realized a total RNA-Seq experiment, analyzing human retinal pigment epithelium cells treated by the oxidant agent N-retinylidene-N-retinylethanolamine (A2E), considering three independent experimental groups (untreated control cells, cells treated for 3 h and cells treated for 6 h). Differentially expressed lncRNAs were filtered out, explored with specific tools and databases, and finally subjected to pathway analysis. We detected 3,3'-overlapping ncRNAs, 107 antisense, 24 sense-intronic, four sense-overlapping and 227 lincRNAs very differentially expressed throughout all considered time points. Analyzed lncRNAs could be involved in several biochemical pathways related to compromised response to oxidative stress, carbohydrate and lipid metabolism impairment, melanin biosynthetic process alteration, deficiency in cellular response to amino acid starvation, unbalanced regulation of cofactor metabolic process, all leading to retinal cell death. The explored lncRNAs could play a relevant role in retinitis pigmentosa etiopathogenesis, and seem to be the ideal candidate for novel molecular markers and therapeutic strategies.

LncRNA HCP5 promotes cell proliferation and inhibits apoptosis via miR-27a-3p/IGF-1 axis in human granulosa-like tumor cell line KGN

This study aimed to reveal the potential roles of long non-coding RNA HCP5 (lncRNA HCP5) and its potential molecular mechanism in polycystic ovarian syndrome (PCOS). The human granulosa-like tumor cell line KGN was used for assessing the effects of HCP5 in the proliferation and apoptosis of granulosa cells (GCs). The results showed that downregulation of HCP5 suppressed cell proliferation through arresting cell cycle progression at G1 phase, and induced the apoptosis via activating mitochondrial pathway, while overexpression of HCP5 played the opposite effects in KGN cells. We predicted and confirmed miR-27a-3p was a directly target to HCP5 and it could directly bind with insulin-like growth factor-1 (IGF-1). Next, we performed gain- and loss-of-functions approaches by transfecting miR-27a-3p inhibitor into HCP5 knocking down cells and transfecting miR-27a-3p mimics into HCP5 overexpressing cells. The results demonstrated that downregulation and upregulation of miR-27a-3p could block the effects on the proliferation and apoptosis mediated by silencing and overexpressing HCP5 in KGN cells. Additionally, miR-27a-3p inhibitor remarkably reversed the IGF-1 decrease regulated by knocking down HCP5 and miR-27a-3p mimics inhibited the IGF-1 increase modulated by overexpressing HCP5 in KGN cells. Furthermore, we observed that the promoted cell vitality and reduced apoptosis mediated by enforced expression of HCP5 could be alleviated when the KGN cells transfected with IGF-1 siRNA. Our findings indicate that HCP5 might be a potential regulatory factor for development of PCOS through regulating the miR-27a-3p/IGF-1 axis.

Long noncoding RNAs in cancer: From discovery to therapeutic targets

Long noncoding RNAs (lncRNAs) have recently gained considerable attention as key players in biological regulation; however, the mechanisms by which lncRNAs govern various disease processes remain mysterious and are just beginning to be understood. The ease of next-generation sequencing technologies has led to an explosion of genomic information, especially for the lncRNA class of noncoding RNAs. LncRNAs exhibit the characteristics of mRNAs, such as polyadenylation, 5' methyl capping, RNA polymerase II-dependent transcription, and splicing. These transcripts comprise more than 200 nucleotides (nt) and are not translated into proteins. Directed interrogation of annotated lncRNAs from RNA-Seq datasets has revealed dramatic differences in their expression, largely driven by alterations in transcription, the cell cycle, and RNA metabolism. The fact that lncRNAs are expressed cell- and tissue-specifically makes them excellent biomarkers for ongoing biological events. Notably, lncRNAs are differentially expressed in several cancers and show a distinct association with clinical outcomes. Novel methods and strategies are being developed to study lncRNA function and will provide researchers with the tools and opportunities to develop lncRNA-based therapeutics for cancer.

