Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures

Plasma expression level of Hsa_circ_0099734 is associated with atrial fibrillation and its poor prognosis

BACKGROUND

Atrial fibrillation (AF) is a common arrhythmia characterized by severe complications such as stroke, resulting in high disability and mortality rates. A circular RNA (circRNA) hsa_circ_0099734 was found significantly expressed in the atrial tissue of AF patients and controls in our previous work. In this study, we aim to reveal the association between hsa_circ_0099734 and AF as well as its poor prognosis, offering novel perspectives for clinical treatment.

METHODS

A 1:1 matched case-control study was designed to examine the association between hsa_circ_0099734 and AF. A prospective cohort study was conducted to investigate the association between hsa_circ_0099734 and AF prognosis using Cox proportional hazards regression analysis.

RESULTS

An elevated plasma level of hsa_circ_0099734 was an independent risk factor for AF in a multivariable conditional logistic regression model (OR 3.23, 95 % CI: 1.11-9.44; P = 0.032). Regarding the prognostic role of hsa_circ_0099734, the multivariable Cox regression analysis indicated that a high level of hsa_circ_0099734 in plasma was an independent risk factor for stroke in patients with AF (HR 2.87, 95 % CI: 1.90-4.35; P < 0.001), and also an independent risk factor for all-cause mortality in AF patients (HR 3.16, 95 % CI: 2.25-4.45; P < 0.001). Adding hsa_circ_0099734 to the CHA2DS2-VA score provided better reclassification and net clinical benefit than the ABC risk score.

CONCLUSIONS

The plasma level of hsa_circ_0099734 was associated with AF risk and the occurrence of stroke or all-cause mortality in AF patients. Hsa_circ_0099734 has the potential to be a non-invasive biomarker for predicting AF and its poor prognosis.

Hsa_circ_0000231 Accelerates Cell Autophagy and Promotes Cell Proliferation and Invasion of Colorectal Cancer via miR-140-3p/Bcl-2 Axis

Accumulating evidence indicated that circular RNAs (circRNAs) directly sponge to microRNAs (miRNAs),(miRNAs), which in turn regulate the gene expression and affect the malignancy behavior at the posttranscriptional level. However, the expression levels, function, and mechanism of circ_0000231 in colorectal cancer (CRC) are largely unknown. The expression levels of circ_0000231, miR-140-3p, and Bcl-2 in 110 CRC tissues and matched normal colorectal tissues were detected by qRT-PCR method. circ_0000231 and Bcl-2 were suppressed by siRNA, and miR-140-3p was overexpressed by RNA mimics in CRC cell lines. The function-based experiments were conducted to detect the proliferation and migratory abilities in CRC cell lines. RNA pull-down, RNA immunoprecipitation (RIP), and dual-fluorescence reporter assay were conducted to verify the association among circ_0000231, miR-140-3p, and Bcl-2. Western blot analysis and mRFP-GFP-LC3 adenovirus were used to detect the autophagy level affected by circ_0000231, miR-140-3p, and Bcl-2 axis. Downregulated circ_0000231 significantly suppressed the proliferation and migratory abilities of CRC cells by suppressing autophagy and promoting G0/G1 phase arrest. Furthermore, RNA pull-down, RIP, and dual-fluorescence reporter assays confirmed that circ_0000231 regulates the expression of Bcl-2 by directly targeting miR-140-3p. More importantly, circ_0000231 promoted the levels of autophagy via the miR-140-3p/Bcl-2 axis in CRC. Our study demonstrated that circ_0000231, as a tumor promotor, enhances the level of autophagy by regulating Bcl-2 via targeting miR-140-3p. Moreover, circ_0000231 might serve as a diagnostic and prognostic indicator and a novel molecular target for CRC therapy.

Circular RNAs in gynecological cancer: From molecular mechanisms to clinical applications (Review)

Circular RNAs (circRNAs) have emerged as promising biomarkers and therapeutic targets in gynecological cancer. The present review explored developments in circRNA research in ovarian, endometrial and cervical cancer. circRNA biogenesis, functions and roles in cancer pathogenesis have been discussed, focusing on their potential as diagnostic and prognostic markers. Furthermore, circRNAs mechanisms of action, including miRNA sponging, protein scaffolding and peptide encoding were examined, highlighting specific circRNAs implicated in each cancer type and their clinical significance. The unique properties of circRNAs, such as stability and tissue-specific expression, make them ideal candidates for biomarker development. By synthesizing the currently available literature and identifying future research directions, the present review underscored circRNAs potential to improve gynecological cancer management through novel diagnostic tools, prognostic markers and targeted therapies.

