Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy

Analysis of the lncRNA-miRNA-mRNA network to explore the regulation mechanism in human traumatic brain injury

Traumatic brain injury (TBI) refers to brain dysfunction with or without traumatic structural injury induced by an external force. Nevertheless, the molecular mechanism of TBI remains undefined. Differentially expressed (DE) lncRNAs, DEmRNAs and DEmiRNAs were selected between human TBI tissues and the adjacent histologically normal tissue by high-throughput sequencing. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis of overlapping DEmRNAs between predicted mRNAs of DEmiRNAs and DEmRNAs. The competitive endogenous RNA (ceRNA) network of lncRNA-miRNA-mRNA was established in light of the ceRNA theory. In the ceRNA network, the key lncRNAs were screened out. Then key lncRNAs related ceRNA subnetwork was constructed. After that, qRT-PCR was applied to validate the expression levels of hub genes. 114 DElncRNAs, 1807 DEmRNAs and 6 DEmiRNAs were DE in TBI. The TBI-related ceRNA network was built with 73 lncRNA nodes, 81 mRNA nodes and 6 miRNAs. According to topological analysis, two hub lncRNAs (ENST00000562897 and ENST00000640877) were selected to construct the ceRNA subnetwork. Subsequently, key lncRNA-miRNA-mRNA regulatory axes constructed by two lncRNAs including ENST00000562897 and ENST00000640877, two miRNAs including miR-6721-5p and miR-129-1-3p, two mRNAs including ketohexokinase (KHK) and cyclic nucleotide-gated channel beta1 (CNGB1), were identified. Furthermore, qRT-PCR results displayed that the expression of ENST00000562897, KHK and CNGB1 were significantly decreased in TBI, while the miR-6721-5p expression levels were markedly increased in TBI. The results of our study reveal a new insight into understanding the ceRNA regulation mechanism in TBI and select key lncRNA-miRNA-mRNA axes for prevention and treatment of TBI.

SLC26A4-AS1 Aggravates AngII-induced Cardiac Hypertrophy by Enhancing SLC26A4 Expression

BACKGROUND

It has been reported that solute carrier family 26 members 4 antisense RNA 1 (SLC26A4-AS1) is highly related to cardiac hypertrophy.

OBJECTIVE

This research aims to investigate the role and specific mechanism of SLC26A4-AS1 in cardiac hypertrophy, providing a novel marker for cardiac hypertrophy treatment.

METHODS

Angiotensin II (AngII) was infused into neonatal mouse ventricular cardiomyocytes (NMVCs) to induce cardiac hypertrophy. Gene expression was detected by quantitative real-time PCR (RT-qPCR). Protein levels were evaluated via western blot. Functional assays analyzed the role of SLC26A4-AS1. The mechanism of SLC26A4-AS1 was assessed by RNA-binding protein immunoprecipitation (RIP), RNA pull-down, and luciferase reporter assays. The P value <0.05 was identified as statistical significance. Student's t-test evaluated the two-group comparison. The difference between different groups was analyzed by one-way analysis of variance (ANOVA).

RESULTS

SLC26A4-AS1 is upregulated in AngII-treated NMVCs and promotes AngII-induced cardiac hypertrophy. SLC26A4-AS1 regulates its nearby gene solute carrier family 26 members 4 (SLC26A4) via functioning as a competing endogenous RNA (ceRNA) to modulate the microRNA (miR)-301a-3p and miR-301b-3p in NMVCs. SLC26A4-AS1 promotes AngII-induced cardiac hypertrophy via upregulating SLC26A4 or sponging miR-301a-3p/miR-301b-3p.

CONCLUSION

SLC26A4-AS1 aggravates AngII-induced cardiac hypertrophy via sponging miR-301a-3p or miR-301b-3p to enhance SLC26A4 expression.

Integration of RNA molecules data with prior-knowledge driven Joint Deep Semi-Negative Matrix Factorization for heart failure study

Heart failure (HF) is the main manifestation of cardiovascular disease. Recent studies have shown that various RNA molecules and their complex connections play an essential role in HF’s pathogenesis and pathological progression. This paper aims to mine key RNA molecules associated with HF. We proposed a Prior-knowledge Driven Joint Deep Semi-Negative Matrix Factorization (PD-JDSNMF) model that uses a hierarchical nonlinear feature extraction method that integrates three types of data: mRNA, lncRNA, and miRNA. The PPI information is added to the model as prior knowledge, and the Laplacian constraint is used to help the model resist the noise in the genetic data. We used the PD-JDSNMF algorithm to identify significant co-expression modules. The elements in the module are then subjected to bioinformatics analysis and algorithm performance analysis. The results show that the PD-JDSNMF algorithm can robustly select biomarkers associated with HF. Finally, we built a heart failure diagnostic model based on multiple classifiers and using the Top 13 genes in the significant module, the AUC of the internal test set was up to 0.8714, and the AUC of the external validation set was up to 0.8329, which further confirmed the effectiveness of the PD-JDSNMF algorithm.

A Survey on Computational Methods for Investigation on ncRNA-Disease Association through the Mode of Action Perspective

Molecular and sequencing technologies have been successfully used in decoding biological mechanisms of various diseases. As revealed by many novel discoveries, the role of non-coding RNAs (ncRNAs) in understanding disease mechanisms is becoming increasingly important. Since ncRNAs primarily act as regulators of transcription, associating ncRNAs with diseases involves multiple inference steps. Leveraging the fast-accumulating high-throughput screening results, a number of computational models predicting ncRNA-disease associations have been developed. These tools suggest novel disease-related biomarkers or therapeutic targetable ncRNAs, contributing to the realization of precision medicine. In this survey, we first introduce the biological roles of different ncRNAs and summarize the databases containing ncRNA-disease associations. Then, we suggest a new trend in recent computational prediction of ncRNA-disease association, which is the mode of action (MoA) network perspective. This perspective includes integrating ncRNAs with mRNA, pathway and phenotype information. In the next section, we describe computational methodologies widely used in this research domain. Existing computational studies are then summarized in terms of their coverage of the MoA network. Lastly, we discuss the potential applications and future roles of the MoA network in terms of integrating biological mechanisms for ncRNA-disease associations.

Transcriptome Sequencing Data Reveal LncRNA-miRNA-mRNA Regulatory Network in Calcified Aortic Valve Disease

Background

Calcified aortic valve disease (CAVD) is one of the most common valvular heart diseases in the elderly population. However, no effective medical treatments have been found to interfere with the progression of CAVD, and specific molecular mechanisms of CAVD remain unclear.

Materials and Methods

Transcriptome sequencing data of GSE55492 and GSE148219 were downloaded from the European Nucleotide Archive, and the microarray dataset, GSE12644 was acquired from the Gene Expression Omnibus database. Software, including FastQC, HISAT2, samtools, and featureCounts was applied to generate the read count matrix. The “Limma” package in R was utilized to analyze differentially expressed genes (DEGs). Thereafter, weighted gene co-expression network analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the protein-protein interaction (PPI) network were used to identify hub genes associated with CAVD, which were further validated by receiver operating characteristic curve (ROC) analysis using GSE12644. The long non-coding RNA (LncRNA)-mediated regulatory network was established based on the differentially expressed LncRNAs and hub genes, which were detected using quantitative real-time PCR (qRT-PCR) in clinical samples and valve interstitial cells. Moreover, CIBERSORT was used to calculate the expression distribution of immune cell infiltration in CAVD.

Results

A total of 126 DEGs were included in the PPI network. PI3K-Akt signaling pathway, ECM-receptor interaction, hematopoietic cell lineage, cell adhesion molecules, and focal adhesion were the most enriched pathways revealed by KEGG. Four LncRNAs, including TRHDE-AS1, LINC00092, LINC01094, and LINC00702 were considered the differentially expressed LncRNA. SPP1, TREM1, GPM6A, CCL19, CR1, NCAM1, CNTN1, TLR8, SDC1, and COL6A6 were the 10 hub genes identified to be associated with CAVD. Moreover, the calcified aortic valve samples had a greater level of Tregs, naïve B cells, and M0 macrophages than the noncalcified ones, whereas CAVD samples had a lower M2 macrophage expression compared to the noncalcified valve tissues.

Conclusion

The current study identified SPP1, TREM1, TLR8, SDC1, GPM6A, and CNTN1 as hub genes that could potentially be associated with CAVD. The LINC00702–miR-181b-5p–SPP1 axis might participate in the development of CAVD. Additionally, M2 macrophages, Tregs, naïve B cells, and M0 macrophages might possibly play a role in the initiation of CAVD.

Identification and Validation of Apparent Imbalanced Epi-lncRNAs Prognostic Model Based on Multi-Omics Data in Pancreatic Cancer

Background: Globally, pancreatic adenocarcinoma is a recognized cause of pancreatic death (PAAD) associated with high mortality. Long non-coding RNAs (lncRNAs) play an important role in several biological processes in pancreatic cancer.