Effect of astragalosides on long non-coding RNA expression profiles in rats with adjuvant-induced arthritis

Rheumatoid arthritis (RA) is an autoimmune disease of unknown etiology, which occurs in ~1.0% of the general population. Increasing studies have suggested that long non-coding RNAs (lncRNAs) may serve important roles in various biological processes and may be associated with the pathogenesis of different types of disease, including RA. Astragalosides (AST) has been used as a traditional Chinese medicine for the treatment of RA. However, the mechanism underlying its therapeutic effect has remained unclear to date. Thus, there is an urgent need to elucidate the possible mechanism of AST in the treatment of RA from the perspective of lncRNAs. In the present study, the lncRNAs and mRNAs of a vehicle group, animal model group and AST treatment (control) group were determined by Arraystar Rat lncRNA/mRNA microarray. The differentially expressed genes with a fold change >1.5 and P<0.05 were selected and analyzed. Gene Ontology (GO) and pathway analysis was performed using the Database for Annotation, Visualization and Integration Discovery, and the coding-non-coding gene co-expression network was drawn based on the correlation analysis between the differentially expressed lncRNAs and mRNAs. Based on node degree and the correlation between bioinformatics analysis and RA, the critical differentially expressed lncRNAs were selected, analyzed and verified by reverse transcription-quantitative PCR (RT-qPCR) analysis. The results showed that, following AST treatment, up to 75 lncRNAs and 247 mRNAs were found to be differentially expressed among the three groups. GO and pathway analysis manifested that 135 GO terms and 17 pathways were enriched by differentially expressed genes. Four lncRNAs (MRAK012530, MRAK132628, MRAK003448 and XR_006457) were selected as the critical lncRNAs and their trend in expression showed consistency between the RT-qPCR and microarray data. In conclusion, AST had a regulatory effect on differentially expressed lncRNAs during the development of RA, and four lncRNAs could be selected as critical therapeutic targets of AST.

Genome-wide methods for investigating long noncoding RNAs

Long noncoding RNAs (lncRNAs) are large RNA transcripts that do not code for proteins but exert their effects in the form of RNA. To date many thousands of lncRNAs have been identified, their molecular functions and mechanisms of action however are largely unknown. The development of high-throughput experimental technologies, such as ChIRP (Chromatin isolation by RNA purification), CHART (Capture Hybridization Analysis of RNA Targets), RAP (RNA antisense purification), RIP (RNA Immunoprecipitation), CLIP (cross-linking and immunoprecipitation) and RNA pull-down, has led to a rapid expansion of lncRNA research and resulted in many publicly-available databases. This review provides an overview of the current methodologies available for discovering and investigating functions of lncRNAs in various human diseases. A comparison and application of these methods are also included. Finally, this paper surveys current databases containing annotations, interactome networks and functions of lncRNAs. The appropriate use of these methods and databases will provide not only high-resolution functional features of lncRNAs, but also enhance our understanding of the underlying mechanisms by which lncRNAs regulate a variety of biological processes.

Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology

Cardiovascular diseases (CVDs) affect the heart and the vascular system with a high prevalence and place a huge burden on society as well as the healthcare system. These complex diseases are often the result of multiple genetic and environmental risk factors and pose a great challenge to understanding their etiology and consequences. With the advent of next generation sequencing, many non-coding RNA transcripts, especially long non-coding RNAs (lncRNAs), have been linked to the pathogenesis of CVD. Despite increasing evidence, the proper functional characterization of most of these molecules is still lacking. The exploration of conservation of sequences across related species has been used to functionally annotate protein coding genes. In contrast, the rapid evolutionary turnover and weak sequence conservation of lncRNAs make it difficult to characterize functional homologs for these sequences. Recent studies have tried to explore other dimensions of interspecies conservation to elucidate the functional role of these novel transcripts. In this review, we summarize various methodologies adopted to explore the evolutionary conservation of cardiovascular non-coding RNAs at sequence, secondary structure, syntenic, and expression level.