Circular RNAs: key players in tumor immune evasion

Immune responses against tumor antigens play a role in confining tumor growth. In response, cancer cells developed several mechanisms to bypass or defeat these anti-tumor immune responses-collectively referred to as "tumor immune evasion". Recent studies have shown that a group of non-coding RNAs, namely circRNAs affect several aspects of tumor immune evasion through regulation of activity of CD8 + T cells, regulatory T cells, natural killer cells, cytokine-induced killer cells or other immune cells. Understanding the role of circRNAs in this process facilitate design of novel therapies for enhancing the anti-tumor capacity of immune system. This review provides an outline of different roles of circRNAs in the tumor immune evasion.

Circular RNAs in glioma progression: Fundamental mechanisms and therapeutic potential: A review

Gliomas are the most common primary malignant brain tumors, characterized by aggressive invasion, limited therapeutic options, and poor prognosis. Despite advances in surgery, radiotherapy, and chemotherapy, the median survival of glioma patients remains disappointingly low. Therefore, identifying glioma-associated therapeutic targets and biomarkers is of significant clinical importance. Circular RNAs (circRNAs) are a class of naturally occurring long non-coding RNAs (lncRNAs), notable for their stability and evolutionary conservation. Increasing evidence indicates that circRNA expression is dysregulated in gliomas compared to adjacent non-tumor tissues and contributes to the regulation of glioma-related biological processes. Furthermore, numerous circRNAs function as oncogenes or tumor suppressors, mediating glioma initiation, progression, and resistance to temozolomide (TMZ). Mechanistically, circRNAs regulate glioma biology through diverse pathways, including acting as miRNA sponges, binding RNA-binding proteins (RBPs), modulating transcription, and even encoding functional peptides. These features highlight the potential of circRNAs as diagnostic and prognostic biomarkers, as well as therapeutic targets for glioma. This review summarizes the dysregulation and functions of circRNAs in glioma and explores key mechanisms through which they mediate tumor progression, including DNA damage repair, programmed cell death (PCD), angiogenesis, and metabolic reprogramming. Our aim is to provide a comprehensive perspective on the multifaceted roles of circRNAs in glioma and to highlight their potential for translational application in targeted therapy.

Construction of a competing endogenous RNA regulatory network in pterygium and role of hsa_circ_0081682 in fibroblast proliferation, migration, and apoptosis

Pterygium is a fibrovascular growth associated with chronic inflammation, tissue remodeling, and angiogenesis, which invades the cornea. Circular RNAs (circRNAs) are emerging as pivotal role in many diseases, but their role in pterygium remains unclear. We performed circRNA and miRNA expression profiling on pterygium and conjunctival tissues, then the circRNA-miRNA-mRNA regulatory network was constructed. Bioinformatics was used to predict downstream pathways. Pterygium fibroblasts were used for experiments assessing proliferation (CCK8, EdU), migration (wound healing, transwell), and apoptosis (AnnexinV-FITC/PI). We identified 162 differentially expressed circRNAs and 96 miRNAs. Key pathways involved in pterygium pathogenesis, including focal adhesion and PI3K-Akt signaling, were predicted. Hsa_circ_0081862 was downregulated in pterygium tissues and fibroblasts, inhibiting fibroblast proliferation and migration while promoting apoptosis. This research constructed a ceRNA network and identified hsa_circ_0081682 as the potential diagnostic marker for pterygium. This research contributes to the understanding of biochemical basis of pterygium, which may facilitate the development of targeted strategies for its management and prevention.

hsa_circ_0015388 Reduces Macrophage Derived Reactive Oxygen Species in Crohn's Disease

BACKGROUND

Crohn's disease (CD) is a refractory inflammatory bowel disease with an unclear etiology. CircularRNA (circRNA) has been highlighted as a novel class of functional noncoding RNAs associated with the pathogenesis of various diseases. However, the functions of circRNA in CD remain unclear.

METHODS

Biopsies were obtained from noninflammatory sites in the terminal ileum of the CD group (n = 4) and non-CD group (n = 4) and analyzed for circRNA expression using RNA sequencing. The significantly altered circRNAs were validated in the CD group (n = 45) and non-CD group (n = 15) using quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Transcriptome analysis was conducted using circRNA-downregulated macrophage-like THP-1 cells. Reactive oxygen species (ROS) levels, cytokine mRNA expression, phagocytosis, and migration were evaluated in circRNA-downregulated THP-1 cells.

