Circular RNAs are abundant, conserved, and associated with ALU repeats

Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective

Bioinformatics has significantly advanced RNA-based therapeutics, particularly circular RNAs (circRNAs), which outperform mRNA vaccines, by offering superior stability, sustained expression, and enhanced immunogenicity due to their covalently closed structure. This review highlights how bioinformatics and computational biology optimise circRNA vaccine design, elucidates internal ribosome entry sites (IRES) selection, open reading frame (ORF) optimisation, codon usage, RNA secondary structure prediction, and delivery system development. While circRNA vaccines may not always surpass traditional vaccines in stability, their production efficiency and therapeutic efficacy can be enhanced through computational strategies. The discussion also addresses challenges and future prospects, emphasizing the need for innovative solutions to overcome current limitations and advance circRNA vaccine applications.

Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses

Herpesviruses require the host transcriptional machinery, inducing significant changes in gene expression to prioritize viral transcripts. We examined alpha- and gamma-herpesvirus alterations to a type of alternative splicing, namely circular RNA (circRNA) synthesis. We developed "Circrnas in Host And viRuses anaLysis pIpEline" (CHARLIE) to facilitate viral profiling. This method identified thousands of back-splicing variants, including circRNA common to lytic and latent phases of infection. Ours is the first report of Herpes Simplex Virus-1 circRNAs, including species derived from ICP0 and the latency-associated transcript. We characterized back-splicing cis- and trans-elements, and found viral circRNAs resistant to spliceosome perturbation and lacking canonical splice donor-acceptors. Subsequent loss-of-function studies of host RNA ligases (RTCB, RLIG1) revealed instances of decreased viral back splicing. Using eCLIP and 4sU-Sequencing, we determined that the KSHV RNA-binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work explores unique splicing mechanisms driven by lytic infection, and identifies a class of transcripts with the potential to function in replication, persistence, or tumorigenesis.

Circ_DLG1 facilitates cell proliferation and metastasis of esophageal squamous cell carcinoma via upregulating MAP3K9

BACKGROUND

Circ_DLG1 is found to be aberrantly expressed in esophageal squamous cell carcinoma (ESCC) tissues, but its role in the progression of ESCC remains to be elucidated.

METHODS

The expression of circ_DLG1, miR-338-3p and mitogen-activated protein kinase kinase kinase 9 (MAP3K9) was measured by qRT-PCR. Cell cycle, viability, migration and invasion were investigated using flow cytometry, MTT assay and transwell assay, respectively. The protein levels of MAP3K9, p38, phosphor p38 (p-p38), ERK1/2 (ERKs), phosphor ERKs (p-ERKs) were detected by western blot. Dual-luciferase reporter assay and RIP assay were performed to verify the putative relationship between miR-338-3p and circ_DLG1 or MAP3K9. Animal experiments were performed to ascertain the role of circ_DLG1 in vivo.

RESULTS

Circ_DLG1 expression was elevated in ESCC tissues, plasma and cells. Circ_DLG1 knockdown inhibited cell proliferation, migration and invasion. MAP3K9 was highly expressed in ESCC, and its overexpression rescued the effects of circ_DLG1 knockdown on cell proliferation and metastasis. Besides, circ_DLG1 positively regulated MAP3K9 expression by competitively targeting miR-338-3p. Also, miR-338-3p inhibition or MAP3K9 overexpression recovered the inhibiting effect of circ_DLG1 knockdown on the phosphorylated levels of p38 and ERKs. In addition, circ_DLG1 knockdown blocked the tumor growth in vivo by regulating the miR-338-3p/MAP3K9 axis.

CONCLUSION

Circ_DLG1 promoted malignant progression of ESCC by mediating the miR-338-3p/MAP3K9/p38/ERK pathway, indicating that targeted inhibition of the circ_DLG1/miR-338-3p/MAP3K9/p38/ERK axis might be an effective strategy for the treatment of ESCC.

Circular RNA in liver cancer research: biogenesis, functions, and roles

Liver cancer, characterized by its insidious nature, aggressive invasiveness, and propensity for metastasis, has witnessed a sustained increase in both incidence and mortality rates in recent years, underscoring the urgent need for innovative diagnostic and therapeutic approaches. Emerging research indicates that CircRNAs (circular RNAs) are abundantly and stably present within cells, with their expression levels closely associated with the progression of various malignancies, including hepatocellular carcinoma. In the context of liver cancer progression, circRNAs exhibit promising potential as highly sensitive diagnostic biomarkers, offering novel avenues for early detection, and also function as pivotal regulatory factors within the carcinogenic process. This study endeavors to elucidate the biogenesis, functional roles, and underlying mechanisms of circRNAs in hepatocellular carcinoma, thereby providing a fresh perspective on the pathogenesis of liver cancer and laying a robust foundation for the development of more precise and effective early diagnostic tools and therapeutic strategies.

Study on the mechanism of hsa_circ_0074763 regulating the miR-3667-3P/ACSL4 axis in liver fibrosis

This study aimed to investigate the involvement of hsa_circ_0074763 in the activation of HSCs (hepatic stellate cells ) and liver fibrosis. Additionally, it aimed to conduct a preliminary analysis of the molecular mechanism targeting miR-3667-3p/ACSL4 (Long-chain acyl-CoA synthetase 4), thereby providing novel molecular targets for liver fibrosis. The GEO database was utilized to identify differentially expressed hsa_circ_0074763 and determined its subcellular localization in LX-2 cells using fluorescence in situ hybridization. Bioinformatics analysis was employed for result prediction, and the interaction between hsa_circ_0074763 and miR-3667-3P was confirmed using dual-luciferase reporter gene assay. ACSL4 mediated ferroptosis was detected with kit. Hsa_circ_0074763 exhibits high expression levels in the fibrosis model. Validation through dual-luciferase reporter gene assays confirms the interaction between hsa_circ_0074763 and miR-3667-3P. Functional cell experiments demonstrate that overexpression of hsa_circ_0074763 promotes proliferation of LX-2 cells, elevates inflammation levels, and inhibits apoptosis. Additionally, ACSL4 has been identified as a direct target of miR-3667-3P, with overexpression of hsa_circ_0074763 counteracting the inhibitory effect on ACSL4 by suppressing miR-3667-3P. Overexpression of ACSL4 increased the expression levels of ROS (Lipid Oxidation), Iron (Ferro Orange) and MDA (Malondialdehyde), and decreased the expression levels of GPX4 (Glutathione peroxidase 4) and GSH (Glutathione). Our finding suggests that overexpression of hsa_circ_0074763 likely enhances the HSC activation through modulation of the miR-3667-3P/ACSL4 axis. Therefore, hsa_circ_0074763 holds potential as a therapeutic target for liver fibrosis.

The Application of Non-Coding RNAs as Biomarkers, Therapies, and Novel Vaccines in Diseases

Non-coding RNAs (ncRNAs) are a class of RNAs that largely lack the capacity to encode proteins. They have garnered significant attention due to their central regulatory functions across numerous cellular and physiological processes at transcriptional, post-transcriptional, and translational levels. Over the past decade, ncRNA-based therapies have gained considerable attention in the diagnosis, treatment, and prevention of diseases, and many studies have revealed a significant relationship between ncRNAs and diseases. At the same time, due to their tissue specificity, an increasing number of projects have focused on the application of ncRNAs as biomarkers in diseases, as well as the design and development of novel ncRNA-based vaccines and therapies for clinical use. These ncRNAs may also drive research into the potential molecular mechanisms and complex pathogenesis of related diseases. However, new biomarkers need to be validated for their clinical effectiveness. Additionally, to produce safe and stable RNA products, factors such as purity, precise dosage, and effective delivery methods must be ensured to achieve optimal bioactivity. These challenges remain key issues in the clinical application of ncRNAs. This review summarizes the prospects of ncRNAs as potential biomarkers, as well as the current research status and clinical applications of ncRNAs in therapies and vaccines, and discusses the challenges and expectations of ncRNAs in disease diagnosis and drug therapy.