Knockdown of long noncoding RNA urothelial carcinoma associated 1 inhibits colorectal cancer cell proliferation and promotes apoptosis via modulating autophagy

Long noncoding RNA urothelial carcinoma associated 1 (UCA1) has been implicated in the growth and metastasis of colorectal cancer (CRC), and autophagy contributes to tumorigenesis and cancer cell survival. However, the regulatory role of UCA1 in CRC cell viability by modulating autophagy remains unclear. In the present study, a significant positive correlation was observed between UCA1 and microtubule-associated protein 1 light chain 3 (LC3) levels, and the elevated UCA1 was negatively correlated with the PKB/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway in 293T cells. Downregulation of UCA1 inhibited autophagy activation and cell proliferation, whereas the apoptosis was increased and the cell cycle was arrested in G2 stage. The next results showed that UCA1 was markedly upregulated in Caco-2 cells. Knockdown of UCA1 significantly decreased the LC3-II and autophagy-related gene 5 (ATG5) protein levels and resulted in an increase in p62 expression. Conversely, the autophagy activator rapamycin (RAPA) reversed the effects. Furthermore, downregulated UCA1 decreased Caco-2 cells population in the G1 phase and increased the cells number in G2 phage. The cell proliferation was inhibited, and apoptosis rate was promoted. More important, RAPA could also abrogate the changes induced by knockdown of UCA1. Collectively, these data demonstrated that downregulated UCA1 induced autophagy inhibition, resulting in suppressing cell proliferation and promoting apoptosis, which suggested that UCA1 might serve as a potential new oncogene to regulate CRC cells viability by modulating autophagy.

High‑throughput sequencing reveals differentially expressed lncRNAs and circRNAs, and their associated functional network, in human hypertrophic scars

Growing evidence suggests that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are involved in the occurrence and development of tumors and fibrotic diseases. However, the integrated analysis of lncRNA and circRNA expression, alongside associated co-expression and competing endogenous RNA (ceRNA) networks, has not yet been performed in human hypertrophic scars (HS). The present study compared the expression levels of lncRNAs, circRNAs and mRNAs in human HS and normal skin tissues by high-throughput RNA sequencing. Numerous differentially expressed lncRNAs, circRNAs and mRNAs were detected. Subsequently, five aberrantly expressed lncRNAs and mRNAs, and six circRNAs were measured to verify the RNA sequencing results by reverse transcription-quantitative polymerase chain reaction. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for the dysregulated genes, in order to elucidate their principal functions. In addition, a coding-noncoding gene co-expression (CNC) network and ceRNA network were constructed for specific significantly altered genes. The CNC network analysis suggested that AC048380.1 and LINC00299 were associated with metastasis-related genes, including inhibin subunit βA (INHBA), SMAD family member 7 (SMAD7), collagen type I α1 chain (COL1A1), transforming growth factor β3 (TGFβ3) and MYC proto-oncogene, bHLH transcription factor (MYC). Inhibitor of DNA binding 2 was associated with the lncRNAs cancer susceptibility 11, TGFβ3-antisense RNA 1 (AS1), INHBA-AS1, AC048380.1, LINC00299 and LINC01969. Circ-Chr17:50187014_50195976_-, circ-Chr17:50189167_50194626_-, circ-Chr17:50189167_ 50198002_- and circ-Chr17:50189858_50195330_- were also associated with INHBA, SMAD7, COL1A1, TGFβ3 and MYC. COL1A1 and TGFβ3 were associated with circ-Chr9:125337017_125337591_+ and circ-Chr12:120782654_120784593_-. The ceRNA network indicated that INHBA-AS1 and circ-Chr9:125337017_125337591_+ were ceRNAs of microRNA-182-5p targeting potassium voltage-gated channel subfamily J member 6, ADAM metallopeptidase with thrombospondin type 1 motif 18, SRY-box 11, MAGE family member L2, matrix metallopeptidase 16, thrombospondin 2, phosphodiesterase 11A and collagen type V a1 chain. These findings suggested that lncRNAs and circRNAs may act as ceRNAs, which are implicated in the pathophysiology and development of human HS, and lay a foundation for further insight into the novel regulatory mechanism of lncRNAs and circRNAs in hypertrophic scarring.

Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives

Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.

Non-coding RNAs in aneurysmal aortopathy

Aortic aneurysms represent a major public health burden, and currently have no medical treatment options. The pathophysiology behind these aneurysms is complex and variable, depending on location and underlying cause, and generally involves progressive dysfunction of all elements of the aortic wall. Changes in smooth muscle behavior, endothelial signaling, extracellular matrix remodeling, and to a variable extent inflammatory signaling and cells, all contribute to the dilation of the aorta, ultimately resulting in high mortality and morbidity events including dissection and rupture. A large number of researchers have identified non-coding RNAs as crucial regulators of aortic aneurysm development, both in humans and in animal models. While most work to-date has focused on microRNAs, intriguing information has also begun to emerge regarding the role of long-non-coding RNAs. This review summarizes the currently available data regarding the involvement of non-coding RNAs in aneurysmal aortopathies. Going forward, these represent key potential therapeutic targets that might be leveraged in the future to slow or prevent aortic aneurysm formation, progression and rupture.

Circulating lncRNA NEAT1 correlates with increased risk, elevated severity and unfavorable prognosis in sepsis patients

OBJECTIVE

To investigate the correlation of circulating long non-coding RNA nuclear-enriched abundant transcript 1 (lncRNA NEAT1) expression with disease risk, severity, prognosis and inflammatory cytokine levels in sepsis patients.

METHODS

152 sepsis patients and 150 health controls (HCs) were enrolled in this study. Plasma and serum samples were obtained from sepsis patients and HCs, and lncRNA NEAT1 expression in plasma was determined by quantitative polymerase chain reaction, while levels of inflammatory cytokines in serum were detected by enzyme linked immune sorbent assay.

RESULTS

LncRNA NEAT1 expression was remarkably higher in sepsis patients than in HCs (P < 0.001). Receiver operating characteristic (ROC) curve disclosed a good predictive value of lncRNA NEAT1 expression for sepsis risk with area under curve (AUC) of 0.730 (95% CI: 0.740-0.861). Subsequent multivariate logistic regression analysis demonstrated that lncRNA NEAT1 expression was independently associated with higher sepsis risk (P < 0.001). In sepsis patients, lncRNA NEAT1 expression was also observed to be positively correlated with Acute Physiology and Chronic Health Evaluation (APACHE) II score (P < 0.001), serum tumor necrosis factor-α (P < 0.001), interleukin (IL)-1β (P = 0.043), IL-6 (P = 0.001) and IL-8 (P = 0.038), while negatively correlated with IL-10 (P < 0.001). In addition, lncRNA NEAT1 expression was increased in non-survivors compared to survivors (P = 0.006), and ROC curve revealed a good prognostic value of lncRNA NEAT1 for non-survivor risk with AUC 0.641 (95% CI: 0.536-0.746).

CONCLUSION

Circulating lncRNA NEAT1 correlates with increased disease risk, elevated severity and unfavorable prognosis as well as higher expression of pro-inflammatory cytokines in sepsis patients.