RESULTS

CircularRNA sequencing analysis revealed significant differences in 31 circRNAs between the CD group and non-CD group. Quantitative reverse transcriptase-polymerase chain reaction analysis for each circRNA demonstrated significant upregulation of hsa_circ_0015388 in the CD group. Hsa_circ_0015388 was expressed in THP-1 cells, but not in HCEC-1CT and Caco-2/bbe. Transcriptome analysis in THP-1 cells transfected with scramble or hsa_circ_0015388 siRNA (small interfering RNA) showed a significant alteration in innate immune response related pathway. Reactive oxygen species production was significantly increased in the hsa_circ_0015388 downregulated THP-1 cells. Reactive oxygen species induction in the hsa_circ_0015388 knocked down THP-1 was diminished by the inhibition of TNFSF10.

CONCLUSION

A comprehensive analysis of circRNA expression revealed that 31 circRNAs were dysregulated in the CD group. Hsa_circ_0015388 is expressed in macrophages and negatively regulates ROS function inhibiting the TNFSF10 pathway. This study first revealed that hsa_circ_0015388 plays a role in the pathogenesis of CD by suppressing ROS production in macrophages.

Circ_RPPH1 promotes bladder urothelium carcinoma proliferation and EMT by recruiting and binding to EIF4 A3

BACKGROUND

The involvement of circ_RPPH1 in bladder urothelial carcinoma (BUC) remains unclear, as well as the underlying mechanism.

METHODS

Circ_RPPH1 levels in BUC cells and tissues were measured via RT-qPCR. Downregulation of circ_RPPH1 was assessed using colony formation, CCK-8, wound healing, and Transwell assays to evaluate proliferation, migration, and invasion. RIP and RNA pull-down confirmed circ_RPPH1 binding to EIF4A3, while immunoblotting analyzed EIF4A3 and EMT-related proteins.

RESULTS

High circ_RPPH1 levels in BUC correlated with tumor invasion depth. Its knockout suppressed proliferation, invasion, and EMT, while circ_RPPH1 overexpression reduced EIF4A3 binding to N-cadherin and Vimentin mRNA, promoting EMT.

CONCLUSION

Circ_RPPH1 promotes tumor growth and EMT in BUC by inhibiting EIF4A3-mediated mRNA regulation, activating the EIF4A3/N-cadherin/Vimentin pathway.

Development of Mathematical Models Using circRNA Combinations (circTulp4, circSlc8a1, and circStrn3) in Mouse Brain Tissue for Postmortem Interval Estimation

The postmortem interval (PMI) is defined as the time interval between physiological death and the examination of the corpse, playing a critical role in forensic investigations. Traditional PMI estimation methods are often influenced by subjective and environmental factors. Circular RNAs (circRNAs), known for their stability, abundance, and conservation in brain tissue, show promise as biomarkers for PMI estimation. However, research on circRNAs in this context remains limited. This study aimed to develop PMI estimation models using circRNAs across multiple temperatures. By employing semi-quantitative reverse transcription-PCR, circTulp4, circSlc8a1, and circStrn3 were identified as reliable biomarkers for mouse brain tissue. Mathematical models were constructed using the reference genes 28S rRNA, mt-co1, and circCDR1as. At 4 °C, most equations had p-values below 0.05, with the equation using circSlc8a1 as a marker exhibiting the highest goodness of fit. Validation results indicated that the equation using circTulp4 as the reference gene had the highest accuracy. When applying the combined aforementioned three circRNAs, the equation using circCDR1as as the reference gene showed better accuracy. At 25 °C, all equations had R2 values greater than 0.86, but most cubic equations had p-values above 0.05. Validation results demonstrated that the circTulp4/mt-co1 equation had the highest accuracy. When applying combined circRNAs, the R2 values improved, and long-term PMI estimation was more accurate than short-term PMI estimation. At 35 °C, the linear equations had significantly poorer goodness of fit compared to nonlinear equations, and nonlinear equations exhibited better accuracy than linear equations. When applying the combined aforementioned three circRNAs, the accuracy of the three reference genes was similar, and the accuracy of long-term PMI estimation was consistently higher than that of short-term estimation. For the three-dimensional models, all R2 values exceeded 0.75 with p-values significantly below 0.0001. Validation results demonstrated higher accuracy at 25 °C and 35 °C, with superior performance for long-term PMI estimation. In summary, this study constructed PMI estimation models under multiple temperature conditions based on highly expressed circRNAs in mouse brain tissue, highlighting circTulp4, circSlc8a1, and circStrn3 as novel biomarkers. These findings offer a complementary tool for PMI estimation, particularly for long-term PMI estimation.

Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene

The scarecrow (scro) gene encodes a fly homolog of mammalian Nkx2.1, which is vital for early fly development and for optic lobe development. Previously, scro was reported to produce a circular RNA in addition to traditional mRNAs. In this study, we report 12 different scro circular RNAs, which are either mono or multiexonic forms. The most abundant ones are circScro(2) carrying the second exon (E2) only and bi-exonic circScro(3,4) having both the third (E3) and fourth exon (E4). Levels of circScro(2) show an age-dependent increase in adult heads, supporting a general trend of high accumulation of circular RNAs in aged fly brains. In silico analysis of the introns flanking circular RNA exons predicts 2 pairs of intronic complementary sequences; 1 pair residing in introns 1 and 2 and the other in introns 2 and 4. The first pair was demonstrated to be essential for the circScro(2) production in cell-based assays; furthermore, deletion of the region including intronic complementary sequence components in the intron-2 reduces in vivo production of both circScro(2) and circScro(3,4) by 80%, indicating them to be essential for the biogenesis of the 2 circular RNAs. Besides the intronic complementary sequence, the intron regions immediately abutting exons seem to be responsible for a basal level of circular RNA formation. Moreover, ectopic intronic complementary sequence derived from the laccase2 locus is comparably effective in circScro production, buttressing the importance of the hairpin loop structure formed by intronic complementary sequence for the biogenesis of circular RNA. Last, overexpressed scro alters outcomes of both linear and circular RNAs from the endogenous scro locus, suggesting that Scro plays a direct or indirect role in regulating the expression levels of either or both forms.

CircRNAs in the tumor microenvironment: new frontiers in cancer progression and therapy

The tumor microenvironment (TME), a dynamic ecosystem which including immune cells, cancer-associated fibroblasts (CAFs), endothelial cells, pericytes and acellular components, is orchestrating cancer progression through crosstalk between malignant cells and stromal components and increasingly recognized as a therapeutic frontier. Within this intricate network, circular RNAs (circRNAs) have emerged as pivotal regulators due to their unique covalently closed structures, which confer exceptional stability and multifunctional capabilities. This regulation is mediated through multiple mechanisms, such as acting as microRNA (miRNA) sponges, interacting with proteins, and, in certain instances, encoding functional peptides. The interaction between circRNAs and the TME not only affects cancer growth and metastasis but also influences immune evasion and therapeutic resistance. Elucidating the mechanisms by which circRNAs orchestrate these interactions is essential for identifying novel diagnostic biomarkers and developing effective therapeutic strategies. Such insights are expected to bridge gaps in current cancer biology, offering promising avenues for precision oncology and ultimately improving clinical outcomes for cancer patients.

Circular RNAs modulate cell death in cardiovascular diseases

Cardiovascular diseases (CVDs) remain a global health challenge, with programmed cell death (PCD) mechanisms like apoptosis and necroptosis playing key roles in the progression. Circular RNAs (circRNAs) have recently been recognized as crucial regulators of gene expression, especially in modulating PCD. In current researches, circRNA regulation of apoptosis is the most studied area, followed by autophagy and ferroptosis. Notably, the regulatory role of circRNAs in pyroptosis and necroptosis has also begun to attract attention. From a mechanistic perspective, circRNAs influence cellular processes through several modes of action, including miRNA sponging, protein interactions, and polypeptide translation. Manipulating circRNAs and their downstream targets through inhibition or overexpression offers versatile therapeutic options for CVD treatment. Continued investigation into circRNA-mediated mechanisms may enhance our understanding of CVD pathophysiology and underscore their potential as novel and promising therapeutic targets.

Effects of circPICALM-miR-132-PHKB regulated by METTL3 on proliferation of porcine skeletal muscle satellite cells

Circular RNA (circRNA) is ubiquitously expressed in highly differentiated eukaryotes, playing an extremely vital regulatory role in muscle growth and development. In this study, we identified circPICALM, a novel circRNA which consists of exons 5 to 9 of the PICALM gene, exhibiting differential expression in the longissimus dorsi muscle (LD) of adult (QA) and newborn (QN) Queshan Black pigs. CircPICALM is resistant to RNase R, mainly located in the cytoplasm with potential coding capacities. When circPICALM was over-expressed in porcine skeletal muscle satellite cells (PSMSCs), there was a significant decrease in the expression levels of PCNA, CDK4, CDK1 and CCND1, which consequently inhibited the proliferation of PSMSCs. Conversely, miR-132, a target molecule of circPICALM, was found to promote the proliferation of PSMSCs. In addition, circPICALM can up-regulate the expression of the target gene PHKB by competitively adsorbing miR-132. The circPICALM-ssc-miR-132-PHKB regulatory axis is regulated by METTL3, which increases the m6A level of both PSMSCs and circPICALM, thereby promoting the proliferation of PSMSCs. Overall, this study furnishes a fundamental reference for further in-depth exploration of the specific molecular mechanisms underlying m6A modification and circPICALM in muscle development and progression.