Loss of age-accumulated crh-1 circRNAs ameliorate amyloid β-induced toxicity in a C. elegans model for Alzheimer's disease

Circular RNAs (circRNAs) are non-coding RNAs mostly derived from exons of protein-coding genes via a back-splicing process. The expression of hundreds of circRNAs accumulates during healthy aging and is associated with Alzheimer's disease (AD), which is characterized by the accumulation of amyloid-beta (Aβ) proteins. In C. elegans, many circRNAs were previously found to accumulate during aging, with loss of age-accumulated circRNAs derived from the CREB gene (circ-crh-1) to increase mean lifespan. Here, we used C. elegans to study the effects of age-accumulated circRNAs on the age-related onset of Aβ-toxicity. We found that circ-crh-1 mutations delayed Aβ-induced muscle paralysis and lifespan phenotypes in a transgenic C. elegans strain expressing a full-length human Aβ-peptide (Aβ1-42) selectively in muscle cells (GMC101). The delayed Aβ phenotypic defects were associated with the inhibition of Aβ aggregate deposition, and thus, genetic removal of circ-crh-1 alleviated Aβ-induced toxicity. Consistent with a detrimental role for age-accumulated circRNAs in AD, the expression level of circ-crh-1 expression is elevated after induction of Aβ during aging, whereas linear crh-1 mRNA expression remains unchanged. Finally, we found that the delayed onset of Aβ-induced paralysis observed in circ-crh-1 mutants is dependent on the col-49 collagen gene. Taken together, our results show that the loss of an age-accumulated circRNA exerts a protective role on Aβ-induced toxicity, demonstrating the utility of C. elegans for studying circRNAs in AD and its relationship to aging.

CircRNAs: a novel potential strategy to treat breast cancer

Breast cancer is among the most prevalent malignant tumors worldwide, with triple-negative breast cancer (TNBC) being the most aggressive subtype and lacking effective treatment options. Circular RNAs (circRNAs) are noncoding RNAs that play crucial roles in the development of tumors, including breast cancer. This article examines the progress of research on circRNAs in breast cancer, focusing on four main areas: 1) breast cancer epidemiology, classification, and treatment; 2) the structure, discovery process, characteristics, formation, and functions of circRNAs; 3) the expression, mechanisms, clinical relevance, and recent advances in the study of circRNAs in breast cancer cells and the immune microenvironment, particularly in TNBC; and 4) the challenges and future prospects of the use of circRNAs in BC research.

Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases

The bulk of RNA produced from the genome of complex organisms consists of a very large number of transcripts lacking protein translational potential and collectively known as noncoding RNAs (ncRNAs). Initially thought to be mere products of spurious transcriptional noise, ncRNAs are now universally recognized as pivotal players in cell regulatory networks across a broad spectrum of biological processes. Owing to their critical regulatory roles, ncRNA dysfunction is closely associated with the etiopathogenesis of various human malignancies, including cancer. As such, ncRNAs represent valuable diagnostic biomarkers as well as potential targets for innovative therapeutic intervention. In this review, we focus on microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two most extensively studied classes in the field of ncRNA biology. After outlining key concepts of miRNA and lncRNA biogenesis pathways, we examine their multiple roles in mediating epigenetic regulation of gene expression and chromatin organization. Finally, by providing numerous examples of specific miRNAs and lncRNAs, we discuss how dysregulation of these mechanisms contributes to the onset and/or progression of various human diseases.

Nucleic acid therapeutics: Past, present, and future

Nucleic acid therapeutics have become increasingly recognized in recent years for their capability to target both coding and non-coding sequences. Several types of nucleic acid modalities, including siRNA, mRNA, aptamer, along with antisense oligo, have been approved by regulatory bodies for therapeutic use. The field of nucleic acid therapeutics has been brought to the forefront by the rapid development of vaccines against COVID-19, followed by a number of approvals for clinical use including much anticipated CRISPR-Cas9. However, obstacles such as the difficulty of achieving efficient and targeted delivery to diseased sites remain. This review provides an overview of nucleic acid therapeutics and highlights substantial advancements, including critical engineering, conjugation, and delivery strategies, that are paving the way for their growing role in modern medicine.

HAS-CIRCpedia-5280 sponges miR-4712-5p inhibited colon cancer autophagyinduced by human beta-defensin-1

BACKGROUND

Among all malignancies, colorectal cancer ranks third in incidence rate and second in mortality rate. Human beta-defensin-1 (hBD-1) has broad-spectrum antimicrobial properties, and it plays an important role in the tumor microenvironment. Circular ribonucleic acids (circRNAs) regulate the proliferation and progression of colorectal cancer cells via cancer-related signaling pathways.

METHODS

Cell proliferation was assessed using the Cell Counting Kit-8 assay to determine the optimal hBD-1 concentration. Intracellular autophagic vesicles were visualized via monodansylcadaverine staining. In addition, the levels of AKT and mammalian target of rapamycin (mTOR)-associated signaling proteins were analyzed via Western blot analysis. CircRNA microarrays and quantitative real-time polymerase chain reaction were used to identify differentially expressed circRNAs in colon cancer cell lines. The functional role of HAS-CIRCpedia-5280 in vitro was demonstrated by overexpressing HAS-CIRCpedia-5280 and inhibiting miR-4712-5p. HAS-CIRCpedia-5280 could be a sponge of miR-4712-5p, mimicking the effect induced by HAS-CIRCpedia-5280 overexpression in colon cancer cells.

RESULTS

hBD-1 inhibited the proliferation of colon cancer cells and increased the number of intracellular autophagic vesicles. In addition, hBD-1 inhibited the AKT/mTOR signaling pathway, thereby enhancing cellular autophagy. Further, the interaction of HAS-CIRCpedia-5280 and miR-4712-5p was investigated. hBD-1 upregulated the expression level of HAS-CIRCpedia-5280 and downregulated the expression level of miR-4712-5p in colon cancer cells. Subsequently, the overexpression of HAS-CIRCpedia-5280 or the inhibition of miR-4712-5p activated the AKT/mTOR signaling pathway, leading to cellular autophagy inhibition. Conversely, the mimicry of miR-4712-p counteracted the effect of HAS-CIRCpedia 5280 overexpression in colon cancer cells by inhibiting the activation of the AKT/mTOR signaling pathway and, thereby, enhancing cellular autophagy.

CONCLUSION

hBD-1 can have an inhibitory effect against cell proliferation in colon cancer SW-620/HCT-116 cells via the HAS-CIRCpedia-5280/miR-4712-5p-mediated activation of autophagy.

DMGAT: predicting ncRNA-drug resistance associations based on diffusion map and heterogeneous graph attention network

Non-coding RNAs (ncRNAs) play crucial roles in drug resistance and sensitivity, making them important biomarkers and therapeutic targets. However, predicting ncRNA-drug associations is challenging due to issues such as dataset imbalance and sparsity, limiting the identification of robust biomarkers. Existing models often fall short in capturing local and global sequence information, limiting the reliability of predictions. This study introduces DMGAT (diffusion map and heterogeneous graph attention network), a novel deep learning model designed to predict ncRNA-drug associations. DMGAT integrates diffusion maps for sequence embedding, graph convolutional networks for feature extraction, and GAT for heterogeneous information fusion. To address dataset imbalance, the model incorporates sensitivity associations and employs a random forest classifier to select reliable negative samples. DMGAT embeds ncRNA sequences and drug SMILES using the word2vec technique, capturing local and global sequence information. The model constructs a heterogeneous network by combining sequence similarity and Gaussian Interaction Profile kernel similarity, providing a comprehensive representation of ncRNA-drug interactions. Evaluated through five-fold cross-validation on a curated dataset from NoncoRNA and ncDR, DMGAT outperforms seven state-of-the-art methods, achieving the highest area under the receiver operating characteristic curve (0.8964), area under the precision-recall curve (0.8984), recall (0.9576), and F1-score (0.8285). The raw data are released to Zenodo with identifier 13929676. The source code of DMGAT is available at https://github.com/liutingyu0616/DMGAT/tree/main.

