Insights into circular RNAs: their biogenesis, detection, and emerging role in cardiovascular disease

Non-coding RNAs as therapeutic targets and biomarkers in ischaemic heart disease

The adult heart is a complex, multicellular organ that is subjected to a series of regulatory stimuli and circuits and has poor reparative potential. Despite progress in our understanding of disease mechanisms and in the quality of health care, ischaemic heart disease remains the leading cause of death globally, owing to adverse cardiac remodelling, leading to ischaemic cardiomyopathy and heart failure. Therapeutic targets are urgently required for the protection and repair of the ischaemic heart. Moreover, personalized clinical biomarkers are necessary for clinical diagnosis, medical management and to inform the individual response to treatment. Non-coding RNAs (ncRNAs) deeply influence cardiovascular functions and contribute to communication between cells in the cardiac microenvironment and between the heart and other organs. As such, ncRNAs are candidates for translation into clinical practice. However, ncRNA biology has not yet been completely deciphered, given that classes and modes of action have emerged only in the past 5 years. In this Review, we discuss the latest discoveries from basic research on ncRNAs and highlight both the clinical value and the challenges underscoring the translation of these molecules as biomarkers and therapeutic regulators of the processes contributing to the initiation, progression and potentially the prevention or resolution of ischaemic heart disease and heart failure.

Roles and mechanisms of circular RNA in respiratory system cancers

Circular RNAs (circRNAs) constitute a class of endogenous non-coding RNAs (ncRNAs) that lack a 5'-ended cap and 3'-ended poly (A) tail and form a closed ring structure with covalent bonds. Due to its special structure, circRNA is resistant to Exonuclease R (RNaseR), making its distribution in the cytoplasm quite rich. Advanced high-throughput sequencing and bioinformatics methods have revealed that circRNA is highly conserved, stable, and disease- and tissue-specific. Furthermore, increasing research has confirmed that circRNA, as a driver or suppressor, regulates cancer onset and progression by modulating a series of pathophysiological mechanisms. As a result, circRNA has emerged as a clinical biomarker and therapeutic intervention target. This article reviews the biological functions and regulatory mechanisms of circRNA in the context of respiratory cancer onset and progression.

CircSEPT9 promotes breast cancer progression by regulating PTBP3 expression via sponging miR-625-5p

BACKGROUND

Breast cancer (BC) is a common malignancy which threatens the health of women. Circular RNAs (circRNAs) are critical factors in multiple cancers, including BC. The aim of this experiment was to investigate the molecular mechanisms of circRNA Septin 9 (circSEPT9) in the progression of BC.

METHODS

CircSEPT9, microRNA-625-5p (miR-625-5p) and polypyrimidine tract-binding protein 3 (PTBP3) levels were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Western blot was performed to detect the protein levels of PTBP3, E-cadherin and vimentin. Cell counting kit-8 assay (CCK8) and thymidine analog 5-ethynyl-2'-deoxyuridine (EDU) was utilized for proliferation examination. Flow cytometry was conducted to measure apoptosis. Transwell assay and wound healing assay to investigate the migration of BC cells. Glucose uptake and lactate production were determined by specific kits. Additionally, dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were utilized to verify the interaction. A murine xenograft model was established to investigate the function of circSEPT9 in BC in vivo.

RESULTS

Overexpression of circSEPT9 was found in BC tissues and cells. Silencing circSEPT9 impeded BC cell proliferation, migration, epithelial-mesenchymal transition (EMT) and glycolytic metabolism but facilitated cell apoptosis in vitro. Meanwhile, circSEPT9 knockdown constrained tumor growth in vivo. MiR-625-5p was targeted by circSEPT9. The influence of silencing circSEPT9 on BC cell function was regained by miR-625-5p inhibitor. Furthermore, miR-625-5p regulated BC cell malignant phenotypes via downregulating PTBP3.

