Functional lncRNA-miRNA-mRNA networks in rabbit carotid atherosclerosis

Role of long non-coding RNA TCONS_02443383 in regulating cell adhesion and peroxisome proliferator-activated receptor (PPAR) signaling genes in atherosclerosis: A New Zealand white rabbit model study

OBJECTIVE

In this study, we performed RNA sequencing (RNA-seq) on the abdominal aorta tissue of New Zealand rabbits and investigated the potential association of lncRNA TCONS_02443383 with the development of AS through bioinformatics analysis of the sequencing data. The obtained results were further validated using quantitative real-time polymerase chain reaction (qRT-PCR).

METHOD

We induced an AS model in New Zealand rabbits by causing balloon injury to the abdominal aorta vascular wall and administering a high-fat diet. We then upregulated the expression level of the lncRNA TCONS_02443383 by injecting lentiviral plasmids through the ear vein. RNA sequencing (RNA-seq) was performed on the abdominal aorta tissues. We conducted Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway and Gene Ontology (GO) analyses.

RESULT

The overexpression of the lncRNA TCONS_02443383 led to an upregulation of peroxisome proliferator-activated receptor (PPAR) signaling pathways as well as genes related to cell adhesion.

CONCLUSION

The overexpression of the lncRNA TCONS_02443383 can inhibit the occurrence and development of AS by upregulating peroxisome proliferator-activated receptor (PPAR) signaling pathways and genes related to cell adhesion.

LncRNA RASSF8-AS1 knockdown displayed antiproliferative and proapoptotic effects through miR-188-3p/ATG7 pathway in ox-LDL-treated vascular smooth muscle cells

BACKGROUND

Long noncoding RNA (lncRNA)-mediated changes in gene expression contribute to atherosclerosis (AS) development. However, the roles of numerous lncRNAs in AS have not been fully elucidated. Here, we aimed to investigate the potential role of lncRNA RASSF8-AS1 (RASSF8-AS1) in autophagy of human aortic vascular smooth muscle cells (HA-VSMCs).

METHODS

RASSF8-AS1 expression in patients with AS was extracted from the Gene Expression Omnibus (GEO) database. RASSF8-AS1 and microRNA-188-3p (miR-188-3p) expression was analyzed in 20 enrolled patients with AS. HA-VSMCs were treated with oxidized low-density lipoprotein (ox-LDL) (25, 50, 75, and 100 µg/mL) for 24 h. Loss- or gain-of-function of RASSF8-AS1, miR-1883p, and autophagy-related 7 (ATG7) was studied using the transfected HA-VSMCs. Cell viability was assessed using Cell Counting Kit-8 (CCK-8). Apoptosis was detected with annexin V-fluorescein isothiocyanate (FITC) and propidium iodide (PI). Relative luciferase reporter assay was used to confirm the targeting relationship of miR-188-3p to RASSF8-AS1 or ATG7. Gene expression was detected by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot.

RESULTS

RASSF8-AS1 was enriched in the serum of patients with AS and ox-LDL-treated HA-VSMCs. Ox-LDL induced proliferation and autophagy while inhibiting the apoptosis of HA-VSMCs, which was abated by RASSF8-AS1 knockdown. RASSF8-AS1 downregulated miR-188-3p of ox-LDL-treated HA-VSMCs. RASSF8-AS1 knockdown caused an increase in miR-188-3p, which inhibited proliferation and autophagy and induced the apoptosis of ox-LDL-treated HA-VSMCs. miR-188-3p inhibited ATG7 expression in ox-LDL-treated HA-VSMCs. RASSF8-AS1 elevated ATG7 and induced autophagy through sponging miR-188-3p in ox-LDL-treated HA-VSMCs.

CONCLUSIONS

RASSF8-AS1 regulated autophagy by targeting miR-188-3p, a messenger RNA-binding miRNA that increases ATG7 level, which may be a new target molecule for the prevention and prognosis of AS.

The roles and mechanisms of miR-26 derived from exosomes of adipose-derived stem cells in the formation of carotid atherosclerotic plaque

BACKGROUND

This study explored the serum concentrations of miR-26 in patients with carotid atherosclerosis (CAS) and defined the roles and mechanisms of miR-26 derived from the exosomes of adipose-derived stem cells (ADSC-exos).