SRSF3 and hnRNP A1-mediated m6A-modified circCDK14 regulates intramuscular fat deposition by acting as miR-4492-z sponge

The intramuscular fat (IMF) content of yak beef is critical for determining its quality. Circular RNAs (circRNAs) are a group of endogenous non-coding RNAs that have emerged as important factors in the regulation of IMF deposition. However, the molecular mechanisms through which circRNAs regulate IMF deposition, particularly in yaks, remain unclear. In the present study, a novel circRNA, circCDK14 (originating from the yak's CDK14 gene), was identified by sequencing and RNase R treatment. In our previous study, we successfully established a ceRNA network map and identified miR-4492-z, which interacts with circCDK14. Furthermore, using methylation prediction software, we predicted two genes, SRSF3 and hnRNP A1, that have a strong binding relationship with circCDK14; existing research has confirmed their close association with m6A methylation modifications. On the basis of these findings, we comprehensively evaluated the effects of circCDK14, miR-4492-z, SRSF3 and hnRNP A1 on the proliferation and differentiation of yak intramuscular pre-adipocytes using EdU, CCK-8, BODIPY, Oil Red O and qRT-PCR analyses. Mechanistically, the interaction between circCDK14 and miR-4492-z was validated using a dual-luciferase reporter gene assay and rescue experiments. RIP assays revealed the binding interaction of circCDK14 with SRSF3 and hnRNP A1. The MeRIP experiments showed modification of circCDK14 methylation, with SRSF3 and hnRNP A1 promoting the methylation and translocation of circCDK14 from the nucleus to the cytoplasm. In summary, our results suggest that m6A-modified circCDK14 plays a crucial role as an miR-4492-z sponge in regulating IMF deposition in yaks and that the nuclear export of circCDK14 correlates with the expression levels of SRSF3 and hnRNP A1. This study provides a theoretical basis for the improvement of yak meat quality and promotes the development of molecular yak breeding.

Recent advances and perspectives on the development of circular RNA cancer vaccines

Engineered circular RNAs (circRNAs) are emerging as promising platforms for RNA-based vaccines in cancer treatment. We summarize the recent advances of design, synthesis, and delivery of circRNA-based cancer vaccines, and highlight the applications and challenges of circRNA vaccines in cancer therapy. Further enhancements are required in areas such as antigen selection, targeted delivery, multidimensional crosstalks, and clinical trial assessments to advance the efficacy and safety of circRNA vaccines in cancer.

Predicting circRNA-Drug Resistance Associations Based on a Multimodal Graph Representation Learning Framework

Circular RNA (circRNA) is a class of noncoding RNA that is highly conserved and exhibit exceptional stability. Due to its function as a microRNA sponge, circRNA has gained significant attention as an essential biomarker and potential drug target in the pathogenesis of several cancers. Although many circRNAs have been identified to play a role in cancer resistance, traditional methods are time-consuming and expensive. In this context, computational methods offer a promising way to facilitate the discovery process. However, most existing prediction models focus on the association between circRNAs and drug resistance, without considering the corresponding disease-related information in the circRNA-drug resistance association. Incorporating disease-related information into the prediction of circRNA-drug resistance associations could potentially improve the efficiency and speed of discovering and developing circRNA-targeting drugs. We propose a computational framework, named GraphCDD, for predicting the association between circRNA and drug resistance. Our model utilizes data from three sources, namely circRNA, disease, and drug, to construct three similarity networks that represent the features of circRNA, disease, and drug, respectively. We utilize a multimodal graph neural network to acquire efficient representations of circRNAs, diseases, and drugs by integrating various types of information, and establish a predictive model. The experimental results have validated the effectiveness of our model and provided a promising method in predicting potential associations between circRNA and drug resistance.

Circular RNAs in cancer stem cells: Insights into their roles and mechanisms (Review)

Cancer stem cells (CSCs) represent a small, yet pivotal subpopulation of tumor cells that play significant roles in tumor initiation, progression and therapeutic resistance. Circular RNAs (circRNAs) are a distinct class of RNAs characterized by their closed‑loop structures, lacking 5' to 3'ends. There is growing evidence that circRNAs are integral to the development and regulation of CSCs. Aberrant expression of circRNAs in CSCs can contribute to oncogenic properties and drug resistance. Specifically, oncogenic circRNAs modulate CSC behavior via key signaling pathways, thereby promoting CSC self‑renewal and maintenance, as well as tumor progression. This review summarizes the latest research on the functional roles and regulatory mechanisms of circRNAs in CSC behavior and discusses potential applications and challenges of targeting circRNAs in CSCs. Understanding the intricate interactions between circRNAs and CSCs may lead to novel therapeutic strategies that effectively combat treatment resistance and improve patient outcomes.

Research progress of circular RNA FOXO3 in diseases (review)

Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs with a closed-loop structures, and they exert crucial regulatory functions in diverse biological processes and disease development through the modulation of linear RNA transcription, downstream gene expression, and protein translation, among others. Circular RNA FOXO3(circFOXO3, Hsa_circ_0006404) originates from exon 2 of the FOXO3 gene and exhibits widespread cytoplasmic expression in eukaryotic cells. It shows specific expression in different tissues or cells. Recent research has associated circFOXO3 with various diseases such as cancer, cardiovascular diseases, neurological disorders, senescence, and inflammation. However, a comprehensive review of the research progress of circFOXO3 in human diseases has not been conducted. In this paper, we provide a systematic review of the latest advances in circFOXO3 research in diseases, elucidate its biological functions and potential molecular mechanisms, and discuss the future directions and challenges in circRNAs research to provide valuable references and inspiration for research in this field.

Insights into non-coding RNAS: biogenesis, function and their potential regulatory roles in acute kidney disease and chronic kidney disease

Noncoding RNAs (ncRNAs) have emerged as pivotal regulators of gene expression, and have attracted significant attention because of their various roles in biological processes. These molecules have transcriptional activity despite their inability to encode proteins. Moreover, research has revealed that ncRNAs, especially microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are linked to pervasive regulators of kidney disease, including anti-inflammatory, antiapoptotic, antifibrotic, and proangiogenic actions in acute and chronic kidney disease. Although the exact therapeutic mechanism of ncRNAs remains uncertain, their value in treatment has been studied in clinical trials. The numerous renal diseases and the beneficial or harmful effects of NcRNAs on the kidney will be discussed in this article. Afterward, exploring the biological characteristics of ncRNAs, as well as their purpose and potential contributions to acute and chronic renal disease, were explored. This may offer guidance for treating both acute and long-term kidney illnesses, as well as insights into the potential use of these indicators as kidney disease biomarkers.

CircNIPBLL modulates the inflammatory response against Eimeria tenella infection via sponging gga-miR-2954

Coccidiosis, a parasitic disease caused by Eimeria protozoa that parasitizes intestinal tissues of chicken, poses a challenge to the development of the poultry industry. circRNAs are a class of circular RNA macromolecules crucial in the immune response to pathogens. Previous studies have shown that gga-miR-2954 inhibits the inflammatory response to Eimeria tenella (E. tenella) infection. In this study, we screened the key circRNA (circNIPBLL) regulating gga-miR-2954 using a co-expression network. The RNase R and Actinomycin D assays showed that the circular structure of the circNIPBLL was stable. Besides, the circNIPBLL expression was mainly distributed in the cytoplasm but did not have coding capacity. Overexpression of circNIPBLL significantly promoted the production of the IL-6, IL-1β, TNF-α, and IL-8 in sporozoite-stimulated DF-1 cells, whereas circNIPBLL knockdown significantly inhibited these effects. Moreover, circNIPBLL induced apoptosis of DF-1 cells stimulated by sporozoites. Mechanistically, circNIPBLL functioned as a sponge for gga-miR-2954, and overexpression of circNIPBLL rescued the effect of gga-miR-2954 mimic on the inflammatory response of DF-1 cells stimulated with sporozoites. Taken together, this study suggested that circNIPBLL modulated the inflammatory response against E. tenella infection by sponging gga-miR-2954, which may provide novel insights into the immune mechanisms of chicken resistance to E. tenella.

Exosomal CircMFN2 Enhances the Progression of Pituitary Adenoma via the MiR-146a-3p/TRAF6/NF-κB Pathway

BACKGROUND

 Pituitary adenoma (PA) is a common intracranial endocrine tumor, but no precise target has been found for effective prediction and treatment of PA.