CONCLUSION

circSEPT9 contributed to the malignant progression of BC by up-regulating PTBP3 via sponging miR-625-5p.

hsa_circ_0008500 regulates Benzo(a)pyrene-loaded gypsum-induced inflammation and apoptosis in human bronchial epithelial cells via activation of Ahr/C-myc pathways

Polycyclic aromatic hydrocarbons (PAHs) are major organic pollutants attached to fine particulate matter in the atmosphere. They induce lung inflammation, asthma, and other lung diseases. Exploring the toxic mechanism of PAHs on lung epithelial cells may provide a theoretical basis for the prevention and treatment of respiratory diseases induced by PAHs. In our study, 16 human bronchial epithelial (16HBE) cells were exposed to different concentrations of gypsum dust, Benzo(a)pyrene (BaP), and BaP-loaded gypsum dust for 24 hours. Gypsum dust loaded with BaP significantly increased the cytotoxicity of 16HBE cells, enhanced the production of lactate dehydrogenase (LDH), interleukin-6 (IL-6) and interleukin-8 (IL-8), induced cell apoptosis, and upregulate the expression of hsa_circ_0008500 (circ_0008500). The mechanism was studied with a BaP-loaded gypsum dust concentration of 1.25 mg/mL. StemRegenin 1 (SR1) pretreat significantly reduced the release of LDH, IL-6, and IL-8 and decreased the protein levels of Ahr、XAP2, C-myc, and p53. Second-generation sequencing indicated that circ_0008500 was highly expressed after 16HBE induced by BaP-loaded gypsum dust. Functional experiments confirmed that circ_0008500 promoted the inflammation and apoptosis of 16HBE cells induced by BaP-loaded gypsum dust by regulating the Ahr signaling pathway. Our study showed that fine particulate matter adsorption of BaP significantly increased the toxic effect of BaP on cells. By activating the Ahr/C-myc pathway, circ_0008500 promoted inflammation and apoptosis of 16HBE cells induced by BaP-loaded gypsum dust.

Exosome derived from tumor-associated macrophages: biogenesis, functions, and therapeutic implications in human cancers

Tumor-associated macrophages (TAMs), one of the most abundant immune cell types in the tumor microenvironment (TME), account for approximately 50% of the local hematopoietic cells. TAMs play an important role in tumorigenesis and tumor development through crosstalk between various immune cells and cytokines in the TME. Exosomes are small extracellular vesicles with a diameter of 50-150 nm, that can transfer biological information (e.g., proteins, nucleic acids, and lipids) from secretory cells to recipient cells through the circulatory system, thereby influencing the progression of various human diseases, including cancer. Recent studies have suggested that TAMs-derived exosomes play crucial roles in malignant cell proliferation, invasion, metastasis, angiogenesis, immune responses, drug resistance, and tumor metabolic reprogramming. TAMs-derived exosomes have the potential to be targeted for tumor therapy. In addition, the abnormal expression of non-coding RNAs and proteins in TAMs-derived exosomes is closely related to the clinicopathological features of patients with cancer, and these exosomes are expected to become new liquid biopsy markers for the early diagnosis, prognosis, and monitoring of tumors. In this review, we explored the role of TAMs-derived exosomes in tumorigenesis to provide new diagnostic biomarkers and therapeutic targets for cancer prevention.

Downregulated M6A modification and expression of circRNA_103239 promoted the progression of glioma by regulating the miR-182-5p/MTSS1 signalling pathway

Glioma is a common type of tumor in the central nervous system, and the mortality is high. The prognosis of advanced glioma patients remains poor, and the therapeutic strategies need to be developed. The roles of circRNAs in glioma remain largely unknown. The aim of this study was to explore the functions circRNA_103239 in the biological behaviour changes of glioma cells. The expression of circRNA_103239 in clinical samples and glioma cells were examined using RT-qPCR. The targets of circRNA_103239 were predicted using bioinformatics approach. Gain- and loss-of-function study were carried out. The proliferation of transfected cells were evaluated by CCK-8 assay. Migratory and invasive activities of the cells were examined using wound healing, colony formation and transwell assay. Tumor growth was also evaluated in vivo. The results indicated that the expression of circRNA_103239 was predominantly detected in the cytoplasma of glioma cells. In addition, the expression of circRNA_103239 was down-regulated in glioma, and up-regulated circRNA_103239 inhibited the progression of glioma. Furthermore, miR-182-5p was the novel target of circRNA_103239 in glioma, and MTSS1 was the putative downstream molecule of circRNA_103239/miR-182-5p axis. Additionally, circRNA_103239 suppressed the progression of glioma in a miR-182-5p/MTSS1 dependent manner. Moreover, circRNA_103239 inhibited tumour growth in vivo, and the expression of circRNA_103239 was regulated by METTL14-mediated m6A modification. In summary, in normal cells, METTL14 mediated the m6A modification and expression of circRNA_103239, which sponging miR-182-5p and inducing the expression of MTSS1, subsequently inhibiting the EMT; whereas in glioma cells, downregulated METTL14 induced downregulated m6A modification and expression of circRNA_103239, further resulting in the up-regulation of miR-182-5p and down-regulation of MTSS1, consequently promoting the EMT of glioma cells and triggering the progression of tumor.