METHODS

The carotid artery width was diagnosed by ultrasound examination in patients with different degrees of CAS. The serum levels of total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) in patients were detected by biochemistry. The serum levels of miR-26 were determined by quantitative polymerase chain reaction (qPCR). A model of CAS in ApoE-/- mice fed with a rich-fat diet was established to analyze the regulatory effects of serum miR-26 on blood lipids in mice. Adipose mesenchymal stem cell lines transfected with miR-26 were established. The regulatory relationship between the expression levels of inflammatory factors, including tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and IL-1β, and the expression levels of miR-26 in the supernatant of each group of cells was determined by qPCR. The ADSC-exos were extracted from ADSCs and injected into model mice through the tail vein. The therapeutic effect of ADSCs expressing miR-26 on model mice was evaluated by detecting the levels of inflammatory factors and blood lipids in the serum of the mice.

RESULTS

The degree of atherosclerosis (AS) was positively associated with the intima-media thickness (IMT) of the carotid artery. The serum levels of miR-26 in patients were inversely correlated with the levels of blood lipids (TC, TG, and LDL-C), and positively correlated with HDL-C levels. Similarly, in the CAS mouse model, the serum levels of miR-26 were inversely correlated with the levels of blood lipids (TC, TG, and LDL-C), and positively correlated with HDL-C level. In ADSCs transfected with miR-26, the miR-26 expression in the cell supernatant was negatively regulated by the expression of inflammatory factors, TNF-α, IL-6, and IL-1β, in the cell supernatant. ADSC-exos expressing miR-26 has positive effects on correcting blood lipids and inflammatory factors in the mouse model of CAS.

CONCLUSIONS

miR-26 has an active role in CAS and may be a novel target for the treatment of CAS in the future.

Identification of Biomarkers of Autophagy-Related Genes Between Early and Advanced Carotid Atherosclerosis

Background

Accumulating evidence demonstrates that autophagy is important in inhibiting inflammation and cholesterol efflux. It suggested the autophagy may be a treatment of atherosclerosis. Thus, we screened autophagy-related mRNA to explore their mechanism of scientific basis for early diagnosis and therapy of atherosclerosis.

Methods

The GSE28829 datasets were assessed to analyze differentially expressed genes by GEO2R. And autophagy-related hub genes were identified by HADb. The biological function of autophagy-related DEmRNAs was examined by Metascape. The construction of a protein–protein network was explored by String. Cytohubba was utilized to screen hub genes. Analysis of DEmiRNA-mRNA pairs was executed by DIANA microT-CDS database. Finally, correlation analysis was carried out to identify the relationship between DEARGs and clinical and prognostic factors.

Results

A number of 1087 DEGs and 19 autophagy-related DEmRNAs were identified in advanced carotid atherosclerotic plaque compared with the early. The biological function containing development and growth was enriched. Moreover, we screened the top hub nodes with the highest degrees. MicroRNAs (miRNAs) are confirmed to participate in genesis and progression of atherosclerosis, so we further analyzed the miRNA–mRNA regulatory network genes with four hub genes to explore their potential mechanism in atherosclerosis. Then, we revealed co-expression of four key genes CTSB, ITGB1, CXCR4, TNFSF10 and autophagy-related genes. As for the clinical factors, hypertension factor showed higher expression of ITGB1. The probability of coronary heart disease factor was significantly increased with high expression of CTSB and CXCR4, as well as low expression of ITGB1 and TNFSF10. Diabetes factor tended to express distinguished levels of CTSB and ITGB1. TNFSF10 was highly expressed in both hyperlipidemia and ischemic stroke factor.

Conclusion

CTSB, ITGB1, CXCR4 and TNFSF10 may be critical in atherosclerosis development and were thought to be potential diagnostic biomarkers for atherosclerosis.

The lncRNA DANCR promotes development of atherosclerosis by regulating the miR-214-5p/COX20 signaling pathway

BACKGROUND

Although long non-coding RNA differentiation antagonizing non-protein coding RNA (DANCR) has been reported to be involved in atherosclerosis (AS) development, its specific mechanism remains unclear.