Coding circular RNA in human cancer

circular RNA (circRNA) is a covalently closed single-stranded RNA that lacks 5' and 3' ends and has long been considered a noncoding RNA. With the development of high-throughput sequencing and bioinformatics technology, the understanding of circRNA has become increasingly advanced. Recent studies have shown that some cytoplasmic circRNAs can be effectively translated into detectable proteins, further indicating the importance of circRNA in cellular pathology and physiological functions. Internal ribosome entry site (IRES) and N6-methyladenosine (m6A) mediated cap-independent translation initiation are considered potential mechanisms of circRNA translation. Multiple circRNAs have been shown to play crucial roles in human cancer. This paper provides an overview of the nature and functions of circRNA and describes the possible mechanisms underlying the initiation of circRNA translation. We summarized the emerging functions of circRNA-encoded proteins in human cancer. Finally, we discuss the therapeutic potential of circRNAs and the challenges of research in this field. This review on circRNA translation will reveal a hidden human proteome and enhance our understanding of the importance of circRNAs in human malignant tumors.

Whole transcriptome sequencing-based identification and functional prediction of salt-tolerant-related circular RNAs in ZM-4 (Malus zumi)

CircRNAs, are a class of covalently closed non-coding RNAs; they have been identified in many plants and play an important role in the response to abiotic stresses. However, little is known about the response of the circRNAs of salt-tolerant apple rootstock resources in response to salt stress. In this study, the leaves and roots of the salt-tolerant Malus resource, ZM-4, and the salt-sensitive rootstock M9T337, were used as test materials and were exposed to 75 mmol/L NaCl stress for 0 h and 24 h. A total of 2502 circRNAs were identified, and 218 and 242 circRNAs were uniquely expressed in M9T337 and ZM-4, respectively. Furthermore, it was shown that the up-regulated parental genes of the differentially expressed circRNAs were enriched in the metabolic pathways and the biosynthesis of secondary metabolites pathway in the leaves and roots of ZM-4 under salt stress, respectively. There were potential regulatory networks of ceRNA among 150 circRNAs, 139 miRNAs, and 397 mRNAs. Novel_circ_000845 and novel_circ_000266 could target and inhibit the expression of mdm-miR156 and up-regulate the expression of the salt-responsive gene SPL6. Six circRNAs, including novel_circ_000898 and novel_circ_001519, could target and inhibit the expression of mdm-miR10995 and up-regulate the expression of the salt-responsive gene COBL7. In conclusion, this study laid the foundation for the post-transcriptional molecular regulation mechanism of salt tolerance in apple rootstock resources.

Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities

Circular RNAs (circRNAs) are emerging as important regulatory molecules in both host and viral systems, acting as microRNA sponges, protein decoys or scaffolds, and templates for protein translation. Host-derived circRNAs are increasingly recognized for their roles in immune responses, while virus-encoded circRNAs, especially those from DNA viruses, have been shown to modulate host cellular machinery to favor viral replication and immune evasion. Recently, RNA virus-encoded circRNAs were also discovered, but evidence suggests that they might be generated using a different mechanism compared to the circRNAs produced from the host and DNA viruses. This review highlights recent advances in our understanding of both host and virus-derived circRNAs, with a focus on their biological roles and contributions to pathogenesis. Furthermore, we discuss the potential of circRNAs as biomarkers and their application as therapeutic targets or scaffolds for RNA-based therapies. Understanding the roles of circRNAs in host-virus interactions offers novel insights into RNA biology and opens new avenues for therapeutic strategies against viral diseases and associated cancers.

The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

Acute myeloid leukaemia (AML) is a prevalent haematologic malignancy characterized by significant heterogeneity. Despite the application of aggressive therapeutic approaches, AML remains associated with poor prognosis. Circular RNAs (circRNAs) constitute a unique class of single-stranded RNAs featuring covalently closed loop structures that are ubiquitous across species. These molecules perform crucial regulatory functions in the pathogenesis of various diseases through diverse mechanisms, including acting as miRNA sponges, interacting with DNA or proteins, and encoding functional proteins/polypeptides. Recently, numerous circRNAs have been confirmed to have aberrant expression patterns in AML patients. In particular, certain circRNAs are closely associated with specific clinicopathological characteristics and thus have great potential as diagnostic/prognostic biomarkers and therapeutic targets in AML. Herein, we systematically summarize the biogenesis, degradation, and functional mechanisms of circRNAs while highlighting their clinical relevance. We also outline a series of online databases and analytical tools available to facilitate circRNA research. Finally, we discuss the current challenges and future research priorities in this evolving field.