Association of the rs1870634 Variant in Long Intergenic Non-protein Coding RNA 841 with Coronary Artery Disease: A GWAS-Replication Study in an Iranian Population

Recent genome-wide association studies (GWAS) identified a list of single-nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD). Replication of GWAS findings in different population corroborated the observed association in the parent GWAS. In this study, we aimed to replicate the association of rs1870634, a GWAS identified SNP, to CAD in an Iranian population. The study population consisted of 267 subjects undergoing coronary angiography coronary angiography including 155 CAD patients and 112 non-CAD age- and gender-matched controls. The genotype determination of rs1870634 SNP performed using high-resolution melting analysis (HRM) technique. Our results revealed that the GG genotype frequency was significantly higher in CAD patients compared with controls (P = 0.03). The results of binary logistic regression suggested that this genotype was significantly associated with CAD risk adjustment for age, BMI, sex, TC, and LDL-C lipid levels (OR of 2.78, 95% CI (1.10-7.01), P = 0.03). Moreover, our results showed that the GG+TG genotypes were 2.52 times more likely to develop CAD (95% CI 1.05-6.03) than TT genotype carriers after adjusting for age, sex, and lipid profiles (P = 0.037). These data showed that the GG genotype could be associated with increased risk of CAD in a sample of Iranian population.

Microarray analysis of the expression profile of lncRNAs reveals the key role of lncRNA BC088327 as an agonist to heregulin‑1β‑induced cell proliferation in peripheral nerve injury

Heregulin‑1β is capable of promoting the nerve regeneration of acellular nerve allografts with skin‑derived precursor differentiated Schwann cell (SC) therapy in peripheral nerve injury. Long non‑coding RNAs (lncRNAs) serve important roles in the regulation of gene transcription and trans-lation in multiple biological processes, but its association with the repair of peripheral nerve injury is unexplored. Therefore, in the present study, the aim was to identify novel indicators for peripheral nerve injury, and to detect whether there is an association between lncRNA expression and the treatment effect of heregulin‑1β on this disorder. The expression status of lncRNAs and mRNAs in a well‑built rat model with sciatic nerve injury was investigated using microarray assays. Based on the results of the microarray assays and quantitative polymerase chain reaction validation, it was inferred that lncRNA BC088327 was upregulated to the largest extent among all the lncRNAs. According to these findings, the role of BC088327 in peripheral nerve injury was further assessed by detecting the cell viability, cell cycle and apoptosis in a hypoxic SC cell model after suppressing the expression of BC088327 using specific small interfering RNA. Based on the results of the lncRNA microarray assay, 805 lncRNAs were significantly differentially expressed, among which, 323 lncRNAs were upregulated and 482 lncRNAs were downregulated. Based on the results of the mRNA microarray assay, 1,293 lncRNAs were significantly differentially expressed, including 603 upregulated and 690 downregulated lncRNAs. Moreover, knockdown of lncRNA BC088327 suppressed cell viability and induced cell apoptosis and S-phase cell cycle arrest in the SCs. In conclusion, expression profile changes of lncRNAs in peripheral nerve injuries were closely associated with treatment with heregulin‑1β. lncRNA BC088327 may play a synergistic role with heregulin‑1β in repairing peripheral injury, which has the potential be a biomarker for the detection of peripheral injury and a medical target for the development of therapeutic modalities.

Long non-coding RNA CRNDE promotes gallbladder carcinoma carcinogenesis and as a scaffold of DMBT1 and C-IAP1 complexes to activating PI3K-AKT pathway

Deleted in malignant brain tumors 1 (DMBT1) is deleted during cancer progression and as a potential tumor-suppressor gene in various types of cancer. However, its role in Gallbladder cancer remains poorly understood. DMBT1 has low-expression and deletion of copy number were detected in normal tissues and GBC cancer tissues by qRT-PCR. Knockdown of DMBT1 increased migration and invasion and overexpressed DMBT1 impaired migration and invasion in GBC cells. We also evaluated the molecular mechanism of DMBT1 by RNA sequencing and GSEA analysis. RNA-Pulldown and RIP assay authenticated CRNDE can specified binding with DMBT1 and c-IAP1. Downregulation of DMBT1 resulted in significant change of gene expression (at least 2-fold) in PI3K-AKT pathway, increased expression of MMP-9, JUK-1, ERK and AKT, activating PI3K-AKT pathway lead to GBC carcinogenesis.We for the first time reported, DMBT1 as a prognosis biomarker, is low-expressed in GBC tumors, and CRNDE act as a scaffold to recruit the DMBT1 and c-IAP1, promotes the PI3K-AKT pathway. Our study reveals DMBT1 may be an important contributor to GBC cancer development.