METHODS

 Quantitative reverse transcription polymerase chain reaction (qRT‒PCR) analysis showed that circMFN2 could affect the expression of miR-146a-3p in PA samples. Moreover, we used Western blotting to evaluate the expression levels of TRAF6 and NF-κB markers. The EdU assay, scratch wound healing assay, and Matrigel invasion assay were performed to assess the potential function of this pathway in PA cells. Based on the bioinformatic analysis including KEGG, gene ontology (GO) analysis, and microarray analysis, we evaluated the efficacy of circMFN2 as a potential biomarker for diagnosing PA, and we aimed to determine the mechanism of action in PA cells.

RESULTS

 Our findings indicate that there is a significant increase in the expression of circMFN2 in tissues, serum, and exosomes in the invasive group compared with the noninvasive and normal groups. Furthermore, this difference was statistically significant both preoperatively and postoperatively. To clarify its function, we downregulated this gene, and the experimental results suggested that the motility and proliferative capacity were reduced in vitro. In addition, rescue assays showed that miR-146a-3p could successfully reverse the inhibitory effect of circMFN2 knockdown on motility and proliferation in PA cells. Moreover, downregulation of circMFN2 and miR-146a-3p significantly changed the expression of TRAF6 and NF-κB.

CONCLUSION

 This study identified that circMFN2 regulates miR-146a-3p to promote adenoma development partially via the TRAF6/NF-κB pathway and may be a potential therapeutic target for PA.

CircMRP4 orchestrates podocytes injury via the miR-499-5p/RRAGB/mTORC1 axis in diabetic kidney disease

Diabetic kidney disease2 (DKD) is a chronic complication of diabetes characterized by kidney damage due to persistent hyperglycemia. A growing number of evidence indicated that circular RNAs3 (circRNAs) play a crucial role in diabetes and associated complications. However, the function and mechanism of circRNAs in DKD remain unclear. Herein, we investigated the expression profiles of circRNAs in DKD mice compared to non-diabetic mice using RNA-seq analysis. A novel circRNA, circMRP4, derived from the circularization of Multidrug resistance-associated protein 44 (MRP4) was identified. The expression of circMRP4 was significantly increased in both kidney tissues of DKD and mouse podocytes exposed to high glucose5 (HG). In addition, knockdown of circMRP4 alleviated podocytes apoptosis and inflammation induced by HG, while circMRP4 overexpression resulted in the opposite impact. Dual-luciferase reporter, RNA immunoprecipitation and RNA pull-down assay demonstrated that circMRP4 could directly target miR-499-5p which was closely associated with podocytes apoptosis and inflammation. Furthermore, circMRP4 was found to act as a sponge for miR-499-5p, leading to the upregulation of its target RRAGB, thereby activating the mTORC1/P70S6K signaling. In summary, our findings suggested that circMRP4 mediated podocytes apoptosis and inflammation in DKD by modulating the miR-499-5p/RRAGB/mTORC1/P70S6K axis, highlighting circMRP4 as a potential therapeutic target for DKD.

Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism

Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3' and 5' ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.

Circular RNA in Pancreatic Cancer: Biogenesis, Mechanism, Function and Clinical Application

Circular RNAs (circRNAs) are a class of novel RNA molecules featured by single-strand covalently closed circular structure, which not only are extensively found in eukaryotes and are highly conserved, but also conduct paramount roles in the occurrence and progression of pancreatic cancer (PC) through diverse mechanisms. As recent studies have demonstrated, circRNAs typically exhibit tissue-specific and cell specific expression patterns, with strong potential as biomarkers for disease diagnosis and prognosis. On the basis of their localization and specific interactions with DNA, RNA, and proteins, circRNAs are considered to possess specific biological functions by acting as microRNA (miRNA) sponges, RNA binding protein (RBP) sponges, transcriptional regulators, molecular scaffolds and translation templates. On that account, further addressing the technical difficulties in the detection and research of circRNAs and filling gaps in their biological knowledge will definitely push ahead this comparatively young research field and bring circRNAs to the forefront of clinical practice. Thus, this review systematically summarizes the biogenesis, function, molecular mechanisms, biomarkers and therapeutic targets of circRNAs in PC.

Multiple roles of circular RNAs in prostate cancer: from the biological basis to potential clinical applications

Prostate cancer is an important health concern affecting men. Circular RNAs (circRNAs) play an important molecular biological role in regulating gene expression due to their unique structure. Studies have revealed the involvement of circRNAs in many human diseases. In prostate cancer, circRNAs can act as oncogenes or tumour suppressor genes and affect cancer cell proliferation, invasion, resistance to chemotherapy and, consequently, disease progression. Accordingly, prostate cancer-related circRNAs are expected to serve as new targets in early clinical diagnosis and targeted therapy, but the various roles of circRNAs in prostate cancer have not been fully elucidated. This article reviews the molecular pathological roles of circRNA in prostate cancer and explores its prospects as a translational medicine in clinical treatment and prognostic evaluation.

Role of circular RNAs in cancer therapy resistance

Over the past decade, circular RNAs (circRNAs) have gained recognition as a novel class of genetic molecules, many of which are implicated in cancer pathogenesis via different mechanisms, including drug resistance, immune escape, and radio-resistance. ExosomalcircRNAs, in particular, facilitatecommunication between tumour cells and micro-environmental cells, including immune cells, fibroblasts, and other components. Notably, micro-environmental cells can reportedly influence tumour progression and treatment resistance by releasing exosomalcircRNAs. circRNAs often exhibit tissue- and cancer-specific expression patterns, and growing evidence highlights their potential clinical relevance and utility. These molecules show strong promise as potential biomarkers and therapeutic targets for cancer diagnosis and treatment. Therefore, this review aimed to briefly discuss the latest findings on the roles and resistance mechanisms of key circRNAs in the treatment of various malignancies, including lung, breast, liver, colorectal, and gastric cancers, as well as haematological malignancies and neuroblastoma.This review will contribute to the identification of new circRNA biomarkers for the early diagnosis as well as therapeutic targets for the treatment of cancer.

CircAKT3 promotes prostate cancer proliferation and metastasis by enhancing the binding of RPS27A and RPL11

BACKGROUND

Metastatic prostate cancer (PCa) is a leading cause of mortality among PCa patients. Although circular RNAs (circRNAs) are recognized for their pivotal roles in tumorigenesis, the specifics of their influence within the context of PCa have yet to be fully elucidated.

METHODS

RT-qPCR was conducted to evaluate circAKT3 expression in PCa cells and in both tumor and adjacent noncancerous tissues. The oncogenic role of circAKT3 was confirmed through a combination of in vitro and in vivo experiments. Mechanistic investigations using RNA-pulldown, RNA immunoprecipitation (RIP), fluorescence in situ hybridization (FISH), immunofluorescence (IF), and Chromatin Immunoprecipitation (ChIP) assays explored how circAKT3 modulates c-Myc activity via interactions with RPS27A and RPL11. Additionally, Western Blotting and further in vitro and in vivo studies assessed circAKT3's influence on PCa progression through MST1.

RESULTS

This research identified the function and regulation of circAKT3, a circRNA derived from exons 2 to 8 of the kinase-b3 (AKT3) gene, in human PCa cells. CircAKT3 was significantly correlated with clinical indicators of disease severity, including D'Amico risk classification, the Gleason score, and pT stage. Both in vitro and in vivo experiments demonstrated that circAKT3 knockdown inhibited PCa cell proliferation, migration, and invasion. Lipid nanoparticles encapsulating si-circAKT3 (LNP-si-circAKT3) effectively suppressed the growth of bone tumors formed by PCa cells. Mechanistically, circAKT3 acted as a protein scaffold between ribosomal protein S27a (RPS27A) and ribosomal protein L11 (RPL11), promoting their cytoplasmic translocation and reducing nuclear RPL11 levels, ultimately diminishing RPL11's interaction with c-Myc and resulting in enhanced c-Myc-driven suppression of macrophage stimulating 1 (MST1) expression. Consequently, the decreased MST1 led to PCa progression and metastasis. CircAKT3 formation was facilitated by both flanking Alu elements and the RNA binding protein Quaking (QKI). Additionally, downregulation of the RNA helicase URH49 resulted in the nuclear accumulation of circAKT3, finally suppressing MST1 expression.