Methods: The gene expression profile of PAAD patients were obtained from The Cancer Genome Atlas (TCGA) database. The limma package was used to identify epigenetic disorders of lncRNAs and PCG. Subsequently, the genomic characteristics and landscape of lncRNAs were explored. The pancreatic cancer-related lncRNAs gene set from Lnc2Cancer v3.0 were collected and the difference between cancer samples and normal samples were analysed. A prognostic model consisting of five epigenetic lncRNA (epi-lncRNAs) was established by univariate and multivariate Cox proportional hazards regression analyses and was verified across different data sets. Finally, the expression of core epi-lncRNAs was identified by PCR experiment.

Results: A total of 2237 epi-lncRNAs, 11855 non-epi-lncRNAs, 13518 epi-PCGs, and 6097 non-epi-PCGs, were identified. The abnormal frequency of lncRNAs in pancreatic cancer was much lower than that in PCG, and 138 epi-lncRNAs were enriched in human cancer-related lncRNAs. Epi-lncRNAs had a higher number with longer lengths and a greater number of transcripts. Epi-lncRNAs associated with epigenetic disorders had a higher number of exons, gene length, and isomers as compared to non-epi-lncRNAs. Further, the five pancreatic cancer-specific epi-lncRNA genes (AL161431.1, LINC00663, LINC00941, SNHG10, and TM4SF1-AS1) were identified. Based on these five pancreatic cancer-specific epis-lncRNAs, a prognostic model for pancreatic cancer was established. The RT-PCR result confirmed that AL161431.1, LINC00663, LINC00941, and SNHG10 expressions in pancreatic cancer samples were higher as compared to normal pancreatic samples; the expression of TM4SF1-AS1 in pancreatic cancer cells was significantly lower than that in normal pancreatic samples.

Conclusions: Epigenetic abnormalities could promote abnormal lncRNA expression in pancreatic cancer and may play an important role in its progression.

Construction and Analysis of lncRNA-Associated ceRNA Network in Atherosclerotic Plaque Formation

Atherosclerosis (AS) is a vascular disease with plaque formation. Unstable plaques can be expected to result in cardiovascular disease, such as myocardial infarction and stroke. Studies have verified that long noncoding RNAs (lncRNAs) play a critical role in atherosclerotic plaque formation (APF), including MALAT1, GAS5, and H19. A ceRNA network is a combination of these two interacting processes, which regulate the occurrence and progression of many diseases. However, lncRNA-associated ceRNA network in terms of APF is limited. This study sought to discover novel potential biomarkers and ceRNA network for APF. We designed a triple network based on the lncRNA-miRNA and mRNA-miRNA pairs obtained from lncRNASNP and starBase. Differentially expressed genes (DEGs) and lncRNAs in human vascular tissues derived from the Gene Expression Omnibus database (GSE43292, GSE97210) were systematically selected and analyzed. A ceRNA network was constructed by hypergeometric test, including 8 lncRNAs, 243 miRNAs, and 8 mRNAs. APF-related ceRNA structure was discovered for the first time by combining network analysis and statistical validation. Topological analysis determined the key lncRNAs with the highest centroid. GO and KEGG enrichment analysis indicated that the ceRNA network was primarily enriched in “regulation of platelet-derived growth factor receptor signaling pathway,” “negative regulation of leukocyte chemotaxis,” and “axonal fasciculation.” A functional lncRNA, HAND2-AS1, was identified in the ceRNA network, and the main miRNA (miRNA-570-3p) regulated by HAND2-AS1 was further screened. This present study elucidated the important function of lncRNA in the origination and progression of APF and indicated the potential use of these hub nodes as diagnostic biomarkers and therapeutic targets.

Characterization and Validation of ceRNA-Mediated Pathway–Pathway Crosstalk Networks Across Eight Major Cardiovascular Diseases

Pathway analysis is considered as an important strategy to reveal the underlying mechanisms of diseases. Pathways that are involved in crosstalk can regulate each other and co-regulate downstream biological processes. Furthermore, some genes in the pathways can function with other genes via the relationship of the competing endogenous RNA (ceRNA) mechanism, which has also been demonstrated to play key roles in cellular biology. However, the comprehensive analysis of ceRNA-mediated pathway crosstalk is lacking. Here, we constructed the landscape of the ceRNA-mediated pathway–pathway crosstalk of eight major cardiovascular diseases (CVDs) based on sequencing data from ∼2,800 samples. Some common features shared by numerous CVDs were uncovered. A fraction of the pathway–pathway crosstalk was conserved in multiple CVDs and a core pathway–pathway crosstalk network was identified, suggesting the similarity of pathway–pathway crosstalk among CVDs. Experimental evidence also demonstrated that the pathway crosstalk was functioned in CVDs. We split all hub pathways of each pathway–pathway crosstalk network into three categories, namely, common hubs, differential hubs, and specific hubs, which could highlight the common or specific biological mechanisms. Importantly, after a comparison analysis of the hub pathways of networks, ∼480 hub pathway-induced common modules were identified to exert functions in CVDs broadly. Moreover, we performed a random walk algorithm on the hub pathway-induced sub-network and identified 23 potentially novel CVD-related pathways. In summary, our study revealed the potential molecular regulatory mechanisms of ceRNA crosstalk in pathway–pathway crosstalk levels and provided a novel routine to investigate the pathway–pathway crosstalk in cardiology. All CVD pathway–pathway crosstalks are provided in http://www.licpathway.net/cepathway/index.html.

Transcriptome sequencing reveals a lncRNA-mRNA interaction network in extramammary Paget's disease

Background

Extramammary Paget’s disease (EMPD) is a rare malignant intraepidermal adenocarcinoma that is poorly understood. Regulatory long noncoding RNAs (lncRNAs) are characterized in many species and shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in different diseases, especially in cancer studies. In the present study, we used high-throughput sequencing to reveal the lncRNA–mRNA interaction network in extramammary Paget’s disease.

Methods

High-throughput sequencing was used to identify differentially expressed lncRNA and mRNA profiles between EMPD patients and healthy controls. Then, a series of bioinformatics analyses were conducted to construct the lncRNA–mRNA interaction network, which was finally confirmed in vitro.

Results

Six pairs of EMPD tumor and normal skin samples were collected and sequenced to identify the differentially expressed lncRNA and mRNA profiles between EMPD and healthy controls. A total of 997 differentially expressed mRNAs and 785 differentially expressed lncRNAs were identified. The GO and KEGG analyses show that epidermal development and cell adhesion play important roles in EMPD. The results of the lncRNA–mRNA interaction network analysis suggested that NEAT1, PGAP1, FKBP5 and CDON were the pivotal nodes of the network and that lncRNA NEAT1 might regulate mRNA PGAP1, FKBP5 and CDON. The results of the quantitative real-time RT–PCR performed in ten other patients for NEAT1, PGAP1, FKBP5 and CDON were consistent with those of the sequencing analysis. Moreover, an in vitro experiment confirmed the interactions between NEAT1 and PGAP1, FKBP5 and CDON in human immortalized keratinocytes.

Conclusion

These findings suggest that the lncRNA–mRNA interaction network based on four pivotal nodes, NEAT1, PGAP1 FKBP5 and CDON, may play an important role in EMPD, which will contribute to a deeper understanding of the pathogenesis of EMPD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-021-01135-2.

Emerging Advances of Non-coding RNAs and Competitive Endogenous RNA Regulatory Networks in Asthma

Asthma is a chronic inflammatory disease characterized by airway remodeling and bronchial hyperresponsiveness. A variety of effector cells and cytokines jointly stimulate the occurrence of inflammatory response in asthma. Although the pathogenesis of asthma is not entirely clear, the possible roles of non-coding RNAs (ncRNAs) have been recently demonstrated. NcRNAs are non-protein-coding RNA molecules, such as circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which are involved in the regulation of a variety of biological processes. Mounting studies have shown that ncRNAs play pivotal roles in the occurrence and progression of asthma via competing endogenous RNA (ceRNA) regulatory networks. However, the specific mechanism and clinical application of ncRNAs and ceRNA regulatory networks in asthma have not been fully elucidated, which are worthy of further investigation. This paper comprehensively summarized the current progress on the roles of miRNAs, lncRNAs, circRNAs, and ceRNA regulatory networks in asthma, which can provide a better understanding for the disease pathogenesis and is helpful for identifying novel biomarkers for asthma.

Construction and Characterization of Long Non-Coding RNA-Associated Networks to Reveal Potential Prognostic Biomarkers in Human Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) is one type of the malignant tumors with high morbidity and mortality. The molecular mechanism of LUAD is still unclear. Studies demonstrate that lncRNAs play crucial roles in LUAD tumorigenesis and can be used as prognosis biomarkers. Thus, in this study, to identify more robust biomarkers of LUAD, we firstly constructed LUAD-related lncRNA-TF network and performed topological analyses for the network. Results showed that the network was a scale-free network, and some hub genes with high clinical values were identified, such as lncRNA RP11-173A16 and TF ZBTB37. Module analysis on the network revealed one close lncRNA module, which had good prognosis performance in LUAD. Furthermore, through integrating ceRNAs strategy and TF regulatory information, we identified some lncRNA-TF positive feedback loops. Prognostic analysis revealed that ELK4- and BDP1-related feedback loops were significant. Secondly, we constructed the lncRNA-m6A regulator network by merging all the high correlated lncRNA-m6A regulator pairs. Based on the network analysis results, some key m6A-related lncRNAs were identified, such as MIR497HG, FENDRR, and RP1-199J3. We also investigated the relationships between these lncRNAs and immune cell infiltration. Results showed that these m6A-related lncRNAs were high correlated with tumor immunity. All these results provide a new perspective for the diagnostic biomarker and therapeutic target identification of LUAD.