METHODS

DANCR expression levels in blood samples of AS patients and oxidized low-density lipoprotein (ox-LDL) treated vascular smooth muscle cells (VSMCs) and human umbilical vein endothelial cells (HUVECs) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The small interfering RNA targeting DANCR (si-DANCR) was used to silence DANCR expression. Cell viability was assessed by CCK-8 assay. Cell apoptosis was evaluated by flow cytometry. Levels of inflammatory cytokines, anti-oxidative enzyme superoxide dismutase (SOD) activity, and malonaldehyde (MDA) were detected by specific commercial kits. An animal AS model was established to confirm the role of DANCR/microR-214-5p/COX20 (the chaperone of cytochrome c oxidase subunit II COX2) in AS development.

RESULTS

DANCR was significantly increased in the blood samples of AS patients and ox-LDL treated VSMCs and HUVECs. DANCR downregulation obviously increased viability and reduced apoptosis of ox-LDL-treated VSMCs and HUVECs. Meanwhile, DANCR downregulation reduced the levels of inflammatory cytokines, including interleukin (IL)-6 (IL-6), IL-1beta (IL-1β), IL-6 and tumor necrosis factor (TNF)-alpha (TNF-α) and MDA while increasing the SOD level in ox-LDL-treated VSMCs and HUVECs. DANCR regulated COX20 expression by acting as a competing endogenous RNA (ceRNA) of miR-214-5p. Rescue experiments demonstrated that miR-214-5p downregulation obviously attenuated si-DANCR-induced protective effects on ox-LDL-caused endothelial injury.

CONCLUSIONS

Our results revealed that DANCR promoted AS progression by targeting the miR-214-5p/COX20 axis, suggesting that DANCR might be a potential therapeutic target for AS.

Role of long intergenic non-protein coding RNA 00152 in pancreatic cancer glycolysis via the manipulation of the microRNA-185-5p/Krüppel-like factor 7 axis

The current study set out to investigate the role of long intergenic non-protein coding RNA (LINC) 00152 in pancreatic cancer (PC) cell glycolysis with the microRNA (miR)-185-5p/Krüppel-like factor 7 (KLF7) axis. Firstly, PC tissues and cells as well as the control ones were collected from 53 PC patients, and assessed for LINC00152 expression patterns. Besides, PC cells with the most differentially expressed LINC00152 were selected for further experiments. When LINC00152 was silenced or overexpressed, PC cell glucose consumption, lactic acid production, adenosine triphosphate and levels of glycolysis-associated enzymes were detected. In addition, the binding relation between LINC00152 and miR-185-5p as well as the target relation between miR-185-5p and KLF7 was clarified and validated. Additionally, xenograft transplantation was performed to confirm the in vitro experiments. It was found that LINC00152 was over-expressed in PC, and it predicted a poor prognosis. Besides, LINC00152 knockdown inhibited PC cell glycolysis. Moreover, LINC00152 could specifically targeted miR-185-5p. Meanwhile, LINC00152 exhaustion blocked PC cell glycolysis through the up-regulation of miR-185-5p. Lastly, LINC00152 inhibition targeted miR-185-5p to quench KLF7, therefore suppressing PC cell tumorigenesis and glycolysis. Collectively, our findings indicated that silencing LINC00152 restricted PC cell glycolysis via promoting miR-185-5p and reducing KLF7.

Diagnostic and Prognostic Significance of miR-675-3p in Patients With Atherosclerosis