Circulating lnc-ITSN1-2 expression presents a high value in diagnosis of rheumatoid arthritis and correlates with disease activity

This study was aimed to investigate the correlation of lnc-ITSN1-2, lnc-APOC3-2 and lnc-AL355149.1 expressions in plasma by qPCR with rheumatoid arthritis (RA) risk and disease activity. 30 RA patients and 30 health controls (HC) were enrolled in this study. Plasma sample were collected from RA patients before any treatment carried out and HCs. Top 3 RA related long non-coding RNAs (lncRNAs) (lnc-ITSN1-2, lnc-APOC3-2 and lnc-AL355149.1) were selected by a computational framework prediction. The expression of lnc-ITSN1-2, lnc-APOC3-2 and lnc-AL355149.1 were determined by qPCR method. Age (P=0.350) and gender (P=0.542) were similar between RA patients and HCs. lnc-ITSN1-2 level was extremely increased in RA patients compared with HCs (P<0.001), while both lnc-APOC3-2 and lnc-AL355149.1 expressions were numerically higher in RA patients but with no statistical significance (P=0.152 and P=0.139 respectively). Receiver Operating Characteristic (ROC) curves were performed and we found lnc-ITSN1-2 disclosed a great diagnostic value for RA with area under curve (AUC) 0.898, 95% CI 0.813-0.983, and sensitivity was 90.0% and specificity was 80.0% respectively at the best cut-off point. In addition, plasma lnc-ITSN1-2 level was illuminated to be positively associated with erythrocyte sedimentation rate (ESR) (P=0.049), C-reactive protein (CRP) (P<0.001) and disease activity score in 28 joints (DAS28) (P=0.007). Circulating lnc-ITSN1-2 expression was observed to be a novel and convincing biomarker for RA diagnosis as well as disease management.

Identification of long non-coding RNA 00312 and 00673 in human NSCLC tissues

Non-small cell lung cancer (NSCLC) is a fatal disease to human health. Despite the advanced progresses in cancer therapy during the past decades, NSCLC still remains the leading cause of cancer death worldwide. The long non‑coding RNAs (lncRNAs) recently have been considered as key regulators of tumor malignant. Previous studies identified that long non‑coding RNAs, linc00312 and linc00673 are markedly associated with lung cancer. However, current understanding of the two lncRNAs involving in NSCLC remains unclear. The aim of the present study was to profile their expression and clinicopathological significance in 76 patients' NSCLC tissues compared to non‑tumor tissues using reverse transcription-quantitative polymerase chain reaction. Data have indicated that the linc00312 expression level was significantly decreased in NSCLC tissues (P<0.001), while a higher linc00673 level has been detected in the same tumor tissues (P<0.01). In addition, the low expression of linc00312 was associated with the Tumor‑Node‑Metastasis stage of NSCLC (P<0.05), whereas the high expression of linc00673 was related with the histological types of NSCLC (P<0.05). In conclusion, lncRNA 00312 and 00673 may serve as potential novel biomarkers for lung cancer early diagnosis, which may play a vital role in treatments of NSCLC.