A New Story of the Three Magi: Scaffolding Proteins and lncRNA Suppressors of Cancer

Scaffolding molecules exert a critical role in orchestrating cellular response through the spatiotemporal assembly of effector proteins as signalosomes. By increasing the efficiency and selectivity of intracellular signaling, these molecules can exert (anti/pro)oncogenic activities. As an archetype of scaffolding proteins with tumor suppressor property, the present review focuses on MAGI1, 2, and 3 (membrane-associated guanylate kinase inverted), a subgroup of the MAGUK protein family, that mediate networks involving receptors, junctional complexes, signaling molecules, and the cytoskeleton. MAGI1, 2, and 3 are comprised of 6 PDZ domains, 2 WW domains, and 1 GUK domain. These 9 protein binding modules allow selective interactions with a wide range of effectors, including the PTEN tumor suppressor, the β-catenin and YAP1 proto-oncogenes, and the regulation of the PI3K/AKT, the Wnt, and the Hippo signaling pathways. The frequent downmodulation of MAGIs in various human malignancies makes these scaffolding molecules and their ligands putative therapeutic targets. Interestingly, MAGI1 and MAGI2 genetic loci generate a series of long non-coding RNAs that act as a tumor promoter or suppressor in a tissue-dependent manner, by selectively sponging some miRNAs or by regulating epigenetic processes. Here, we discuss the different paths followed by the three MAGIs to control carcinogenesis.

Long non-coding RNAs in cardiac hypertrophy

Cardiac hypertrophy (CH) is generally considered adaptive responses that may occur after myocardial infarction, pressure overload, volume overload, inflammatory heart muscle disease, or idiopathic dilated cardiomyopathy, whereas long-term stimulation eventually leads to heart failure (HF). However, the current molecular mechanisms involved in CH are unclear. Recently, increasing evidences reveal that long non-coding RNAs (lncRNAs) play vital roles in CH. Different lncRNAs can promote or inhibit the pathological process of CH by different mechanisms, while the regulation of lncRNAs expression can improve CH. Thus, CH-related lncRNAs may become a novel field of research on CH.

Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis

Background: Atrial fibrillation (AF) is the most common arrhythmia. We aimed to construct competing endogenous RNA (ceRNA) networks associated with the susceptibility and persistence of AF by applying the weighted gene co-expression network analysis (WGCNA) and prioritize key genes using the random walk with restart on multiplex networks (RWR-M) algorithm.

Methods: RNA sequencing results from 235 left atrial appendage samples were downloaded from the GEO database. The top 5,000 lncRNAs/mRNAs with the highest variance were used to construct a gene co-expression network using the WGCNA method. AF susceptibility- or persistence-associated modules were identified by correlating the module eigengene with the atrial rhythm phenotype. Using a module-specific manner, ceRNA pairs of lncRNA–mRNA were predicted. The RWR-M algorithm was applied to calculate the proximity between lncRNAs and known AF protein-coding genes. Random forest classifiers, based on the expression value of key lncRNA-associated ceRNA pairs, were constructed and validated against an independent data set.

Results: From the 21 identified modules, magenta and tan modules were associated with AF susceptibility, whereas turquoise and yellow modules were associated with AF persistence. ceRNA networks in magenta and tan modules were primarily involved in the inflammatory process, whereas ceRNA networks in turquoise and yellow modules were primarily associated with electrical remodeling. A total of 106 previously identified AF-associated protein-coding genes were found in the ceRNA networks, including 16 that were previously implicated in the genome-wide association study. Myocardial infarction–associated transcript (MIAT) and LINC00964 were prioritized as key lncRNAs through RWR-M. The classifiers based on their associated ceRNA pairs were able to distinguish AF from sinus rhythm with respective AUC values of 0.810 and 0.940 in the training set and 0.870 and 0.922 in the independent test set. The AF-related single-nucleotide polymorphism rs35006907 was found in the intronic region of LINC00964 and negatively regulated the LINC00964 expression.

Conclusion: Our study constructed AF susceptibility- and persistence-associated ceRNA networks, linked genetics with epigenetics, identified MIAT and LINC00964 as key lncRNAs, and constructed random forest classifiers based on their associated ceRNA pairs. These results will help us to better understand the mechanisms underlying AF from the ceRNA perspective and provide candidate therapeutic and diagnostic tools.

Identification of functional lncRNAs through constructing a lncRNA-associated ceRNA network in myocardial infarction

Myocardial infarction (MI) is a type of coronary heart disease, which refers to the ischemic necrosis of the heart muscle. A large number of studies have discussed the mechanism of MI from the perspective of competing endogenous RNA (ceRNA) network. However, the mechanisms underlying the function of lncRNAs in MI have still not been explained in an explicit manner. Therefore, we constructed a scale-free lncRNA-associated ceRNA network to identify some crucial lncRNAs in MI. Results showed that the given disease genes for MI were involved in the network, the degrees of which were significantly larger than the other nodes of the network. For measuring the network centrality, we then constructed a hub subnetwork. The miRNAs and mRNAs in the hub subnetwork have been validated to function in MI-related biological function. In addition, we identified 2 MI-related functional modules from the lncRNA-associated ceRNA network, which suggested that lncRNA exerted function in local network. Enrichment analysis showed that these functional modules corresponded to some similar and different pathways related to cardiovascular disease. More importantly, 3 MI-related crucial lncRNAs, CTD-3092A11.2, RP5-821D11.7 and CTC-523E23.1 were detected as potential biomarkers, which may be involved in MI-related biological progresses. Our study identified 20 functional lncRNAs based on ceRNA network analysis, which may provide novel diagnosis and therapeutic targets for MI from the ceRNA network perspective.

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.

Bioinformatics-Based Analysis of the lncRNA-miRNA-mRNA Network and TF Regulatory Network to Explore the Regulation Mechanism in Spinal Cord Ischemia/Reperfusion Injury

Background

Spinal cord ischemia/reperfusion injury (SCII) is a catastrophic complication involved with cardiovascular, spine, and thoracic surgeries and can lead to paraplegia. Nevertheless, the molecular mechanism of SCII remain ill-defined.

Methods

Expression profiling (GSE138966) data were obtained from GEO database. Then, differentially expressed (DE) lncRNAs and DEmRNAs were screened out with p < 0.05, and | fold change| > 1.5. Aberrant miRNAs expression in SCII was obtained from PubMed. Functional enrichment analysis of overlapping DEmRNAs between predicted mRNAs in miRDB database and DEmRNAs obtained from GSE138966 was performed using cluster Profiler R package. The lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network was established in light of ceRNA theory. The key lncRNAs in the ceRNA network were identified by topological analysis. Subsequently, key lncRNAs related ceRNA-pathway network and transcription factors (TFs)-mRNAs network were constructed. Simultaneously, the expression levels of hub genes were measured via qRT-PCR.

Results

The results in this study indicated that 76 miRNAs, 1373 lncRNAs, and 4813 mRNAs were differentially expressed in SCII. A SCII-related ceRNA network was constructed with 154 ncRNAs, 139 mRNAs, and 51 miRNAs. According topological analysis, six lncRNAs (NONRATT019236.2, NONRATT009530.2, NONRATT026999.2, TCONS_00032391, NONRATT023112.2, and NONRATT021956.2) were selected to establish the ceRNA-pathway network, and then two candidate hub lncRNAs (NONRATT009530.2 and NONRATT026999.2) were identified. Subsequently, two lncRNA-miRNA-mRNA regulatory axes were identified. NONRATT026999.2 and NONRATT009530.2 might involve SCII via miR-20b-5p/Map3k8 axis based on the complex ceRNA network. SP1 and Hnf4a acting as important TFs might regulate Map3k8. Furthermore, qRT-PCR results showed that the NONRATT009530.2, NONRATT026999.2, Map3k8, Hfn4a, and SP1 were significantly upregulated in SCII of rats, while the miR-20b-5p was downregulated.

Conclusion

Our results offer a new insight to understand the ceRNA regulation mechanism in SCII and identify highlighted lncRNA-miRNA-mRNA axes and two key TFs as potential targets for prevention and treatment of SCII.