In recent years, a rising number of studies have confirmed that microRNA (miRNA) plays a prominent role in the early diagnosis and prognostic value assessment of cardiovascular diseases. The current study was conducted to examine the expression of miR-675-3p in atherosclerosis (AS) patients and to evaluate its clinical diagnosis and prognostic value. 110 AS patients and 70 healthy controls were included in the study. Serum miR-675-3p levels were detected by quantitative real-time PCR (qRT-PCR). The clinical diagnostic significance of serum miR-675-3p in AS patients were investigated by the receiver operating characteristic (ROC) curve. The correlation between miRNA and carotid intima-media thickness (CIMT) was analyzed by the Spearman correlation coefficient. The prognostic significance of serum miR-675-3p was evaluated by the Kaplan-Meier method and Cox regression analysis. The patient’s serum miR-675-3p was significantly increased than the healthy individuals (P < 0.05). An increase of carotid intima-media thickness (CIMT) was positively correlated with the promotion of serum miR-675-3p levels. The area under the ROC curve (AUC) was 0.918, with high sensitivity and specificity. miR-675-3p is a key independent predictor of cardiovascular adverse events in AS patients (HR = 5.375, 95%CI = 1.590-18.170, P = 0.007), and patients with elevated miR-675-3p were more likely to have cardiovascular adverse events (log-rank P = 0.030). Increased miR-675-3p can be used as a potential marker for the diagnosis of AS, and was associated with the poor prognosis of AS.

Silencing of OIP5-AS1 Protects Endothelial Cells From ox-LDL-Triggered Injury by Regulating KLF5 Expression via Sponging miR-135a-5p

Background: Long non-coding RNAs (lncRNAs) have been implicated in the pathogenesis of atherosclerosis. LncRNA OIP5 antisense RNA 1 (OIP5-AS1) has been found to be associated with the development of atherosclerosis. In this study, we further investigated the molecular basis of OIP5-AS1 in atherosclerosis pathogenesis.

Methods: Oxidative low-density lipoprotein (ox-LDL) was used to treat human umbilical vein endothelial cells (HUVECs). The levels of OIP5-AS1, miR-135a-5p, and Krüppel-like factor 5 (KLF5) were detected by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot. Cell viability, migration, and apoptosis were evaluated using the Cell Counting Kit-8 (CCK-8), Transwell, and flow cytometry, respectively. The levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) were determined with enzyme-linked immunosorbent assay (ELISA). Targeted interactions among OIP5-AS1, miR-135a-5p, and KLF5 were confirmed by dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Animal studies were performed to assess the role of OIP5-AS1 in atherosclerosis progression in vivo.

Results: Our data showed the significant upregulation of OIP5-AS1 in atherosclerosis serum and ox-LDL-stimulated HUVECs. The silencing of OIP5-AS1 protected against ox-LDL-triggered cytotoxicity in HUVECs and diminished lipids secretion in ApoE^−/− mice. Moreover, OIP5-AS1 functioned as a molecular sponge of miR-135a-5p, and miR-135a-5p was a functional mediator of OIP5-AS1 in regulating ox-LDL-induced HUVEC injury. KLF5 was a direct target of miR-135a-5p, and the increased expression of miR-135a-5p alleviated ox-LDL-induced cytotoxicity by downregulating KLF5. Furthermore, OIP5-AS1 influenced KLF5 expression through sponging miR-135a-5p.

Conclusion: The current work identified that the silencing of OIP5-AS1 protected against ox-LDL-triggered cytotoxicity in HUVECs at least in part by influencing KLF5 expression via acting as a miR-135a-5p sponge.

Constructing a ceRNA-immunoregulatory network associated with the development and prognosis of human atherosclerosis through weighted gene co-expression network analysis

There is now overwhelming experimental and clinical evidence that atherosclerosis (AS) is a chronic inflammatory disease. The recent discovery of a new group of mediators known as competing endogenous RNA (ceRNA) offers a unique opportunity for investigating immunoregulation in AS. In this study, we used gene expression profiles from GEO database to construct a lncRNA-miRNA-mRNA ceRNA network during AS plaque development through weighted gene co-expression network analysis (WGCNA). GO annotation and pathway enrichment analysis suggested that the ceRNA network was mainly involved in the immune response. CIBERSORT and GSVA were used to calculate the immune cell infiltration score and identified macrophage as hub immunocyte in plaque development. A macrophage related ceRNA subnetwork was constructed through correlation analysis. Samples from Biobank of Karolinska Endarterectomy (BiKE) were used to identify prognostic factors from the subnetwork and yielded 7 hub factors that can predict ischemic events including macrophage GSVA score and expression value of AL138756.1, CTSB, MAFB, LYN, GRK3, and BID. A nomogram based on the key factors was established. GSEA identified that the PD1 signaling pathway was negatively associated with these prognostic factors which may explain the cardiovascular side effect of immune checkpoint therapy in anti-tumor treatment.