Diagnosis of acute myocardial infarction using a combination of circulating circular RNA cZNF292 and clinical information based on machine learning

Circulating circular RNAs (circRNAs) are emerging as novel biomarkers for cardiovascular diseases (CVDs). Machine learning can provide optimal predictions on the diagnosis of diseases. Here we performed a proof-of-concept study to determine if combining circRNAs with an artificial intelligence approach works in diagnosing CVD. We used acute myocardial infarction (AMI) as a model setup to prove the claim. We determined the expression level of five hypoxia-induced circRNAs, including cZNF292, cAFF1, cDENND4C, cTHSD1, and cSRSF4, in the whole blood of coronary angiography positive AMI and negative non-AMI patients. Based on feature selection by using lasso with 10-fold cross validation, prediction model by logistic regression, and ROC curve analysis, we found that cZNF292 combined with clinical information (CM), including age, gender, body mass index, heart rate, and diastolic blood pressure, can predict AMI effectively. In a validation cohort, CM + cZNF292 can separate AMI and non-AMI patients, unstable angina and AMI patients, acute coronary syndromes (ACS), and non-ACS patients. RNA stability study demonstrated that cZNF292 was stable. Knockdown of cZNF292 in endothelial cells or cardiomyocytes showed anti-apoptosis effects in oxygen glucose deprivation/reoxygenation. Thus, we identify circulating cZNF292 as a potential biomarker for AMI and construct a prediction model "CM + cZNF292."

Research progress of non-coding RNAs regulation on intramuscular adipocytes in domestic animals

Intramuscular fat (IMF) is the main determinant of the economic value of domestic animal meat, and has a vital impact on the sensory quality characteristics, while the content of IMF is mainly determined by the size and number of intramuscular adipocytes. In recent years, due to the development of sequencing technology and omics technology, a large number of non-coding RNAs have been identified in intramuscular adipocytes. Non-coding RNAs are a kind of RNA regulatory factors with biological functions but without translation function, which mainly include microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These non-coding RNAs regulate the key genes of intramuscular adipocyte growth and development at post-transcriptional level through a variety of regulatory mechanisms, and affect the number and size of intramuscular adipocytes, thus affecting the content of IMF. Here, the review summarizes the candidate non-coding RNAs (miRNAs, lncRNAs, circRNAs) and genes involved in the regulation of intramuscular adipocytes, the related regulation mechanism and signaling pathways, in order to provide reference for further clarifying the molecular regulation mechanism of non-coding RNAs on intramuscular adipocytes in domestic animals.

cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities

Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5' and 3' ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively.

Role of circRNAs in gastric cancer

Circular RNAs (circRNAs) are a large class of non-coding RNAs with single-strand covalently closed loops, formed by reverse splicing, which widely exist in many cell lines and diverse species. Some circRNAs have highly evolutionarily conserved sequences, or tissue-specific or cell-specific expression patterns, and many circRNAs are extremely stable. In the past decades, accumulating evidence has indicated that circRNAs participate in the mechanisms associated with the development of many kinds of tumors, exert important biological functions by acting as microRNA or protein ‘sponges’, transcriptional regulatory factors, and protein translation templates, and play key roles in the occurrence and development of gastric cancer. This review comprehensively summarizes the biogenesis, characteristics, and biological functions of circRNAs, and the molecular mechanisms underlying the role of circRNAs in the carcinogenesis and progression of gastric cancer.

Expression Profile of Pyroptosis-Related Genes and the Associated Regulatory Axis in Primary Gout Patients

Purpose

Analyzed the expression characteristics of pyroptosis-related genes (PRGs) in peripheral blood mononuclear cells (PBMCs) of gout patients by microarray, and constructed ceRNA network to explore the molecular mechanism of RNA-mediated pyroptosis regulation.

Patients and Methods

Human mRNA, lncRNA, circRNA microarray data were used to identify differentially expressed in PBMCs from patients with primary gout and healthy controls. Differential PRGs in PBMCs of gout patients identified by Genecard database and mRNA microarray data. GO and KEGG enrichment analyses of these genes were then conducted. Protein-protein interaction networks and cytoHubba were used to identify hub genes. Combining the lncRNA and circRNA microarray data, a ceRNA network was constructed by Cytoscape to screen out key non-coding RNA molecules that can regulate target PRGs. Finally, the relative expression levels of target miRNA and circRNA in 60 gout patients and 40 healthy subjects were detected by qRT-PCR.