Determination of the key ccRCC-related molecules from monolayer network to three-layer network

Clear cell renal cell carcinoma (ccRCC), with an increasing incidence rate, is one of the ubiquitous cancers. Its pathogenic factors are complicated and the molecular mechanism is not clear. It is essential to analyze the potential key genes related to ccRCC carcinogenesis. In this study, the differentially expressed mRNAs, miRNAs and lncRNAs (DEmRNAs, DEmiRNAs and DElncRNAs) of ccRCC were screened from TCGA database. Then the miRNA-mRNA network, lncRNA-miRNA network and lncRNA-mRNA network were constructed by online database or WGCNA algorithm. Topology attributes of these monolayer networks showed that hsa-mir-155, hsa-mir-200c, hsa-mir-122, hsa-mir-506, hsa-mir-216b, hsa-mir-141, lncRNA AC137723.1 and AC021074.3 are the crucial genes related with the regulatory effects on the proliferation, metastasis and invasion of ccRCC cells. Subsequently, these three monolayer networks were integrated into a lncRNA-miRNA-mRNA multilayer network. Considering node degree, closeness centrality and betweenness centrality, we found hsa-mir-122 is screened out as the only crucial gene in three-layer network. In order to better illustrate the effect of hsa-mir-122 on ccRCC, the lncRNA-hsa-mir-122-mRNA network was constructed with hsa-mir-122 as the center. Pathway analysis of the unique target gene GALNT3 linked to hsa-mir-122 showed that GALNT3 influenced the metabolic process of mucin type O-Glycan biosynthesis. LncRNA AC090377.1 is the unique gene that has target genes among lncRNAs with clinical significance that linked to hsa-mir-122 in the lncRNA-hsa-mir-122-mRNA network. Pathway analysis of AC090377.1 suggested that GUCY2F enriched in phototransduction pathway associated with retina. From monolayer network to three-layer network, hsa-mir-122 is identified as an important molecule in the oncogenesis and progression of ccRCC, offering new strategies to further study of the carcinogenic mechanism of ccRCC.

Transcriptome analysis reveals key pathways that vary in patients with paroxysmal and persistent atrial fibrillation

The present study evaluated mRNA and long non-coding RNA (lncRNA) expression profiles and the pathways involved in paroxysmal atrial fibrillation (ParoAF) and persistent atrial fibrillation (PersAF). Nine left atrial appendage (LAA) tissues collected from the hearts of patients with AF (patients with ParoAF=3; and patients with PersAF=3) and healthy donors (n=3) were analyzed by RNA sequencing. Differentially expressed (DE) mRNAs and lncRNAs were identified by |Log₂ fold change|>2 and P<0.05. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway enrichment, protein-protein interaction network and mRNA-lncRNA interaction network analyses of DE mRNA and mRNA at the upstream/downstream of DE lncRNA were conducted. A total of 285 and 275 DE mRNAs, 575 and 583 DE lncRNAs were detected in ParoAF and PersAF samples compared with controls, respectively. PI3K/Akt and transforming growth factor-β signaling pathways were significantly enriched in the ParoAF_Control and the calcium signaling pathway was significantly enriched in the PersAF_Control. Cis and trans analyses revealed some important interactions in DE mRNAs and lncRNA, including an interaction of GPC-AS2 with dopachrome tautomerase, and phosphodiesterase 4D and cAMP-specific with XLOC_110310 and XLOC_137634. Overall, the present study provides a molecular basis for future clinical studies on ParoAF and PersAF.

Construction of a ceRNA-based lncRNA-mRNA network to identify functional lncRNAs in polycystic ovarian syndrome

Polycystic ovary syndrome (PCOS) is a prevalent endocrine and metabolic disorder in women of childbearing age. Recent studies suggest important roles for lncRNAs in PCOS development. Based on the hypothesis that lncRNAs are able to regulate mRNA functions by competitive binding to shared miRNAs, the present work sought to construct a PCOS-related lncRNA-mRNA network (PCLMN) to identify key lncRNAs with dysregulated expression and potential prognostic and therapeutic relevance. A global background network was constructed after retrieving lncRNA-miRNA and miRNA-mRNA pairs from the lncRNASNP2, miRTarBase and StarBase databases. Based on gene expression profiles from ovarian granulosa cells from PCOS patients and controls in the GEO’s GSE95728 dataset, the PCLMN was then constructed by applying hypergeometric testing. Using topological analysis, we identified 3 lncRNAs (LINC00667, AC073172.1 and H19) ranking within the top-ten gene lists for all three centrality measures. We then explored their subcellular localization, performed functional module analyses, and identified 4 sex hormone-related transcription factors as potential regulators of their expression. Significant associations with inflammation, oxidative stress, and apoptosis-related processes and pathways were revealed for the key lncRNAs in our PCMLN. Further studies verifying the mRNA/lncRNA relationships identified herein are needed to clarify their clinical significance.

Inhibition of lncRNA Gm15834 Attenuates Autophagy-Mediated Myocardial Hypertrophy via the miR-30b-3p/ULK1 Axis in Mice

Emerging evidence reveals that autophagy plays crucial roles in cardiac hypertrophy. Long noncoding RNAs (lncRNAs) are novel transcripts that function as gene regulators. However, it is unclear whether lncRNAs regulate autophagy in cardiac hypertrophy. Here, we identified a novel transcript named lncRNA Gm15834, which was upregulated in the transverse aortic constriction (TAC) model in vivo and the angiotensin-II (Ang-II)-induced cardiac hypertrophy model in vitro and was regulated by nuclear factor kappa B (NF-κB). Importantly, forced expression of lncRNA Gm15834 enhanced autophagic activity of cardiomyocytes and promoted myocardial hypertrophy, whereas silencing of lncRNA Gm15834 attenuated autophagy-induced myocardial hypertrophy. Mechanistically, we found that lncRNA Gm15834 could function as an endogenous sponge RNA of microRNA (miR)-30b-3p, which was downregulated in cardiac hypertrophy. Inhibition of miR-30b-3p enhanced cardiomyocyte autophagic activity and aggravated myocardial hypertrophy, whereas overexpression of miR-30b-3p suppressed autophagy-induced myocardial hypertrophy by targeting the downstream autophagy factor of unc-51-like kinase 1 (ULK1). Moreover, inhibition of lncRNA Gm15834 by adeno-associated virus carrying short hairpin RNA (shRNA) suppressed cardiomyocyte autophagic activity, improved cardiac function, and mitigated cardiac hypertrophy. Taken together, our study identified a novel regulatory axis encompassing lncRNA Gm15834/miR-30b-3p/ULK1/autophagy in cardiac hypertrophy, which may provide a potential therapy target for cardiac hypertrophy.

MiR-128-3p Alleviates Spinal Cord Ischemia/Reperfusion Injury Associated Neuroinflammation and Cellular Apoptosis via SP1 Suppression in Rat

BACKGROUND

Neuroinflammation and cellular apoptosis caused by spinal cord ischemia/reperfusion (I/R) injury result in neurological dysfunction. MicroRNAs (miRs) have crucial functions in spinal cord I/R injury pathogenesis according to previous evidences. Herein, whether miR-128-3p contributes to spinal cord I/R injury by regulating specificity protein 1 (SP1) was assessed.

METHODS

A rat model of spinal cord I/R injury was established by occluding the aortic arch for 14 min. Then, miR-128-3p's interaction with SP1 was detected by dual-luciferase reporter assays. Next, miR-128-3p mimic and inhibitor, as well as adenovirus-delivered shRNA specific for SP1 were injected intrathecally for assessing the effects of miR-128-3p and SP1 on rats with spinal cord I/R injury. SP1, Bax and Bcl-2 expression levels in I/R injured spinal cord tissues were evaluated by Western blotting, while IL-1β, TNF-α, and IL-6 were quantitated by ELISA. Tarlov scores were obtained to detect hind-limb motor function. Evans blue (EB) dye extravasation was utilized to examine blood-spinal cord barrier (BSCB) permeability. Terminal deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL) staining was performed for neuronal apoptosis assessment.

RESULTS

MiR-128-3p expression was decreased, while SP1 amounts were increased in rat spinal cord tissue specimens following I/R. SP1 was identified as a miR-128-3p target and downregulated by miR-128-3p. MiR-128-3p overexpression or SP1 silencing alleviated I/R-induced neuroinflammation and cell apoptosis, and improved Tarlov scores, whereas pretreatment with miR-128-3p inhibitor aggravated the above injuries.

CONCLUSION

Overexpression of miR-128-3p protects neurons from neuroinflammation and apoptosis during spinal cord I/R injury partially by downregulating SP1.

Long non-coding RNA CCAT1 sponges miR-490 to enhance cell proliferation and migration of non-small cell lung cancer

Background

Non‐small cell lung cancer (NSCLC) accounts for 85% of lung cancer which is the most frequently diagnosed malignancy in China. Colon cancer associated transcript 1 (CCAT1) acts as an oncogene in enhancing tumor progression. However, the effects of CCAT1 in NSCLC remain unclear. The purpose of this study was to explore the role of CCAT1 in NSCLC.

Methods

Wound healing and transwell assays were performed to measure cell migration. RT‐qPCR was employed to calculate the mRNA level of CCAT1 and miR‐490.