CONCLUSION

Our findings suggest that circAKT3 acts as a protein scaffold, promoting the interaction between RPS27A and RPL11, thereby influencing c-Myc activity and PCa progression. This study underscores the crucial role of circAKT3 in PCa and its potential as a therapeutic target to impede malignancy progression and metastasis.

CircRNA hsa_circ_0004781 promoted cell proliferation by acting as a sponge for miR-9-5p and miR-338-3p and upregulating KLF5 and ADAM17 expression in pancreatic ductal adenocarcinoma

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive types of solid tumor, and novel strategies must be developed for treating it. Previous studies predominantly utilized circular RNA (circRNA) expression plasmids incorporating Alu elements to facilitate the indirect expression of circRNA.

METHODS

Public databases and bioinformatics tools were used to identify hsa_circ_0004781 that is highly expressed in PDAC and its potential microRNA (miRNA) targets and corresponding mRNA targets. Real hsa_circ_0004781, which is identical to the native form of hsa_circ_0004781 without any exogenous sequences, was prepared through in vitro transcription by using a ribozyme and ion-pair reversed-phase high-performance liquid chromatography (IP-RP HPLC). The biological functions of hsa_circ_0004781 were evaluated using loss-of-function and gain-of-function approaches with circRNA expression plasmids and real hsa_circ_0004781.

RESULTS

Knockdown of hsa_circ_0004781 inhibited the proliferation and migration of PDAC cells, whereas its overexpression produced opposite effects. Hsa_circ_0004781 was identified as a sponge for miR-9-5p and miR-338-3p, and its expression was negatively correlated with that of these miRNAs. Among the targets of miR-9-5p and miR-338-3p, Kruppel-like factor 5 (KLF5) and a disintegrin and metalloproteinase domain 17 (ADAM17) were negatively correlated with survival in patients with PDAC and were inversely regulated by these miRNAs. Furthermore, real hsa_circ_0004781 exhibited the same effects as those of the circRNA expression plasmids.

CONCLUSIONS

This study is the first to use real circRNAs to validate results obtained using circRNA expression plasmids. The results suggest that hsa_circ_0004781 functions as an oncogene, promoting the proliferation of PDAC cells through the miR-9-5p/KLF5 and miR-338-3p/ADAM17 axes. Therefore, hsa_circ_0004781 might be a therapeutic target for PDAC.

Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing

BACKGROUND

Skin wound healing involves a complex gene expression programme that remains largely undiscovered in humans. Circular RNAs (circRNAs) and microRNAs (miRNAs) are key players in this process.

OBJECTIVES

To understand the functions and potential interactions of circRNAs and miRNAs in human skin wound healing.

METHODS

CircRNA, linear RNA and miRNA expression in human acute and chronic wounds were analysed with RNA sequencing and quantitative reverse transcription polymerase chain reaction. The roles of circASH1L(4,5) and miR-129-5p were studied in human primary keratinocytes (proliferation and migration assays, microarray analysis) and ex vivo wound models (histological analysis). The interaction between circASH1L(4,5) and miR-129-5p was examined using luciferase reporter and RNA pulldown assays.

RESULTS

We identified circASH1L(4,5) and its interaction with miR-129-5p, both of which increased during human skin wound healing. Unlike typical miRNA sponging, circASH1L enhanced miR-129 stability and silencing activity by protecting it from target-directed degradation triggered by NR6A1 mRNA. Transforming growth factor-β signalling - crucial in wound healing - promoted circASH1L expression while suppressing NR6A1, thereby increasing the abundance of miR-129 at the post-transcriptional level. CircASH1L and miR-129 enhanced keratinocyte migration and proliferation, crucial processes for the re-epithelialization of human wounds.

CONCLUSIONS

Our study uncovered a novel role for circRNAs as protectors of miRNAs and highlights the importance of regulated miRNA degradation in skin wound healing.

CircMETTL9 targets CCAR2 to induce neuronal oxidative stress and apoptosis via mitochondria-mediated pathways following traumatic brain injury

Traumatic brain injury (TBI) remains a principal factor in neurological disorders, often resulting in significant morbidity due to secondary neuroinflammatory and oxidative stress responses. While circular RNAs are recognized for their high expression levels in the nervous system and play crucial roles in various neurological processes, their specific contributions to the pathophysiology of TBI remain underexplored. In this study, the possible molecular mechanisms through which circMETTL9 modulated oxidative stress and neurological outcomes following TBI were investigated. In vitro model of oxidative stress utilizing SH-SY5Y cells revealed that circMETTL9 knockdown significantly attenuated H₂O₂-induced reactive oxygen species (ROS) production, reduced apoptosis, and preserved mitochondrial function. Additionally, CCAR2 has been identified as a circMETTL9-binding protein by mass spectrometry and RNA immunoprecipitation, with circMETTL9 positively regulating CCAR2 expression. Meanwhile, on the basis of silencing CCAR2, it was verified that the regulation of oxidative stress in SH-SY5Y cells by circMETTL9 was mediated by CCAR2. In vivo experiments using a TBI rat model further confirmed that CCAR2 knockdown alleviated central nervous system (CNS) injury, reduced oxidative stress and apoptosis, and protected mitochondrial integrity following TBI. These findings suggest a novel mechanism by which circMETTL9 targets CCAR2 via mitochondria-mediated Bax/Bcl-2/caspase-3 signaling to regulate apoptosis. CircMETTL9 may provide a viable therapeutic target for mitigating neurological dysfunction following TBI, offering new insights into potential interventions aimed at reducing secondary brain injury.

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.

Circular RNA-Drug Association Prediction Based on Multi-Scale Convolutional Neural Networks and Adversarial Autoencoders

The prediction of circular RNA (circRNA)-drug associations plays a crucial role in understanding disease mechanisms and identifying potential therapeutic targets. Traditional methods often struggle to cope with the complexity of heterogeneous networks and the high dimensionality of biological data. In this study, we propose a circRNA-drug association prediction method based on multi-scale convolutional neural networks (MSCNN) and adversarial autoencoders, named AAECDA. First, we construct a feature network by integrating circRNA sequence similarity, drug structure similarity, and known circRNA-drug associations. Then, unlike conventional convolutional neural networks, we employ MSCNN to extract hierarchical features from this integrated network. Subsequently, adversarial characteristics are introduced to further refine these features through an adversarial autoencoder, obtaining low-dimensional representations. Finally, the learned representations are fed into a deep neural network to predict novel circRNA-drug associations. Experiments show that AAECDA outperforms various baseline methods in predicting circRNA-drug associations. Additionally, case studies demonstrate that our model is applicable in practical related tasks.

Identifying Essential Hub Genes and circRNA-Regulated ceRNA Networks in Hepatocellular Carcinoma

Competitive endogenous RNAs (ceRNAs) absorb microRNAs and subsequently promote corresponding mRNA and long noncoding RNA (lncRNA) expression, which may alter cancer cell malignancy. Thus, dissecting ceRNA networks may reveal novel targets in cancer therapies. In this study, we analyzed differentially expressed genes (DEGs) of mRNAs and lncRNAs, and differentially expressed microRNAs (DE-miRNAs) and circular RNAs (DE-circRNAs) extracted from high-throughput sequencing datasets of hepatocellular carcinoma patients. Based on these data, we identified 26 gene modules using weighted gene co-expression network analysis (WGCNA), of which 5 were associated with tumor differentiation. In these modules, 269 genes were identified by GO and KEGG enrichment and patient's survival correlation analyses. Next, 40 DE-miRNAs, each of which potentially bound a pair of DE-circRNA and hub gene, were discovered. Together with 201 circRNAs and 24 hub genes potentially bound by these miRNAs, 1151 ceRNA networks were constructed. Among them, 75 ceRNA networks consisting of 24 circRNAs, 28 miRNAs and 17 hub genes showed a positive circRNA-hub gene correlation. For validation, we carried out experiments for 4 randomly selected circRNAs regulating 19 potential ceRNA networks and verified 5 of them. This study represents a powerful strategy to identify essential gene networks and provides insights into designing effective therapeutic strategies.