LncRNA PVT1 accelerates malignant phenotypes of bladder cancer cells by modulating miR-194-5p/BCLAF1 axis as a ceRNA

Background: Numerous studies proved that long non-coding RNA (lncRNA) is involved in the progression of multifarious diseases, especially in some carcinomas. As a potential tumor biomarker, plasmacytoma variant translocation 1 gene (PVT1) is involved in the development and progression of multifarious cancers. Nevertheless, the intrinsic and concrete molecular mechanism of PVT1 in bladder cancer still remained unclear, which is also the dilemma faced in many non-coding RNA studies.

Results: Our research revealed that PVT1 was significantly higher expression in bladder carcinoma specimens and cell lines. Further experiments indicated that knockdown or overexpression of PVT1 restrained or promoted the malignant phenotype and WNT/β-catenin signaling in bladder cancer cells. Meanwhile miR-194-5p was in contrast and miR-194-5p could partially reverse the function of PVT1 in malignant bladder tumor cells. As a microRNA sponge, PVT1 actively promotes the expression of b-cells lymphoma-2-associated transcription factor 1 (BCLAF1) to sponge miR-194-5p and subsequently increases malignant phenotypes of bladder cancer cells. Therefore, it performs a carcinogenic effect and miR-194-5p as the opposite function, and serves as an antioncogene in the bladder carcinomas pathogenesis.

Conclusion: PVT1-miR-194-5p-BCLAF1 axis is involved in the malignant progression and development of bladder carcinomas. Experiments revealed that PVT1 has a significant regulatory effect on bladder cancer (BC) and can be used as a clinical diagnostic marker and a therapeutic molecular marker for patients suffering from BC.

Methods: In urothelial bladder carcinoma specimens and cell lines, the relative expression levels of PVT1 and miR-194-5p were detected by quantitative reverse transcription PCR (RT-qPCR). Through experiments such as loss-function and over-expression, the biological effects of PVT1 and miR-194-5p on the proliferation, migration, apoptosis and tumorigenicity were explored in bladder cancer cells. Co-immunoprecipitation, proteomics experiments, dual luciferase reporter gene analysis, western blot and other methods were adopted to investigate the PVT1 potential mechanism in bladder carcinomas.

Role of the lncRNA-mRNA network in atherosclerosis using ox-low-density lipoprotein-induced macrophage-derived foam cells

Atherosclerosis (AS) is the leading cause of coronary heart disease, cerebral infarction, peripheral vascular disease, and other cardiovascular diseases, making it a major risk factor for high morbidity and mortality. Although long non-coding RNAs (lncRNAs) have been reported to play a role in AS, the specific effects of lncRNAs on AS remain largely unknown. Thus the purpose of this study was to explore the roles of mRNAs and lncRNAs in atherosclerosis via an ox-low-density lipoprotein induced macrophage-derived foam cell model. Microarray analysis identified a total of 50 688 mRNAs and 1514 lncRNAs, including 51 lncRNAs and 1730 mRNAs that were significantly dysregulated in the model group (p-adjust < 0.05 and |log 2FC| > 2). The results of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses demonstrated that the dysregulated genes were associated with cell proliferation, cell apoptosis, and inflammatory responses. An lncRNA-mRNA co-expression network was created to further analyze the key regulatory genes. The lncRNAs Brip1os, Gm16586, AU020206, 9430034N14Rik, 2510016D11Rik, LNC_000709, Gm15472, Gm20703, and Dubr were identified as potential biomarkers in macrophage-derived foam cells. Based on 9 lncRNAs and 13 mRNAs, key genes influencing the degree of cell proliferation and cell apoptosis and the subsequent development of AS were identified. Q-PCR verified the key dysregulated genes. Thus, our results suggest potential therapeutic targets for AS and provide avenues for further research on AS pathogenesis.