Results

High expression of CCAT1 was observed in NSCLC tissues and cells, with low expression of miR‐490. CCAT1 promoted the proliferation and metastasis of H1299 and A549 cells, while miR‐490 had the opposite effect. CCAT1 could specifically bind to miR‐490 and regulate its expression. MiR‐490 partially reversed the inhibitory effect of CCAT1 on cell proliferation and metastasis.

Conclusions

The CCAT1/miR‐490 molecular axis has been shown to be important for the treatment of NSCLC.

Knockdown of Long Non-Coding RNA AFAP1-AS1 Promoted Viability and Suppressed Death of Cardiomyocytes in Response to I/R In Vitro and In Vivo

Long non-coding RNA (lncRNA) plays a pivotal role in the development of myocardial infarction (MI). The aim of this study was to investigate the effects of lncRNA actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) on cell cycle, proliferation, and apoptosis. RT-qPCR was used to detect the expression levels of AFAP1-AS1, miR-512-3p, and reticulon 3 (RTN3) in rat model of I/R. The simulated MI environment was constructed. MTT assay and flow cytometry were used to detect changes in cardiomyocyte viability and cell cycle/apoptosis after MI by AFAP1-AS1 silencing or RTN3 silencing. The targeting relationship of miR-512-3p and AFAP1-AS1 and RTN3 in cardiomyocytes was verified by dual luciferase reporter assay. The expression levels of AFAP1-AS1 and RTN3 were significantly upregulated in a rat model of LAD ligation (or MI) ligation, while the expression level of miR-512-3p was significantly reduced. Overexpressed AFAP1-AS1 and RTN3 promoted cardiomyocyte apoptosis and inhibited cardiomyocyte proliferation. MiR-512-3p was a direct target of AFAP1-AS1, and RTN3 was a direct target of miR-512-3p. AFAP1-AS1 promoted the progression of MI by targeting miR-512-3p. AFAP1-AS1 promoted the progression of MI by modulating the miR-512-3p/RTN3 axis. AFAP1-AS1 may be a potential therapy target for MI. Graphical Abstract The role of AFAP1-AS1 in regulating MI injury in vivo. (A) Effect of AFAP1-AS1 in MI injury in vivo. (B) The mRNA level of RTN3 in MI injury in vivo. (C) The protein level of RTN3 in MI injury in vivo. (D) Effect of miR-512-3p in MI model group. (E) TUNEL assay. *P < 0.05, **P < 0.01 vs the sham group; #P < 0.05, ##P < 0.01 vs the MI group.

Replication Study: Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs

As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Phelps et al., 2016) that described how we intended to replicate selected experiments from the paper 'Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs' (Tay et al., 2011). Here, we report the results. We found depletion of putative PTEN competing endogenous mRNAs (ceRNAs) in DU145 cells did not impact PTEN 3'UTR regulation using a reporter, while the original study reported decreased activity when SERINC1, VAPA, and CNOT6L were depleted (Figure 3C; Tay et al., 2011). Using the same reporter, we found decreased activity when ceRNA 3'UTRs were overexpressed, while the original study reported increased activity (Figure 3D; Tay et al., 2011). In HCT116 cells, ceRNA depletion resulted in decreased PTEN protein levels, a result similar to the findings reported in the original study (Figure 3G,H; Tay et al., 2011); however, while the original study reported an attenuated ceRNA effect in microRNA deficient (Dicer^Ex5) HCT116 cells, we observed increased PTEN protein levels. Further, we found depletion of the ceRNAs VAPA or CNOT6L did not statistically impact DU145, wild-type HCT116, or Dicer^Ex5 HCT116 cell proliferation. The original study reported increased DU145 and wild-type HCT116 cell proliferation when these ceRNAs were depleted, which was attenuated in the Dicer^Ex5 HCT116 cells (Figure 5B; Tay et al., 2011). Differences between the original study and this replication attempt, such as variance between biological repeats, are factors that might have influenced the results. Finally, we report meta-analyses for each result.

The roles of long noncoding RNAs in myocardial pathophysiology

Long noncoding RNAs (lncRNAs), more than 200 nt in length, are functional molecules found in various species. These lncRNAs play a vital role in cell proliferation, differentiation, and degeneration and are also involved in pathophysiological processes of cancer and neurodegenerative, autoimmune, and cardiovascular diseases (CVDs). In recent years, emerging challenges for intervention studies on ischemic heart diseases have received much attention. LncRNAs have a key function in the alleviation of myocardial infarction (MI) injury and myocardial ischemia–reperfusion injury. During cardiac hypertrophy (CH) and fibrosis, cardiac cells undergo structural changes and become dysfunctional due to the effects of neurohormonal factors. LncRNAs may serve as important therapeutic targets that promote cardiac remodeling and then retard the development of heart failure (HF). In addition, studies on the roles and mechanisms of action of lncRNAs participating in cardiac pathophysiology via other factors have become the focus of research worldwide. Here, we review the current knowledge on various lncRNAs and their functions in cardiac biology, particularly concentrating on ischemic heart disease, CH, and cardiac fibrosis. We next discuss the predictive value of lncRNAs as diagnostic biomarkers of CVDs.

Comparative genome-wide DNA methylation analysis in myocardial tissue from donors with and without Down syndrome

Down syndrome (DS, trisomy 21) is the most common major chromosomal aneuploidy compatible with life. The additional whole or partial copy of chromosome 21 results in genome-wide imbalances that drive the complex pathobiology of DS. Differential DNA methylation in the context of trisomy 21 may contribute to the variable architecture of the DS phenotype. The goal of this study was to examine the genomic DNA methylation landscape in myocardial tissue from non-fetal individuals with DS. >480,000 unique CpG sites were interrogated in myocardial DNA samples from individuals with (n = 12) and without DS (n = 12) using DNA methylation arrays. A total of 93 highly differentially methylated CpG sites and 16 differentially methylated regions were identified in myocardial DNA from subjects with DS. There were 18 differentially methylated CpG sites in chromosome 21, including 5 highly differentially methylated sites. A CpG site in the RUNX1 locus was differentially methylated in DS myocardium, and linear regression suggests that donors' age, gender, DS status, and RUNX1 methylation may contribute up to ~51% of the variability in RUNX1 mRNA expression. In DS myocardium, only 58% of the genes overlapping with differentially methylated regions codify for proteins with known functions and 24% are non-coding RNAs. This study provides an initial snapshot on the extent of genome-wide differential methylation in myocardial tissue from persons with DS.

FOXD3-AS1 Knockdown Suppresses Hypoxia-Induced Cardiomyocyte Injury by Increasing Cell Survival and Inhibiting Apoptosis via Upregulating Cardioprotective Molecule miR-150-5p In Vitro

Congenital heart disease (CHD) is the most common type of human innate malformation in fetuses. LncRNAs have been pointed to play critical regulatory roles in various types of cardiac development and diseases including CHD. Our study aimed to explore the effects of lncRNA forkhead box D3 antisense RNA 1 (FOXD3-AS1) on hypoxia-induced injury in AC16 cardiomyocytes and the related molecular mechanism. In vitro cell model of CHD was established by stimulating AC16 cells with hypoxia (1% O₂). Expression of FOXD3-AS1 and miR-150-5p was detected by qRT-PCR. Hypoxia-induced injury was evaluated by detecting cell survival, lactate dehydrogenase (LDH) release, apoptosis, and caspase-3/7 activity using MTT, LDH assay, flow cytometry analysis, and caspase-3/7 activity assay, respectively. The regulatory relationship between FOXD3-AS1 and miR-150-5p was explored by luciferase reporter assay, RNA immunoprecipitation (RIP), and qRT-PCR. Results showed that hypoxia exposure caused an upregulation of FOXD3-AS1 and a downregulation of miR-150-5p in AC16 cells. Knockdown of FOXD3-AS1 attenuated reduction of cell survival and increase of LDH release, apoptosis, caspase-3/7 activity, and Bcl-2 associated X (Bax) expression induced by hypoxia in AC16 cells. Notably, we demonstrated that FOXD3-AS1 directly interacted with miR-150-5p to inhibit its expression. miR-150-5p knockdown reinforced the reduction of survival and induction of apoptosis by hypoxia and attenuated the effects of FOXD3-AS1 silencing on the same parameters in AC16 cells. In conclusion, FOXD3-AS1 knockdown protected AC16 cardiomyocytes from hypoxia-induced injury by increasing cell survival and inhibiting apoptosis through upregulating miR-150-5p.