Results

The results revealed 30 differentially expressed PRGs. GO and KEGG analysis of these genes were mainly concentrated in the production and regulation of cytokines, NOD-like receptor signaling pathway and so on. Nine hub genes were screened by PPI network, including IL1B, DDX3X, NLRP3, NLRP9, AIM2, CASP8, P2XR7, CARD8 and IFI16. The has_circRNA_102906\hsa_circRNA_102910\hsa_circRNA_102911-hsa-miR-129-5p-DDX3X\NLRP3\NLRP9 regulatory network was constructed. The expression of has_circRNA_102906, hsa_circRNA_102910, hsa_circRNA_102911 were up-regulated and hsa-miR-129-5p down-regulated in PBMCs of gout patients. The relative expression of hsa_circRNA_102911 was positively correlated with clinical inflammatory indicators associated with gout, and the area under the curve of hsa_circRNA_102911 for gout diagnosis was 0.85 (95% CI: 0.775-0.925; p < 0.001).

Conclusion

There are several differentially expressed PRGs in PBMCs of gout patients, which are involved in the regulation of gout inflammation through multiple pathways. hsa_circRNA_102911-hsa-miR-129-5p-DDX3X\NLRP3\NLRP9 may be the key regulatory pathway for pyroptosis to regulate gout inflammation, and hsa_circRNA_102911 may be a potential biomarker for the diagnosis of primary gout.

Identifying Candidate Circulating RNA Markers for Coronary Artery Disease by Deep RNA-Sequencing in Human Plasma

Advances in RNA sequencing (RNA-Seq) have facilitated transcriptomic analysis of plasma for the discovery of new diagnostic and prognostic markers for disease. We aimed to develop a short-read RNA-Seq protocol to detect mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in plasma for the discovery of novel markers for coronary artery disease (CAD) and heart failure (HF). Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample. We identified fragments from 3986 messenger RNAs (mRNAs), 164 long non-coding RNAs (lncRNAs), 405 putative novel lncRNAs and 227 circular RNAs in plasma. Circulating levels of 160 mRNAs, 10 lncRNAs and 2 putative novel lncRNAs were altered in patients compared with controls (absolute fold change >1.2, p < 0.01 adjusted for multiple comparisons). The most differentially abundant transcripts were enriched in mRNAs encoded by the mitochondrial genome. We did not detect any differences in the plasma RNA profile between patients who developed HF compared with those who did not. In summary, we show that mRNAs, lncRNAs and circular RNAs can be reliably detected in plasma by deep RNA-Seq. Multiple coding and non-coding transcripts were altered in association with CAD, including several mitochondrial mRNAs, which may indicate underlying myocardial ischaemia and oxidative stress. If validated, circulating levels of these transcripts could potentially be used to help identify asymptomatic individuals with established CAD prior to an acute coronary event.

Mechanism and Potential Target of Blood-Activating Chinese Botanical Drugs Combined With Anti-Platelet Drugs: Prevention and Treatment of Atherosclerotic Cardiovascular Diseases

Atherosclerotic cardiovascular diseases (ASCVDs) are the most important diseases that endanger people’s health, leading to high morbidity and mortality worldwide. In addition, various thrombotic events secondary to cardiovascular and cerebrovascular diseases need must be considered seriously. Therefore, the development of novel anti-platelet drugs with high efficiency, and fewer adverse effects has become a research focus for preventing of cardiovascular diseases (CVDs). Blood-activation and stasis-removal from circulation have been widely considered as principles for treating syndromes related to CVDs. Blood-activating Chinese (BAC botanical drugs, as members of traditional Chinese medicine (TCM), have shown to improve hemodynamics and hemorheology, and inhibit thrombosis and atherosclerosis. Modern medical research has identified that a combination of BAC botanical drugs and anti-platelet drugs, such as aspirin or clopidogrel, not only enhances the anti-platelet effects, but also reduces the risk of bleeding and protects the vascular endothelium. The anti-platelet mechanism of Blood-activating Chinese (BAC) botanical drugs and their compounds is not clear; therefore, their potential targets need to be explored. With the continuous development of bioinformatics and “omics” technology, some unconventional applications of BAC botanical drugs have been discovered. In this review, we will focus on the related targets and signaling pathways of anti-atherosclerotic treatments involving a combination of BAC botanical drugs and anti-platelet drugs reported in recent years.