The noncoding circular RNA circHomer1 regulates synaptic development and experience-dependent plasticity in mouse visual cortex

Circular RNAs (circRNAs) are a class of closed-loop, single stranded RNAs whose expression is particularly enriched in the brain. Despite this enrichment and evidence that the expression of circRNAs are altered by synaptic development and in response to synaptic plasticity in vitro, the regulation by and function of the majority of circRNAs in experience-dependent plasticity in vivo remain unexplored. Here, we employed transcriptome-wide analysis comparing differential expression of both mRNAs and circRNAs in juvenile mouse primary visual cortex (V1) following monocular deprivation (MD), a model of experience-dependent developmental plasticity. Among the differentially expressed mRNAs and circRNAs following 3-day MD, the circular and the activity-dependent mRNA forms of the Homer1 gene, circHomer1 and Homer1a respectively, were of interest as their expression changed in opposite directions: circHomer1 expression increased while the expression of Homer1a decreased following 3-day MD. Knockdown of circHomer1 delayed the depression of closed-eye responses normally observed after 3-day MD. circHomer1-knockdown also led to a reduction in average dendritic spine size prior to MD but critically there was no further reduction after 3-day MD, consistent with impaired structural plasticity. circHomer1-knockdown also prevented the reduction of surface AMPA receptors after 3-day MD. Synapse-localized puncta of the AMPA receptor endocytic protein Arc increased in volume after MD but were smaller in circHomer1-knockdown neurons, suggesting that circHomer1 knockdown impairs experience-dependent AMPA receptor endocytosis. Thus, the expression of multiple circRNAs are regulated by experience-dependent developmental plasticity, and our findings highlight the essential role of circHomer1 in V1 synaptic development and experience-dependent plasticity.

Circular RNA circPFKP suppress gastric cancer progression through targeting miR-346/CAMD3 axis

Studies have demonstrated that circular RNAs (circRNAs) exert an important regulatory function in the pathogenesis of various tumors. However, their role in gastric cancer (GC) is still not completely understood. In our study, the differentially expressed circRNAs in GC tissues and matched adjacent normal tissues were analyzed by utilizing gene chips GSE93541, GSE89143, and GSE78092. The expression of has_circ_0006608 (circPFKP), miR-346, and CAMD3 was analyzed through quantitative real-time polymerase chain reaction (qRT-PCR). The CCK-8 assay and Transwell assay were employed to detect the effect of circPFKP on the proliferation, migration, and invasion of gastric cancer cells. The mice xenograft assay was used to assess the function of circPFKP in vivo. The targeting relationship between circPFKP, miR-346, and CAMD3 was predicted by bioinformatics analysis and confirmed by the dual-luciferase reporter assay and RNA pull-down assay. Our results screened and verified that circPFKP was down-regulated in gastric cancer tissues and cells. Overexpression of circPFKP in GC cells can inhibit cell proliferation, migration, invasion, and tumor growth in vivo. Additionally, circPFKP has been shown to act as a sponge for miR-346 to modulate the expression of CAMD3. Finally, we demonstrated that overexpression of CAMD3 or miR-346 inhibitor significantly reversed the effects of si-circPFKP on the proliferation, migration, and invasion of gastric cancer cells. In conclusion, this study provided that circPFKP inhibits the progression of GC via the miR-346/CAMD3 axis, this may provide a noval biomarker for the diagnosis and treatment of GC.

CircBTBD7-420aa Encoded by hsa_circ_0000563 Regulates the Progression of Atherosclerosis and Construction of circBTBD7-420aa Engineered Exosomes

Circular RNAs are associated with cardiovascular disease, including coronary artery disease, but the mechanisms have not been completely elucidated. We found a new protein, circBTBD7-420aa, encoded by hsa_circ_0000563. Our results suggest that circBTBD7-420aa may inhibit the abnormal proliferation and migration of human coronary artery smooth muscle cells by promoting SLC3A2 degradation through the ubiquitin-proteasome pathway. In addition, we constructed engineered exosomes loaded with circBTBD7-420aa that can target vascular smooth muscle cells by modifying peptide fragments targeting osteopontin. This study suggests that circBTBD7-420aa may inhibit the progression of atherosclerosis and serve as a new target for the diagnosis and treatment of coronary artery disease.

Circular RNAs in cancer

Circular RNA (circRNA), a subtype of noncoding RNA, has emerged as a significant focus in RNA research due to its distinctive covalently closed loop structure. CircRNAs play pivotal roles in diverse physiological and pathological processes, functioning through mechanisms such as miRNAs or proteins sponging, regulation of splicing and gene expression, and serving as translation templates, particularly in the context of various cancers. The hallmarks of cancer comprise functional capabilities acquired during carcinogenesis and tumor progression, providing a conceptual framework that elucidates the nature of the malignant transformation. Although numerous studies have elucidated the role of circRNAs in the hallmarks of cancers, their functions in the development of chemoradiotherapy resistance remain unexplored and the clinical applications of circRNA-based translational therapeutics are still in their infancy. This review provides a comprehensive overview of circRNAs, covering their biogenesis, unique characteristics, functions, and turnover mechanisms. We also summarize the involvement of circRNAs in cancer hallmarks and their clinical relevance as biomarkers and therapeutic targets, especially in thyroid cancer (TC). Considering the potential of circRNAs as biomarkers and the fascination of circRNA-based therapeutics, the "Ying-Yang" dynamic regulations of circRNAs in TC warrant vastly dedicated investigations.

Circ_0082374 Promotes the Tumorigenesis and Suppresses Ferroptosis in Non-small Cell Lung Cancer by Up-Regulating GPX4 Through Sequestering miR-491-5p

Circular RNAs (circRNAs) have been identified to be dysregulated in non-small cell lung cancer (NSCLC) and implicated in the progression of this cancer. Here, this work aimed to investigate the role and mechanism of circ_0082374 on NSCLC progression. Levels of circ_0082374, miR-491-5p, GPX4 (glutathione peroxidase 4) and epithelial-mesenchymal transition (EMT)-related proteins were examined by quantitative real-time PCR or western blotting, respectively. Cell proliferation and metastasis were detected using cell counting kit-8, colony formation, EdU, transwell, and Scratch assays. Cell ferroptosis was evaluated by measuring cell survival after the treatment of different ferroptosis inducers or inhibitors, as well as the accumulation of intracellular reactive oxygen species (ROS), ferrous iron (Fe2+) and malondialdehyde (MDA). The binding between miR-491-5p and circ_0082374 or GPX4 was confirmed using dual-luciferase reporter and RNA pull-down assays. In vivo experiments were conducted using murine xenograft assay and immunohistochemistry. Circ_0082374 was a stable circRNA with high expression in NSCLC tissues and cells. Functionally, circ_0082374 silencing suppressed NSCLC cell proliferation and metastasis. Moreover, its down-regulation enhanced ferroptosis by decreasing iron and lipid peroxidation accumulation. Mechanistically, circ_0082374 could indirectly up-regulate GPX4 expression via miR-491-5p, indicating the circ_0082374/miR-491-5p/GPX4 competitive endogenous RNAs (ceRNA) network. Rescue experiments demonstrated that the miR-491-5p/GPX4 axis mediated the regulatory effects of circ_0082374 exerted on NSCLC cells. Moreover, knockdown of circ_0082374 impeded NSCLC growth and EMT via regulating miR-491-5p and GPX4. Circ_0082374 silencing could suppress NSCLC cell proliferation, metastasis and induce ferroptosis through miR-491-5p/GPX4 axis, suggesting a novel therapeutic approach for NSCLC patients.