Circular RNA circATM binds PARP1 to suppress Wnt/β-catenin signaling and induce cell cycle arrest in gastric cancer cells

INTRODUCTION

Gastric cancer (GC) is a common malignancy, which is associated with high rates of morbidity and mortality. Despite therapeutic advancements, there is an overall lack of effective treatment options for patients with GC, particularly those with advanced and metastatic disease. The roles of circular (circ)RNAs in tumorigenesis are being increasingly recognized, among which circRNAs are defined as miRNA/protein sponges, scaffolds, or protein coding templates.

OBJECTIVES

The aim of the present study is to investigate the functions of circATM in GC and elucidate the underlying molecular mechanism.

METHODS

By circRNA sequencing in GC tissues, we identified a novel 526 nt circRNA, circATM, generating from exons 3-6 of the ATM gene. Through circRNA pull-down and RNA immunoprecipitation assays, we identified PARP1 as one of circATM binding proteins. The EdU, colony formation, wound healing, dual-luciferase reporter, cell cycle assays were employed to evaluated circATM functions in vitro. The GC xenograft model was used to determine the role of circATM in vivo.

RESULTS

Knocking down circATM promoted GC cells growth in vivo and in vitro. Meanwhile, the overexpression of circATM increased the levels of p16, p21, and p27, and decreased those of β-catenin and c-Myc. Furthermore, we identified PARP1 as a circATM-interacting partner. Mechanistically, circATM bound to the zinc finger motif of Ⅱ-Ⅲ domains of PARP1 to block its recruitment to sites of DNA damage, triggering cell cycle arrest and sequestering β-catenin from the PARP1/β-catenin/TCF4 complex, leading to the suppression of Wnt/β-catenin signaling. Additionally, circATM facilitated the ubiquitin-proteasome degradation of PARP1, further jeopardizing its ability to mediate DNA damage repair.

CONCLUSION

Taken together, we defined circATM as a novel gastric tumor suppressor via interacting with PARP1, which indicate that circATM may be a promising biomarker for the diagnosis and therapy of GC.

Hsa_circ_0072088 promotes non-small cell lung cancer progression through modulating miR-1270/TOP2A axis

According to the data released by the International Agency for Research on Cancer (IARC) in 2020, lung cancer ranks second among newly diagnosed malignant tumors globally. As a special class of non-coding RNA, circRNA has become a new hotspot in the field of biomarker research. With the continuous deepening of molecular-level investigations, the underlying mechanisms of circRNA are being gradually unveiled. The more widely studied mechanism is the competitive endogenous RNA mechanism of circRNA. Studies related to circRNA expression were searched in GEO database and statistically analyzed using the "limma" package and weighted gene co-expression network analysis. The expression of circRNA, microRNA and mRNA in cells and tissues were examined via qRT-PCR. MTS assay was used to measure cell proliferation, Transwell assay was used to measure cell migration, and apoptosis assay was carried out to detect cell apoptosis. Additionally, a dual-luciferase reporter assay was further executed to explore the targeted binding relationships between circRNA-microRNA and microRNA-mRNA. It was discovered that hsa_circRNA_103809 was differentially highly expressed in non-small cell lung cancer cells, whereas miR-1270 was differentially lowly expressed. The knockdown of circ_0072088 inhibited the cell proliferation and migration, while promoting cell apoptosis. The same biological function was found with the overexpression of miR-1270. The rescue experiment further validated that circ_0072088 could regulate the biological function of cells by influencing miR-1270. Finally, the targeted binding relationship was verified by dual luciferase reporting experiment. In conclusion, circ_0072088 is differentially highly expressed in non-small cell lung cancer and can affect the progression of non-small cell lung cancer through the circ_0072088/miR-1270/TOP2A axis.

Construction of a circRNA-miRNA-mRNA Regulatory Network for the Immune Regulation of Lung Adenocarcinoma

BACKGROUND

Recent research has highlighted the significance of circular RNAs (circRNAs) as pivotal regulators in the progression of tumors and the therapeutic response in non-small cell lung cancer (NSCLC). These circRNAs function through a sponge mechanism, interacting with microRNAs (miRNAs) to modulate mRNA expression levels. Nevertheless, the precise role of the circRNA-miRNA-mRNA regulatory network in immune regulation within lung adenocarcinoma (LUAD) remains inadequately understood.