LINC-PINT suppresses tumour cell proliferation, migration and invasion through targeting miR-374a-5p in ovarian cancer

LncRNA LINC-PINT acts as an important regulator in the development of many cancers. The current study aimed to explore the role of LINC-PINT in the progression of ovarian cancer (OC). LINC-PINT expression level in different FIGO stages of OC and its adjacent tissues, normal HOSE and OC cell lines (A2780, SKOV3, OVCAR3 and HO-8910) was determined by qRT-PCR. Survival analysis on LINC-PINT and OC patients was conducted by Kaplan-Meier. CCK-8, flow cytometry, wound-healing, Transwell assays and western blot were performed to detect the effects of LINC-PINT on proliferation, apoptosis, migration, invasion and EMT process in OC cells. Target gene of LINC-PINT was predicted by Starbase and verified by dual-luciferase reporter assay. The expression of miR-374a-5p in normal and OC tissues, LINC-PINT- or siLINC-PINT-modified OC cells was determined. Moreover, rescue assay was carried out to confirm whether LINC-PINT contributes to the development of OC cells through targeting miR-374a-5p. Low expression of LINC-PINT was observed in OC tissues and cells, noticeably, LINC-PINT expression was even lower in OC tissues with higher FIGO stage. Increased LINC-PINT expression significantly inhibited cell proliferation, promoted apoptosis and suppressed migration, invasion and EMT process, while silencing of LINC-PINT caused the opposite results. Moreover, LINC-PINT sponged miR-374a-5p and overexpressed miR-374a-5p attenuated the effect of up-regulated LINC-PINT on cell viability, migration, invasion and apoptosis. LINC-PINT acts as a tumour suppressor, as it could inhibit cell proliferation, migration, invasion and EMT process, and promote cell apoptosis through down-regulating miR-374a-5p. SIGNIFICANCE OF THE STUDY: Ovarian cancer (OC), which is a frequently diagnosed tumour in female reproductive organs, has a high incidence rate behind cervical cancer and endometrial cancer. LncRNA LINC-PINT acts as an important regulator in the development of many cancers. The current study aimed to explore the role of LINC-PINT in the progression of ovarian cancer (OC) and found that LINC-PINT inhibited cell proliferation, migration invasion and EMT process of OC cell via regulating miR-374a-5p; it might be a potential target for OC treatment.

Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story

MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.

Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer

Background

A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains unclear.

Methods

Based on the competitive endogenous RNA (ceRNA) theory, we constructed a lncRNA-miRNA-mRNA network in oral cancer with the human expression profiles GSE74530 from the Gene Expression Omnibus (GEO) database. We used topological analysis to determine the hub lncRNAs in the regulatory ceRNA network. Then, function enrichment analysis was performed using the clusterProfiler R package. Clinical information was downloaded from The Cancer Genome Atlas (TCGA) database and survival analysis was performed with Kaplan-Meier analysis.

Results

A total of 238 potential co-dysregulated competing triples were obtained in the lncRNA-associated ceRNA network in oral cancer, which consisted of 10 lncRNA nodes, 41 miRNA nodes and 122 mRNA nodes. Additionally, we found lncRNA HCG22 exhibiting superior potential as a diagnostic and prognostic marker of oral cancer.

Conclusions

Our findings provide novel insights to understand the ceRNA regulation in oral cancer and identify a novel lncRNA as a potential molecular biomarker.

Two way network construction and analysis of mRNA, miRNA and lncRNA reveals critical regulators and regulatory modules in cardiovascular diseases

BACKGROUND

Cardiovascular diseases contribute to the leading cause of deaths (31%) in the world population.

OBJECTIVE

The objective of this study is to compile non-coding RNA-gene interaction into a core regulatory network whose dysregulation might play an important role in disease progression.

METHOD

We applied a structured approach to reconstruct the interaction network of lncRNAs, miRNAs and genes involved in cardiovascular diseases. For network construction, we used 'diseasome to interactome' and 'interactome to diseasome' approaches and developed two regulatory networks in heart disorders. In diseasome to interactome approach, starting from a disease-centric network we, expanded the data into an interaction network. However in interactome to diseasome, we used a set of guide genes, miRNAs and lncRNAs to arrive at the common diseases. The disease-centric network in combination with the interaction network will shed light on the interconnected components in a huge diseasome network implicated in heart disorders and manifested through small sub-networks while progressing. Using the above networks we created a sub-networks consisting only of hub genes, miRNAs and lncRNAs on both approaches. The dysregulation of any one of the hubs can lead to a disease condition.

RESULTS

The top ranking hubs common in both the sub-networks were found to be VEGFA, MALAT1, HOTAIR, H19 and hsa-miR-15a. Our network based study reveals an entanglement of regulatory sub-network of miRNAs, lncRNAs and genes in multiple conditions.

CONCLUSION

The identification of hubs in the core triple node network of elements in disease development and progression demonstrates a promising role for network based approaches in targeting critical molecules for drug development.

In Silico Analysis Identifies Differently Expressed lncRNAs as Novel Biomarkers for the Prognosis of Thyroid Cancer

Background

Thyroid cancer (TC) is one of the most common type of endocrine tumors. Long noncoding RNAs had been demonstrated to play key roles in TC. Material and Methods. The lncRNA expression data were downloaded from Co-lncRNA database. The raw data was normalized using the limma package in R software version 3.3.0. The differentially expressed mRNA and lncRNAs were identified by the linear models for the microarray analysis (Limma) method. The DEGs were obtained with thresholds of ∣logFC∣ > 1.5 and P < 0.001. The hierarchical cluster analysis of differentially expressed mRNAs and lncRNAs was performed using CLUSTER 3.0, and the hierarchical clustering heat map was visualized by Tree View.

Results

In the present study, we identified 6 upregulated and 85 downregulated lncRNAs in TC samples. Moreover, we for the first time identified 16 downregulated lncRNAs was correlated to longer disease-free survival time in patients with TC, including ATP1A1-AS1, CATIP-AS1, FAM13A-AS1, LINC00641, LINC00924, MIR22HG, NDUFA6-AS1, RP11-175K6.1, RP11-727A23.5, RP11-774O3.3, RP13-895J2.2, SDCBP2-AS1, SLC26A4-AS1, SNHG15, SRP14-AS1, and ZNF674-AS1.

Conclusions

Bioinformatics analysis revealed these lncRNAs were involved in regulating the RNA metabolic process, cell migration, organelle assembly, tRNA modification, and hormone levels. This study will provide useful information to explore the potential candidate biomarkers for diagnosis, prognosis, and drug targets for TC.

Identifying lncRNA and mRNA Co-Expression Modules from Matched Expression Data in Ovarian Cancer

Long non-coding RNAs (lncRNAs) have been shown to be involved in multiple biological processes and play critical roles in tumorigenesis. Numerous lncRNAs have been discovered in diverse species, but the functions of most lncRNAs still remain unclear. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood. With the advances of high-throughput technologies, the increasing availability of genomic data creates opportunities for deciphering the molecular mechanism and underlying pathogenesis of human diseases. Here, we develop an integrative framework called JONMF to identify lncRNA-mRNA co-expression modules based on the sample-matched lncRNA and mRNA expression profiles. We formulate the module detection task as an optimization problem with joint orthogonal non-negative matrix factorization that could effectively prevent multicollinearity and produce a good modularity interpretation. The constructed lncRNA-mRNA co-expression network and the gene-gene interaction network are used as the network-regularized constraints to improve the module accuracy, while the sparsity constraints are simultaneously utilized to achieve modular sparse solutions. We applied JONMF to human ovarian cancer dataset and the experiment results demonstrate that the proposed method can effectively discover biologically functional co-expression modules, which may provide insights into the function of lncRNAs and molecular mechanism of human diseases.

Network and pathway-based analyses of genes associated with osteoporosis

Osteoporosis (OP) is a disease characterized by bone mass loss, bone microstructure damage, increased bone fragility, and easy fracture. The molecular mechanism underlying OP remains unclear.In this study, we identified 217 genes associated with OP, and formed a gene set [OP-related genes gene set (OPgset)].The highly enriched GOs and pathways showed OPgset genes were significantly involved in multiple biological processes (skeletal system development, ossification, and osteoblast differentiation), and several OP-related pathways (Wnt signaling pathway, osteoclast differentiation, steroid hormone biosynthesis, and adipocytokine signaling pathway). Besides, pathway crosstalk analysis indicated three major modules, with first module consisted of pathways mainly involved in bone development-related signaling pathways, second module in Wnt-related signaling pathway and third module in metabolic pathways. Further, we calculated degree centrality of a node and selected ten key genes/proteins, including TGFB1, IL6, WNT3A, TNF, PTH, TP53, WNT1, IGF1, IL10, and SERPINE1. We analyze the K-core and construct three k-core sub-networks of OPgset genes.In summary, we for the first time explored the molecular mechanism underlying OP via network- and pathway-based methods, results from our study will improve our understanding of the pathogenesis of OP. In addition, these methods performed in this study can be used to explore pathogenesis and genes related to a specific disease.