Exploring precision treatments in immune-mediated inflammatory diseases: Harnessing the infinite potential of nucleic acid delivery

Immune-mediated inflammatory diseases (IMIDs) impose an immeasurable burden on individuals and society. While the conventional use of immunosuppressants and disease-modifying drugs has provided partial relief and control, their inevitable side effects and limited efficacy cast a shadow over finding a cure. Promising nucleic acid drugs have shown the potential to exert precise effects at the molecular level, with different classes of nucleic acids having regulatory functions through varying mechanisms. For the better delivery of nucleic acids, safe and effective viral vectors and non-viral delivery systems (including liposomes, polymers, etc.) have been intensively explored. Herein, after describing a range of nucleic acid categories and vectors, we focus on the application of therapeutic nucleic acid delivery in various IMIDs, including rheumatoid arthritis, inflammatory bowel disease, psoriasis, multiple sclerosis, asthma, ankylosing spondylitis, systemic lupus erythematosus, and uveitis. Molecules implicated in inflammation and immune dysregulation are abnormally expressed in a series of IMIDs, and their meticulous modulation through nucleic acid therapy results in varying degrees of remission and improvement of these diseases. By synthesizing findings centered on specific molecular targets, this review delivers a systematic elucidation and perspective towards advancing and utilization of nucleic acid therapeutics for managing IMIDs.

Unveiling new therapeutic horizons in rheumatoid arthritis: an In-depth exploration of circular RNAs derived from plasma exosomes

Rheumatoid arthritis (RA), a chronic inflammatory joint disease causing permanent disability, involves exosomes, nanosized mammalian extracellular particles. Circular RNA (circRNA) serves as a biomarker in RA blood samples. This research screened differentially expressed circRNAs in RA patient plasma exosomes for novel diagnostic biomarkers. In this study, samples of RA patients with insufficient response to methotrexate (MTX-IR), combined use of tumor necrosis factor inhibitors (TNFi) were followed up for half a year, and 56 circRNA samples of self-test data were stratified into training, testing, and external validation cohorts according to whether American College of Rheumatology 20% improvement criteria (ACR20) was achieved. A diagnostic xgboost model was developed using common hub genes identified by random forest and least absolute shrinkage and selection operator (LASSO), with intersection genes derived from overlapping machine learning-selected genes. Diagnostic performance evaluated via receiver operating characteristic (ROC) curves using pROC for area under the curve (AUC). Optimal LASSO model with 4 circRNAs determined, with AUC > 0.6 for key genes. The model validation performed well on the test set, but not significantly on the validation set. Then, circRNA screening was performed in combination with clinical data, and cross-validation identified hsa-circ0002715, hsa-circ0001946, hsa-circ0000836, and rheumatoid factor (RF) as key genes, among which hsa-circ0002715 and hsa-circ0001946 were emphasized as key markers on the training set. In addition, the morphology and size of exosomes and the expression of CD9 and CD81 verified the successful extraction of exosomes. The qPCR analysis of plasma exosomes in TNFi patients found that the expression of hsa-circ0002715 was higher than that in patients who didn't reach ACR20, and the expression of hsa-circ0001946 was lower than that in patients who didn't reach ACR20. The above studies suggested that hsa-circ0002715 and hsa-circ0001946 may become markers for predicting MTX-IR RA patients and TNFi precision treatment.

The Role of the Dysregulation of circRNAs Expression in Glioblastoma Multiforme

Primary brain tumors that were the most severe and aggressive were called glioblastoma multiforme (GBM). Cancers are caused in part by aberrant expression of circular RNA. Often referred to as competitive endogenous RNA (ceRNA), circRNA molecules act as "miRNA sponges" in cells by decreasing the inhibitory impact of miRNA on their target genes and hence raising the expression levels of those genes. circRNA molecules are rich in miRNA binding sites. The discovery of more structurally diverse and GBM-related circRNAs has great promise for the use of GMB prognostic biomarkers and therapeutic targets, as well as for comprehending the molecular regulatory mechanisms of GBM. In this work, we present an overview of the circRNA expression patterns associated with GBM and offer a potential integrated electrochemical strategy for detecting circRNA with extreme sensitivity in the diagnosis of glioblastoma.

CircRNA expression profiling of the rat thalamus in temporomandibular joint chronic inflammatory pain

Orofacial pain (OFP) induced by temporomandibular disorders (TMDs) is prevalent, affecting approximately 4.6 % of the population. One specific type of TMD is temporomandibular osteoarthritis (TMJOA), a common degenerative disease that significantly impacts patients' quality of life. Differentially expressed circular RNAs (DEcircRNAs) in the thalamus, which serves as a relay station in the orofacial pain transmission pathway, may play a crucial role and serve as potential target markers for inflammation and the progression of inflammatory pain in TMJOA. The aim of this study was to investigate the expression profile of circRNAs in the thalamus of TMJOA. We obtained the circRNA expression profile from the thalamus of a rat model of TMJOA through high-throughput sequencing (HT-seq) and further validated their expression using reverse transcription real-time polymerase chain reaction (RT-qPCR), followed by bioinformatics analysis of the expression data. A total of 425 circRNAs (DESeq2 p- value < 0.05, |log2FoldChange| > 0.0) were identified as significantly differentially expressed by RNA-Seq, comprising 188 up-regulated and 237 down-regulated circRNAs. After validation via RT-qPCR, we employed miRanda software to predict the binding sites of miRNAs for the identified circRNAs to further explore the functions of DEcircRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that DEcircRNAs were primarily enriched in pathways and functions related to synapse development, protein signaling and modification, 'Circadian entertainment', the 'MAPK signaling pathway', and 'Glutamatergic synapse'. These findings suggest that DEcircRNAs in the thalamus play a significant role in the progression of TMJOA and may serve as promising candidate molecular targets for gene therapy.

Mechanisms and therapeutic implications of gene expression regulation by circRNA-protein interactions in cancer

Circular RNAs (circRNAs) have garnered substantial attention due to their distinctive circular structure and gene regulatory functions, establishing them as a significant class of functional non-coding RNAs in eukaryotes. Studies have demonstrated that circRNAs can interact with RNA-binding proteins (RBPs), which play crucial roles in tumorigenesis, metastasis, and drug response in cancer by influencing gene expression and altering the processes of tumor initiation and progression. This review aims to summarize the recent advances in research on circRNA-protein interactions (CPIs) and discuss the functions and mode of action of CPIs at various stages of gene expression, including transcription, splicing, translation, and post-translational modifications in the context of cancer. Additionally, we explore the role of CPIs in tumor drug resistance to gain a deeper understanding of their potential applications in the development of new anti-cancer therapeutic approaches.

Elucidating circRNA-miRNA-mRNA competing endogenous regulatory RNA network during leaf rust pathogenesis in wheat (Triticum aestivum L.)

Advancements in bioinformatic tools and breakthroughs in high throughput RNA sequencing have unveiled the potential role of non-coding RNAs in influencing the overall expression of disease-responsive genes. Owing to the increasing need to develop resilient crop varieties against environmental constraints, our study explores the functional relationship of various non-coding RNAs in wheat during leaf rust pathogenesis. MicroRNAs (miRNAs) and circular RNAs (circRNAs) were retrieved from SAGE and RNA-Seq libraries, respectively, in the susceptible (HD2329) and resistant (HD2329 + Lr28) wheat Near-Isogenic Lines (NILs). Here we explored the previously published circRNAs for their differential expression and correlated the data with the differentially expressed miRNAs (DEMs) through various in silico methods to acquire the target miRNAs of circRNAs and the downstream target mRNAs of miRNAs. Finally, a competing endogenous RNA (ceRNAs) regulatory network was constructed and validated through RT-qPCR method. We have identified the ceRNA regulatory network of four differentially expressed circRNAs (DECs) and five DEMs to highlight their crucial roles in the robust enhancement of the temporal expression profiles of five defense responsive genes (mRNAs) in wheat NILs against leaf rust infection. The study confirms the synergistic expression of circRNAs and mRNAs with an antagonistic correlation with the expression profile of the corresponding miRNAs. The vital role of leaf rust-resistant gene Lr28 has also been highlighted for driving the efficiency of the circRNAs to upregulate target gene expression. Thus, understanding the circRNA-miRNA-target gene interaction during leaf rust pathogenesis can help to identify stress-specific regulatory biomarkers to enhance defense responses in wheat for improved resilience through multi-omics integration of transcriptomics, proteomics and metabolomics.