Functional significance of the long non-coding RNA RP11-169D4.1 as a metastasis suppressor in laryngeal squamous cell carcinoma by regulating CDH1

The present study investigated the expression profile and the function of RP11-169D4.1 and explored its potential mechanisms in laryngeal squamous cell carcinoma. The biological function of RP11-169D4.1 was examined using the MTT assay, flow cytometric analysis, wound healing and transwell assays. The relationship between RP11-169D4.1 and miR-205-5p was discovered by Argonaute 2 protein immunoprecipitation. The target gene of RP11-169D4.1 was CDH1 which was assessed by Pearson's correlation analysis, RT-PCR and western blot assay. We demonstrated that RP11-169D4.1 expression was markedly decreased in LSCC tissues and cell lines. The overexpression of RP11-169D4.1 inhibited the proliferation, migration and invasion of LSCC cell lines as well as promoted apoptosis. We further verified that miR-205-5p had binding sites with RP11‑169D4.1 and that RP11-169D4.1 could regulate the expression of CDH1. Ectopic transfection of RP11-169D4.1 led to a significant reduction in the downstream signaling molecule AKT in LSCC cells. The long non-coding RNA RP11-169D4.1 may serve as a tumor suppressor and a promising therapeutic target in laryngeal cancer, which could inhibit the process of EMT by regulating CDH1.

Reconstruction and analysis of the lncRNA–miRNA–mRNA network based on competitive endogenous RNA reveal functional lncRNAs in rheumatoid arthritis

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population.

Challenges and Opportunities in Linking Long Noncoding RNAs to Cardiovascular, Lung, and Blood Diseases

The new millennium heralds an unanticipated surge of genomic information, most notably an expansive class of long noncoding RNAs (lncRNAs). These transcripts, which now outnumber all protein-coding genes, often exhibit the same characteristics as mRNAs (RNA polymerase II-dependent, 5' methyl-capped, multiexonic, polyadenylated); yet, they do not encode for stable, well-conserved proteins. Elucidating the function of all relevant lncRNAs in heart, vasculature, lung, and blood is essential for generating a complete interactome in these tissues. This is particularly evident because an increasing number of investigators perform RNA-sequencing experiments where, typically, annotated lncRNAs exhibit impressive changes in gene expression. How does one go about evaluating an lncRNA when the sequence of the transcript lends no insight into how it may function within a cell type? Here, we provide a brief overview for the rational study of lncRNAs.

MicroRNAs in idiopathic pulmonary fibrosis: involvement in pathogenesis and potential use in diagnosis and therapeutics

MicroRNAs (miRNAs) are a class of phylogenetically conserved, non-coding short RNAs, 19-22 nt in length which suppress protein expression through base-pairing with the 3'-untranslated region of target mRNAs. miRNAs have been found to participate in cell proliferation, differentiation and apoptosis. Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and high lethality fibrotic lung disease for which currently there is no effective treatment. Some miRNAs have been reported to be involved in the pathogenesis of pulmonary fibrosis. In this review, we discuss the role of miRNAs in the pathogenesis, diagnosis and treatment of IPF.

lncRNA-UCA1 enhances cell proliferation through functioning as a ceRNA of Sox4 in esophageal cancer

Esophageal cancer (EC) is one of the most common gastrointestinal cancers, which leads to the sixth ranking of cancer-related death. Long non-coding RNAs (lncRNAs) play pivotal roles in many biological processes. lncRNA human urothelial carcinoma associated 1 (UCA1) is significantly upregulated and functions as an important oncogene in many types of human cancers. However, the role of UCA1 in EC and its underlying mechanism remains unclear. In the present study, we demonstrated that UCA1 was significantly upregulated in EC tissues and associated with poor prognosis. Overexpression of UCA1 promoted the proliferation of EC cells, while silence of UCA1 inhibited EC cells growth. Furthermore, we found that Sox4 was a direct target gene of UCA1. UCA1 regulated Sox4 expression through functioning as a competing endogenous RNA (ceRNA). UCA1 directly interacted with miR-204 and decreased the binding of miR-204 to Sox4 3'UTR, which suppressed the degradation of Sox4 mRNA by miR-204. This study provides the first evidence that UCA1 promotes cell proliferation through Sox4 in EC, suggesting that UCA1 and Sox4 may be potential therapeutic targets for EC.