MiR-3940-5p promotes granulosa cell proliferation through targeting KCNA5 in polycystic ovarian syndrome

Increased granulosa cell (GC) proliferation may contribute to abnormal folliculogenesis in patients with polycystic ovary syndrome (PCOS), which affects approximately 10% reproductive aged women. However, the mechanisms underlying increased GC proliferation in PCOS remain incompletely understood. In this study, we identified miR-3940-5p as a hub miRNA in GC from PCOS using weighted gene co-expression network analysis (WGCNA), and real-time polymerase chain reaction (RT-PCR) analysis confirmed that miR-3940-5p was significantly increased in GC from PCOS. Enrichment analysis of predicted target genes of miR-3940-5p indicated potential roles of miR-3940-5p in follicular development and cell proliferation regulation. Consistently, functional study confirmed that miR-3940-5p overexpression promoted granulosa cell proliferation. Integrated analysis of mRNA expression profiling data and predicted target genes of miR-3940-5p identified potassium voltage-gated channel subfamily A member 5 (KCNA5) as a potential target of miR-3940-5p, and was validated by luciferase reporter assay. Finally, functional analysis suggested that miR-3940-5p promoted GC proliferation in a KCNA5 dependent manner. In conclusion, miR-3940-5p was a hub miRNA upregulated in GC from PCOS, and promoted GC proliferation by targeting KCNA5.

LncRNA SNHG1 exerts a protective role in cardiomyocytes hypertrophy via targeting miR-15a-5p/HMGA1 axis

Heart failure preceded by pathological cardiac hypertrophy is a leading cause of death. Long noncoding RNA small nucleolar RNA host gene 1 (SNHG1) was reported to inhibit cardiomyocytes apoptosis, but the role and underlying mechanism of SNHG1 in pathological cardiac hypertrophy have not yet been understood. This study was designed to investigate the role and molecular mechanism of SNHG1 in regulating cardiac hypertrophy. We found that SNHG1 was upregulated during cardiac hypertrophy both in vivo (transverse aortic constriction treatment) and in vitro (phenylephrine [PE] treatment). SNHG1 overexpression attenuated the cardiomyocytes hypertrophy induced by PE, while SNHG1 inhibition promoted hypertrophic response of cardiomyocytes. Furthermore, SNHG1 and high-mobility group AT-hook 1 (HMGA1) were confirmed to be targets of miR-15a-5p. SNHG1 promoted HMGA1 expression by sponging miR-15a-5p, eventually attenuating cardiomyocytes hypertrophy. There data revealed a novel protective mechanism of SNHG1 in cardiomyocytes hypertrophy. Thus, targeting of SNHG1-related pathway may be therapeutically harnessed to treat cardiac hypertrophy.

Integrative analysis reveals essential mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) in paroxysmal and persistent atrial fibrillation patients

OBJECTIVE

This study aimed to investigate the functions of mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) in paroxysmal and persistent atrial fibrillation (AF) patients.

METHODS

A total of 9 left atrial appendage (LAA) tissues were collected from patients with AF (ParoAF patients = 3 and PersAF patients = 3) and donors (n=3). Genes and circRNAs were identified by per kilobase per million reads (RPKM) and number of circular reads/number of mapped reads/read length (SRPBM), respectively. Differentially expressed mRNAs (DE mRNAs), lncRNAs (DE lncRNAs), and circRNAs (DE circRNAs) were identified by | log2 (Fold Change) | ≥ 2 and p-value < 0.05. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Protein-protein, mRNA-lncRNA, and circRNA-miRNA interaction networks were constructed. In addition, logistic analysis was conducted among AF and circRNAs.

RESULTS

A total of 285 (116 up-regulated and 169 down-regulated) and 275 (110 up-regulated and 165 down-regulated) DE mRNAs, 575 (276 up-regulated and 299 down-regulated) and 583 (330 up-regulated and 253 down-regulated) DE lncRNAs, and 83 (48 up-regulated and 35 down-regulated) and 99 (58 up-regulated and 41 down-regulated) circRNAs were detected in ParoAF and PersAF, respectively, as compared with control. MAPK signal pathway as well as voltage-dependent, L type, and alpha 1C subunit calcium channel (CACNA1C) might participate in AF occurrence by preventing atrial parasympathetic remodeling. Collagen type I alpha 1 (COL1A1) and COL1A2 mostly participated in the enriched GO and KEGG terms and connected with most of the DE mRNAs. The expression of chr10: 69902697|69948883 was a protective factor against PersAF after adjusting for age (p=0.022, 95% CI: 0.003-0.634).

CONCLUSION

We found that some mRNAs, lncRNAs, circRNAs, and pathways play essential roles in AF pathogenesis and development. Moreover, one protective factor against PersAF was detected.

Long noncoding MIAT acting as a ceRNA to sponge microRNA-204-5p to participate in cerebral microvascular endothelial cell injury after cerebral ischemia through regulating HMGB1

This study is applied to the investigation of the long noncoding RNA myocardial infarction associated transcript's (MIAT's) role in regulating the expression of high-mobility group box 1 (HMGB1) in cerebral microvascular endothelial cell (CMEC) injury after cerebral ischemia by serving as a competitive endogenous RNA (ceRNA) to sponge microRNA-204-5p (miR-204-5p). The cerebral ischemia model of middle cerebral artery occlusion (MCAO) in rats was established by the suture method, in which rats were injected with empty plasmids and MIAT siRNA plasmids. The cerebral ischemia injury model in vitro was established through oxygen glucose deprivation (OGD) in primary cultured CMECs in rats. The cells were transfected with empty plasmids and MIAT siRNA plasmids. The MIAT/miR-204-5p/HMGB1 axis' function in damage and angiogenesis of CMECs were explored. The binding site between MIAT and miR-204-5p along with that between miR-204-5p and HMGB1 was determined. MIAT was overexpressed in MCAO rats' brain tissue and inhibited MIAT attenuated the injury of brain tissue in MCAO rats. Inhibition of MIAT promoted angiogenesis, promoted miR-204-5p expression and inhibited HMGB1 expression in brain tissue of MCAO rats. Inhibition of MIAT reduced CMEC damage, induced angiogenesis of CMECs, increased the number of surviving neurons, promoted miR-204-5p expression and inhibited HMGB1 expression in CMECs treated with OGD. MIAT promoted HMGB1 expression by competitive binding to miR-204-5p to regulate the injury of CMECs after cerebral ischemia. Our study showed that MIAT promoted HMGB1 expression by competitively binding to miR-204-5p to regulate the injury of CMECs after cerebral ischemia.

Mechanism of Caulophyllum robustum Maxim against rheumatoid arthritis using LncRNA-mRNA chip analysis

BACKGROUND

Caulophyllum robustum Maxim (CRM) is a medicinal compound of the Northeast and is commonly used in China for the treatment of rheumatic pain and rheumatoid arthritis (RA). A preliminary study found that CRM has good anti-inflammatory, analgesic and immunosuppressive effects. However, the specific links and targets for its function remain unclear. Our study aimed to provide a mechanism for the action of Caulophyllum robustum Maxim extraction (CRME) against RA and to establish a method for studying disease treatment using Chinese medicine.

METHODS

The 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) method was used to detect the toxicity of CRME in L929 cells, and the concentration ranges of the blank, model, and CRME drug groups were determined. Differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) were identified between the three groups. Gene Ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways of the differentially expressed genes. Expression of Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2 and Egr1 in the blank, model and drug groups was detected by quantitative real-time PCR (qRT-PCR), and the role of CRME on the above factors was determined to ensure consistency with the chip data.

RESULTS

A total of 329 significantly upregulated genes and 141 downregulated genes were identified between the blank and model groups. A total of 218 significantly upregulated genes and 191 downregulated genes were identified between the CRME drug group and model group. CRME has a significant role in multiple pathways involved in the occurrence and development of RA. Additionally, Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2, and Egr1 were observed in modules of the lncRNA-mRNA weighted co-expression network, consistent with the chip data.

CONCLUSIONS

CRME has regulatory effects on inflammatory factors, the histone family, chemokines and their ligands that are related to RA-related cytokines, the RA pathway, the TNF signaling pathway, the Toll receptor-like signaling pathway, the chemokine signaling pathways and other pathways are related to the course of RA.

Identification of functional lncRNAs based on competing endogenous RNA network in osteoblast differentiation

Adult human mesenchymal stem cells have the potential to differentiate into osteoblast, which plays crucial roles in bone regeneration and repair. Some transcriptional factors (TFs), such as BMP-2 and RUNX2, have been demonstrated to control the differentiation processes. It is important to discover more key regulators in osteoblast differentiation. Recently, some studies found long noncoding RNAs (lncRNAs) participating in osteoblast differentiation, such as MALAT1, DANCR, and ANCR. In this study, we performed a network-based computational analysis to investigate the lncRNA-messenger RNA (mRNA) crosstalks via integrating microRNA (miRNA)-RNA interactions, gene coexpression, and protein-protein interactions. First, multiple topology analyses were performed to osteoblast-differentiation-related lncRNA-mRNA network (ODLMN). Several lncRNAs with central topology structures were identified as key regulators. Results showed that these lncRNAs participated in osteoblast differentiation via phosphoinositide 3-kinase (PI3K), mitogen-activated protein kinase, and Ras signals. Previous studies have demonstrated that lncRNAs exert functions by involving in close modules. Second, after performing module searching in ODLMN, two functional modules were identified, which played crucial roles through involving in PI3K/protein kinase B, cyclic adenosine 3',5'-monophosphate, and hypoxia-inducible factor 1 pathways. Third, a subset of core lncRNA-TF crosstalks that might form feedback loops to control the biological processes in osteoblast differentiation was identified. These core lncRNA-TF feedback loops showed more TF binding affinity than other lncRNAs. All these results can help us to uncover the molecular mechanism and provide new targets for bone regeneration and repair.