Circular RNAs in the management of human osteoporosis

BACKGROUND

Osteoporosis (OP) is a metabolic bone disease producing reduction in bone mass with consequent bone fragility. Circular ribonucleic acid (CircRNA) is a form of RNA that forms a loop structure rather than a linear one. CircRNA can be used for therapeutic purposes, including molecular targets or to test new therapies.

SOURCES OF DATA

A systematic search of different databases to July 2024 was performed to define the role of circRNA in OP therapy. Seventeen suitable studies were identified.

AREAS OF AGREEMENT

CircRNAs may be useful in studying metabolic processes in OP and identify possible therapeutic targets and new drug therapies.

AREAS OF CONTROVERSY

The metabolic processes involved in OP are regulated by many genes and cytokines that can be targeted by CircRNAs. However, it is not easy to predict whether the in vitro responses of the studied CircRNAs and their interaction with drugs are also applicable in vivo.

GROWING POINTS

Metabolic processes can be affected by gene dysregulation of CircRNAs on various growth factors. Areas timely for developing research: Despite the predictability of CircRNA pharmacological response in vitro, such pharmacological response cannot be expected to be replicated in vivo.

DATA AVAILABILITY

The data that support the findings of this study are available from the corresponding author.

Circular RNA Formation and Degradation Are Not Directed by Universal Pathways

Circular RNAs (circRNAs) are a class of unique transcripts characterized by a covalently closed loop structure, which differentiates them from conventional linear RNAs. The formation of circRNAs occurs co-transcriptionally and post-transcriptionally through a distinct type of splicing known as back-splicing, which involves the formation of a head-to-tail splice junction between a 5' splice donor and an upstream 3' splice acceptor. This process, along with exon skipping, intron retention, cryptic splice site utilization, and lariat-driven intron processing, results in the generation of three main types of circRNAs (exonic, intronic, and exonic-intronic) and their isoforms. The intricate biogenesis of circRNAs is regulated by the interplay of cis-regulatory elements and trans-acting factors, with intronic Alu repeats and RNA-binding proteins playing pivotal roles, at least in the formation of exonic circRNAs. Various hypotheses regarding pathways of circRNA turnover are forwarded, including endonucleolytic cleavage and exonuclease-mediated degradation; however, similarly to the inconclusive nature of circRNA biogenesis, the process of their degradation and the factors involved remain largely unclear. There is a knowledge gap regarding whether these processes are guided by universal pathways or whether each category of circRNAs requires special tools and particular mechanisms for their life cycles. Understanding these factors is pivotal for fully comprehending the biological significance of circRNAs. This review provides an overview of the various pathways involved in the biogenesis and degradation of different types of circRNAs and explores key factors that have beneficial or adverse effects on the formation and stability of these unique transcripts in higher eukaryotes.

Circular RNAs in glioblastoma

Glioblastoma multiforme (GBM) is the most malignant and common form of brain cancer in adults. The molecular mechanisms underlying GBM progression and resistance are complex and poorly understood. Circular RNAs (circRNAs) are a new class of non-coding RNAsformed by covalently closed loopstructures with no free ends. Their circular structure makes them more stable than linear RNA and resistant to exonuclease degradation. In recent years, they have received significant attention due to their diverse functions in gene regulation and their association with various diseases, including cancer. Therefore, understanding the functions and applications of circRNAs is critical to developing targeted therapeutic interventions and advancing the field of glioblastoma cancer research. In this review, we summarized the main functions of circRNAs and their potential applications in the diagnosis, prognosis and targeted therapy of GBM.

Transcriptome Analysis of Muscle Growth-Related circRNA in the Pacific Abalone Haliotis discus hanna

(1) Background: Animal growth is a complex process, involving the coordination of a wide variety of genes, non-coding RNAs, and pathways. Circular RNAs (circRNAs) belong to a novel class of functional non-coding RNAs (ncRNAs). They have a distinctive ring structure and are involved in various biological processes, including the proliferation, differentiation, and apoptosis of muscle cells. The Pacific abalone Haliotis discus hannai is an economically valuable mollusk species cultivated in China. However, the modulation of muscle growth by circRNAs in this species is poorly understood. (2) Methods: In this study, we analyzed the muscle transcriptomes of 6 H. discus hannai specimens: three small (S_HD) and three large (L_HD) groups via RNA-seq and bioinformatics technology. (3) Results: The results indicated the presence of 11,744 circRNAs in abalone adductor muscle. Furthermore, the L_HD group had 250 significantly differentially expressed circRNAs (106 upregulated and 144 downregulated) relative to the S_HD group. Moreover, the bioinformatics assessment revealed that circRNAs were related to lipid transporter activity, lipid biosynthetic process, fat digestion and absorption, the single-organism metabolic process, the thyroid hormone signaling pathway, and the hippo signaling pathway, which regulates growth. Seventeen key candidate circRNAs were identified, and a core functional circRNA-miRNA-mRNA network associated with abalone muscle growth was described. Gene expression was verified using qRT-PCR, confirming the accuracy of the RNA-seq data. (4) Conclusion: Overall, this investigation furnishes novel evidence for the potential muscle growth modulatory mechanisms in Pacific abalone. These high-quality circRNA data of abalone muscle provide a reference for functional studies on the abalone genome.

Translation of circular RNAs

Circular RNAs (circRNAs) are covalently closed RNAs that are present in all eukaryotes tested. Recent RNA sequencing (RNA-seq) analyses indicate that although generally less abundant than messenger RNAs (mRNAs), over 1.8 million circRNA isoforms exist in humans, much more than the number of currently known mRNA isoforms. Most circRNAs are generated through backsplicing that depends on pre-mRNA structures, which are influenced by intronic elements, for example, primate-specific Alu elements, leading to species-specific circRNAs. CircRNAs are mostly cytosolic, stable and some were shown to influence cells by sequestering miRNAs and RNA-binding proteins. We review the increasing evidence that circRNAs are translated into proteins using several cap-independent translational mechanisms, that include internal ribosomal entry sites, N6-methyladenosine RNA modification, adenosine to inosine RNA editing and interaction with the eIF4A3 component of the exon junction complex. CircRNAs are translated under conditions that favor cap-independent translation, notably in cancer and generate proteins that are shorter than mRNA-encoded proteins, which can acquire new functions relevant in diseases.

Inhibition of mmu_circ_0009303 improves metabolic dysfunction-associated steatotic liver disease by regulating lipid metabolism and oxidative stress

Circular RNAs (circRNAs) play an important role in regulating inflammation and oxidative stress during the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the underlying mechanism is unclear. This study aimed to determine the role of mmu_circ_0009303 in MASLD. We used a bioinformatics approach to identify potential targets and established an in vitro model of MASLD. Oil red O staining, cell transfection and dual-luciferase reporter assay were used to determine the role of mmu_circ_0009303. The results indicated that the mmu_circ_0009303 expression was significantly increased in the MASLD model both in vitro and in vivo and was associated with oxidative stress levels and inflammation. Moreover, bioinformatics analyses revealed that miRNA-182-5p and Foxo3 are targets of mmu_circ_0009303 and miRNA-182-5p, respectively. In the in vitro MASLD model, mmu_circ_0009303 promoted fat deposition in NCTC1469 cells, which was induced by free fatty acid (FFA) through the regulation of miRNA-182-5p/Foxo3. The expression of miRNA-182-5p and Forkhead box O3 (Foxo3) was associated with mmu_circ_0009303 expression in the liver of mice with MASLD, which was induced by a high-fat diet. Furthermore, mmu_circ_0009303 may be involved in regulating the expression of lipid metabolism-related regulatory proteins, such as CPT1A, SLC27A4, ACBD3, SREBP1, FAS, PPARα, and PPARγ. Taken together, mmu_circ_0009303 promotes oxidative stress, inflammation, and excessive fat accumulation in NCTC1469 cells induced by FFA through the regulation of miRNA-182-5p/Foxo3 and lipid metabolism-related regulatory proteins. These findings provide a potential target for the treatment of MASLD.