Biological functions, mechanisms, and clinical significance of circular RNA in pancreatic cancer: a promising rising star

Pancreatic cancer (PC) is a highly malignant solid tumor with insidious onset and easy early metastasis. Despite tremendous efforts devoted to research in this field, the mechanisms underlying PC tumorigenesis and progression remain unclear. Additionally, robust biomarkers and satisfactory therapeutic strategies for clinical use in PC patients are still lacking. Circular RNAs (circRNAs) are a new type of non-coding RNA originating from precursor messenger RNAs, with a covalent continuous closed-loop structure, strong stability and high specificity. Accumulating evidence suggests that circRNAs may participate in PC development and progression. Abnormal expression of circRNAs in PC is considered a vital factor that affects tumor cell proliferation, migration, invasion, apoptosis, angiogenesis and drug resistance. In this review of relevant articles published in recent years, we describe the basic knowledge concerning circRNAs, including their classification, biogenesis, functions and research approaches. Moreover, the biological roles and clinical significance of circRNAs related to PC are discussed. Finally, we note the questions remaining from recent studies and anticipate that further investigations will address these gaps in knowledge in this field. In conclusion, we expect to provide insights into circRNAs as potential targets for specific PC diagnosis and treatment in the future.

Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) with a single-stranded covalently closed-loop structure, and their abnormal expression may participate in the pathogenesis of various human diseases. Currently, knowledge of circRNAs in gout is limited. In this case-control study, human circRNA microarrays were used to identify differentially expressed circRNAs in peripheral blood mononuclear cells (PBMCs) from patients with primary gout (n = 5) and healthy controls (HC; n = 3). Bioinformatics methods were used to analyze significantly different circRNAs (fold change >1.5, p < 0.05). In addition, four significantly differentially expressed circRNAs were selected for quantitative real-time polymerase chain reaction to detect expression levels in 90 gout patients and 60 HC. Subsequently, circRNA-miRNA-mRNA network was established to predict the function of circRNAs of interest. Microarray analysis indicated that 238 circRNAs were upregulated and 41 circRNAs were down-regulated in the gout group (fold change >1.5, p < 0.05). Bioinformatics analysis showed that differentially expressed circRNAs were involved in the pathogenesis of gout via various pathways. Moreover, the expression levels of hsa_circRNA_103657 and hsa_circRNA_000241 were significantly higher in the gout group than those in the HC group, and both correlated significantly with lipid metabolism parameters. Furthermore, the area under the curve of hsa_circRNA_103657 was 0.801 (95% confidence interval (CI): 0.730–0.871; p < 0.001). Our results provide novel insights into the pathogenesis of primary gout. Differentially expressed circRNAs were identified in the PBMCs of gout patients, and these differential circRNAs may play important roles in the development and progression of gout.

Identification of Three Potential circRNA Biomarkers of Polycystic Ovary Syndrome by Bioinformatics Analysis and Validation

Objective

It is well known that circRNAs are closely involved in the progression of various diseases. However, their functions and potential regulatory mechanisms in polycystic ovary syndrome (PCOS) remain largely unknown. In the present study, our aim was to investigate the potential diagnostic value of circRNAs in PCOS.

Methods

The circRNA dataset GSE145296, mRNA dataset GSE155489 and miRNA GSE138572 were downloaded from Gene Expression Omnibus (GEO) database. Then, differentially expressed genes (DEGs) were identified. Based on the potential interactions, a network of cirRNA-related competing endogenous RNAs (ceRNAs) was constructed. Biological functions were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. For further validation, qRT-PCR method was used to detect the expression level of the candidate circRNAs. Then, receiver operating characteristics (ROC) were constructed to evaluate the diagnostic value of the three differentially expressed circRNA (DE-circRNA).

Results

We constructed a network of cirRNA-related ceRNA network. Hsa_circ_0075691, hsa_circ_0075692 and hsa_circ_0085997 were validate to be dysregulated in PCOS.

Conclusion

Hsa_circ_0075691, hsa_circ_0075692 and hsa_circ_0085997 may be potential diagnostic biomarkers of PCOS, but their specific regulatory mechanisms still need to be further studied.