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.

Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease

Background

Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in coronary heart disease (CHD).

Methods

High throughput sequencing were used to identify differentially expressed (DE) lncRNA, miRNA, and mRNA profiles between CHD and healthy control. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene-gene interaction network were constructed and pivotal genes were screened out. Lentivirus-induced shRNA infection and qRT-PCR were performed to validated the gene-gene interactions.

Results

A total of 62 lncRNAs, 332 miRNAs and 366 mRNAs were differentially expressed between CHD and healthy control. GO and KEGG analysis show that immune related molecular mechanisms and biological processes play a role in CHD. The gene-gene interaction network were constructed and visualized based on Pearson correlation coefficients and starBase database. 6 miRNAs in the network were significantly correlated to left ventricular ejection fraction, total choleterol and homocysteine. 2 lncRNAs (CTA-384D8.35 and CTB-114C7.4 (refseq entry LOC100128059)), 1 miRNA (miR-4497), and 1 mRNA (NR4A1) were the pivotal genes. Lentivirus-induced shRNA infection and qRT-PCR had validated the pivotal gene-gene interactions.

Conclusions

These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of CHD from a transcriptomic perspective.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0570-z) contains supplementary material, which is available to authorized users.

lncRNA GAS5 regulates myocardial infarction by targeting the miR-525-5p/CALM2 axis

Long noncoding RNAs (lncRNAs) play critical roles in the pathogenesis of cardiovascular diseases, especially in myocardial infarction (MI). However, the underlying molecular mechanism of how lncRNA involves and affect MI still remains unclear. This study aimed to investigate the expression of lncRNA growth arrest-specific transcript 5 (GAS5) and its effects on myocardial cells' proliferation, cell cycle, and apoptosis. The possible mechanisms involved in GAS5, calmodulin 2 (CALM2), and microRNA (miR)-525-5p were also explored. The messenger RNA (mRNA) level of CALM2, GAS5, and miR-525-5p in postmyocardial infarction (MI) and normal cells were examined by quantitative real-time polymerase chain reaction (RT-qPCR). Western blot analysis assay was conducted to detect the protein levels of CALM2. The changes of cell cycle/apoptosis and cell viability of post-MI myocardial cells (PMMC) were determined by flow cytometry analysis and MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay after knockdown of GAS5 or CALM2, respectively. Dual luciferase reporter assay and RNA-binding protein immunoprecipitation (RIP) assay were performed to verify the targeting relationship between miR-525-5p and GAS5, CALM2 in myocardial. Hypoxic preconditioning was performed in normal cells, which constructed a simulated MI environment, and the effect of GAS5 on cardiomyocyte apoptosis was detected. Our data showed that the expression of GAS5 and CALM2 in PMMC was significantly upregulated, while the expression of miR-525-5p was downregulated. Overexpression of GAS5 and CALM2 profoundly promoted the apoptosis of myocardial cell. However, the proliferation of myocardial cell was inhibited by the upregulation of GAS5 and CALM2. Moreover, GAS5 was proved to be the target of miR-525-5p and GAS5 downregulated the expression of miR-525-5p and CALM2. In addition, lncRNA GAS5 promotes MI, while CALM2 induced MI can be reversed by miR-525-5p. These data suggested that lncRNA GAS5 promoted the development and progression of MI via targeting of the miR-525-5p/CALM2 axis and it has the potential to be explored as a therapeutic target for the treatment of MI in the future.

Systematic analysis of lncRNA expression profiles and atherosclerosis-associated lncRNA-mRNA network revealing functional lncRNAs in carotid atherosclerotic rabbit models

Atherosclerosis, a multifactorial and chronic immune inflammatory disorder, is the main cause of multiple cardiovascular diseases. Researchers recently reported that lncRNAs may exert important functions in the progression of atherosclerosis (AS). Some studies found that lncRNAs can act as ceRNAs to communicate with each other by the competition of common miRNA response elements. However, lncRNA-associated ceRNA network in terms of atherosclerosis is limited. In present study, we pioneered to construct and systematically analyze the lncRNA-mRNA network and reveal its potential roles in carotid atherosclerotic rabbit models. Atherosclerosis was induced in rabbits (n = 3) carotid arteries via a high-fat diet and balloon injury, while age-matched rabbits (n = 3) were treated with normal chow as controls. RNA-seq analysis was conducted on rabbits carotid arteries (n = 6) with or without plaque formation. Based on the ceRNA mechanism, a ternary interaction network including lncRNA, mRNA, and miRNA was generated and an AS-related lncRNA-mRNA network (ASLMN) was extracted. Furthermore, we analyzed the properties of ASLMN and discovered that six lncRNAs (MSTRG.10603.16, 5258.4, 12799.3, 5352.1, 12022.1, and 12250.4) were highly related to AS through topological analysis. GO and KEGG enrichment analysis indicated that lncRNA MSTRG.5258.4 may downregulate inducible co-stimulator to perform a downregulated role in AS through T cell receptor signaling pathway and downregulate THBS1 to conduct a upregulated function in AS through ECM-receptor interaction pathway. Finally, our results elucidated the important function of lncRNAs in the origination and progression of AS. We provided an ASLMN of atherosclerosis development in carotid arteries of rabbits and probable targets which may lay the foundation for future research of clinical applications.

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.

Long noncoding RNA MAGI1-IT1 regulates cardiac hypertrophy by modulating miR-302e/DKK1/Wnt/beta-catenin signaling pathway

Cardiac hypertrophy (CH) is an adaptive cardiac response to overload whose decompensation eventually leads to heart failure or sudden death. Recently, accumulating studies have indicated the implication of long noncoding RNAs (lncRNAs) in CH progression. MAGI1-IT1 is a newly-identified lncRNA that is highly associated with CH, while its specific role in CH progression remains masked. In this study, we uncovered that MAGI1-IT1 was distinctly downregulated in angiotensin (Ang) II-induced hypertrophic H9c2 cells. Also, MAGI1-IT1 overexpression in Ang II-treated H9c2 cells strikingly abolished the enlarged surface area and the enhanced levels of hypertrophic markers such as ANP, BNP, and β-MHC. Mechanically, we found MAGI1-IT1 sponged miR-302e which was identified as a hypertrophy-facilitator here, and that miR-302e upregulation countervailed the inhibition of MAGI1-IT1 overexpression on hypertrophic cells. Moreover, it was confirmed that MAGI1-IT1 boosted DKK1 expression by absorbing miR-302e. Subsequently, we also illustrated that MAGI1-IT1 inactivated Wnt/beta-catenin signaling through a DKK1-dependent pathway. Finally, both the DKK1 inhibition and LiCI (Wnt activator) supplement abrogated the hypertrophy-suppressive impact of MAGI1-IT1 on Ang II-simulated hypertrophic H9c2 cells. Jointly, our findings disclosed that MAGI1-IT1 functioned as a negative regulator in CH through inactivating Wnt/beta-catenin pathway via targeting miR-302e/DKK1 axis, revealing a novel road for CH treatment.

A novel lncRNA-miRNA-mRNA triple network identifies lncRNA TWF1 as an important regulator of miRNA and gene expression in coronary artery disease

Background

Long non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Yet, their mechanisms in coronary artery disease (CAD) are not well understood.

Methods

The expression profile of genes associated to CAD was reannotated into the lncRNA-mRNA biphasic profile. The target microRNA data were used to design a global CAD triple network. Thereafter, we conducted a functional enrichment analysis and clustering using the triple network from the level of topology analyses. The expression of four non-coding RNAs (ncRNAs) was measured by qRT-PCR and the risk of CAD was calculated by nomogram. The prognostic value of three ncRNAs was evaluated using receiver operating characteristic (ROC) curve.

Results

A CAD lncRNA-miRNA-mRNA network was constructed which included 15 mRNAs, 3 miRNAs, 19 edges and one lncRNA. Nomogram showed that four ncRNAs were the risk of CAD. After RT-PCR validation in four ncRNAs between CAD and non-CAD samples, only three ncRNAs had significant meaning for further analysis. ROC curve showed that TWF1 presented an area under curve (AUC) of 0.862, the AUC of hsa -miR-142-3p was 0.856 and hsa -miR126-5p was 0.822. After the pairwise comparison, we found that TWF1 had significant statistical significance (P _TWF1-142 < 0.05 and P _TWF1-126 < 0.01). The results of functional enrichment analysis of interacting gene and microRNA showed that the shared lncRNA TWF1 may be a new factor for CAD.

Conclusions

This investigation on the regulatory networks of lncRNA-miRNA-mRNA in CAD suggests that a novel lncRNA, lncRNA TWF1 is a risk factor for CAD, and expands our understanding into the mechanisms involved in the pathogenesis of CAD.