METHODS AND MATERIALS

We utilized microarray datasets from the GEO NCBI database (GSE101586) to identify differentially expressed circRNAs (DEcircRNAs) in LUAD. CircBank was employed to predict the target miRNAs of DEcircRNAs, which were subsequently intersected with miRNAs from the GSE36681 database. The identified miRNAs were then predicted to target mRNAs using miRDB and miWalk, and intersections with immune-related genes from the IMMPORT database were analyzed. Protein-protein interaction (PPI) networks were constructed using Cytoscape software. The DAVID functional annotation tool was utilized to explore potential biological processes, molecular functions, and KEGG pathways associated with LUAD. Gene expression and Kaplan-Meier survival analyses were conducted to establish a key regulatory network and to assess immune cell infiltration and Pearson correlation for significant target genes. Finally, we selected the most significantly upregulated circRNA with differential expression for validation through in vitro experiments.

RESULTS

Our analysis identified a total of 7 upregulated and 42 downregulated circRNAs, along with 10 significant miRNAs and 20 target mRNAs. KEGG enrichment analysis indicated that these components are primarily enriched in the ErbB signaling pathway. Furthermore, Gene Ontology (GO) analysis revealed significant enrichment in responses to organic substances, cytokine-mediated signaling pathways, cellular responses to cytokines, responses to chemical stimuli, steroid hormone receptor activity, ErbB-3 class receptor binding, oxysterol binding, signal receptor activity, and molecular transducer activity. Notable core mRNAs identified included OAS1, VIPR1, and PIK3R1. Subsequently, we constructed a regulatory network comprising 6 DEcircRNAs, 3 DEmiRNAs, and 3 DEmRNAs. Through ssGSEA and CIBERSORT analyses, we observed significant differences in immune cell infiltration levels between the NSCLC cohort and the control group. Knocking down the expression of hsa_circ_0079557 significantly inhibited the viability, proliferation, migration, and invasion of LUAD cells.

CONCLUSION

We have established a circRNA-miRNA-mRNA regulatory network that offers novel insights into the molecular mechanisms governing immune regulation in LUAD. Future research should aim to translate these findings into clinical applications to enhance patient outcomes.

circ-0001454 alleviates asthma airway inflammation and remodeling via sponging miR-770-5p and regulating cbl-b

Bronchial asthma is a chronic inflammatory disease that has long been a severe threat to human physical and mental health. Circular RNAs (circRNAs) and microRNAs (miRNAs) are involved in regulating various processes in asthma. However, the mechanisms by which these molecules influence the pathophysiological processes of asthma through target gene regulation remain unclear. Our study found that inhibition of miR-770-5p alleviated airway inflammation and remodeling in asthmatic mice. Furthermore, bioinformatics analysis revealed that circ-0001454 harbors binding sites for miR-770-5p, acting as a sponge to adsorb miR-770-5p and function as a competing endogenous RNA (ceRNA), thereby negatively regulating the expression of miR-770-5p. Circ-0001454 not only alleviated airway inflammation and remodeling in asthmatic mice, but also participated in modulating the HDM-induced inflammatory response in BEAS-2B cells. It mitigated bronchial epithelial cell inflammatory damage, reduced oxidative stress, apoptosis, and mitochondrial membrane potential loss. Mechanistically, we observed that circ-0001454 partially alleviated the inflammatory damage of epithelial cells caused by miR-770-5p overexpression excessive reactive oxygen species (ROS) production, apoptosis, and mitochondrial membrane potential disruption. Lastly, we found that circ-0001454 targets miR-770-5p and participates in regulating the expression of cbl-b, which in turn modulates the levels of EGFR, AKT1, and MAPK1 proteins, thereby alleviating inflammation in airway epithelial cells. These findings reveal the role of miR-770-5p in asthma, and how circ-0001454, by binding to miR-770-5p and targeting the gene cbl-b, contributes to the attenuation of airway inflammation, reduction of ROS levels, inhibition of apoptosis, and restoration of mitochondrial membrane potential. This regulation of cbl-b, EGFR, AKT1, and MAPK1 suggests new potential therapeutic targets for asthma treatment.

Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials

Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.

The therapeutic potential of circular RNAs

Over the past decade, research into circular RNA (circRNA) has increased rapidly, and over the past few years, circRNA has emerged as a promising therapeutic platform. The regulatory functions of circRNAs, including their roles in templating protein translation and regulating protein and RNA functions, as well as their unique characteristics, such as increased stability and a favourable immunological profile compared with mRNAs, make them attractive candidates for RNA-based therapies. Here, we describe the properties of circRNAs, their therapeutic potential and technologies for their synthesis. We also discuss the prospects and challenges to be overcome to unlock the full potential of circRNAs as drugs.

Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications

Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

Decoding the regulatory roles of circular RNAs in cardiac fibrosis

Cardiovascular diseases (CVDs) are the primary cause of death globally. The evolution of nearly all types of CVDs is characterized by a common theme: the emergence of cardiac fibrosis. The precise mechanisms that trigger cardiac fibrosis are still not completely understood. In recent years, a type of non-coding regulatory RNA molecule known as circular RNAs (circRNAs) has been reported. These molecules are produced during back splicing and possess significant biological capabilities, such as regulating microRNA activity, serving as protein scaffolds and recruiters, competing with mRNA, forming circR-loop structures to modulate transcription, and translating polypeptides. Furthermore, circRNAs exhibit a substantial abundance, notable stability, and specificity of tissues, cells, and time, endowing them with the potential as biomarkers, therapeutic targets, and therapeutic agents. CircRNAs have garnered growing interest in the field of CVDs. Recent investigations into the involvement of circRNAs in cardiac fibrosis have yielded encouraging findings. This study aims to provide a concise overview of the existing knowledge about the regulatory roles of circRNAs in cardiac fibrosis.

Chi-circ_0009659 modulates goat intramuscular adipocyte differentiation through miR-3431-5p/STEAP4 axis

OBJECTIVE

Circular RNAs (circRNAs) are widely involved in the regulation of lipid deposition in animals, but there are few reports on key circRNAs regulating intramuscular adipocyte differentiation in goats. Therefore, this study took an abundantly expressed in goat adipocytes chi-circ_0009659 as the object.

METHODS

Based on the identification of back splicing site in chi-circ_0009659, its expression level during the goat intramuscular preadipocyte differentiation was detected by quantitative polymerase chain reaction (qPCR) . The chi-circ_0009659 loss-of-function and gain-of-function cell models were obtained by adenovirus and smarter silencer, respectively. and the adipocyte differentiation were explored by Oil Red O staining, Bodipy staining and qPCR. Its major cytoplasmic localization was determined by fluorescence in situ hybridization (FISH), nucleocytoplasmic separation and qPCR. The interaction between chi-circ_0009659, miR-3431-5p, and STEAP family member 4 (STEAP4) was verified by bioinformatics, RNA pull down and dual luciferase reporter assay.

RESULTS

Silencing chi-circ_0009659 inhibited lipid droplet accumulation and the expression of differentiation-determining genes in goat intramuscular adipocytes, while overexpression of chi-circ_0009659 reversed these results. chi-circ_0009659 was predominantly localized to the cytoplasm and could regulate miR-3431 expression which in turn affects STEAP4. Consistent with expectations, miR-3431-5p acted as a negative regulator of GIMPA differentiation, while STEAP4 promoted differentiation.

CONCLUSION

We demonstrated chi-circ_0009659 positively regulates goat intramuscular preadipocyte differentiation by sponging miR-3431-5p to further regulate the expression of STEAP4. This research provides a new reference for in-depth understanding of the effects of circRNA on adipocyte differentiation.

A novel peptide encoded by a rice circular RNA confers broad-spectrum disease resistance in rice plants

Circular RNAs (circRNAs) are a significant class of endogenous RNAs that exert crucial biological functions in human and animal systems, but little is currently understood regarding their roles in plants. Here, we identified a circRNA originating from the back-splicing of exon 4 and exon 5 of a rice gene, OsWRKY9, and named it circ-WRKY9. It is upregulated in rice stripe mosaic virus (RSMV)-infected rice plants. Notably, circ-WRKY9 contains two open reading frames with an internal ribosome entry site. We found that circ-WRKY9 encoded a peptide of 88 amino acids (aa) and named it WRKY9-88aa. Overexpression of WRKY9-88aa suppresses RSMV infection in rice plants, with increased reactive oxygen species production. Furthermore, WRKY9-88aa enhances resistance to blast disease and bacterial leaf blight, suggesting its potential to provide broad-spectrum disease resistance. Our findings provide the first evidence of a peptide encoded by a circRNA in planta and highlight its potential application to control a wide spectrum of plant diseases.

CircRNAs in Colorectal Cancer: Unveiling Their Roles and Exploring Therapeutic Potential

Colorectal cancer (CRC) is the most common malignancy of the digestive system. Although research into the causes of CRC's origin and progression has advanced over the past few decades, many details are still not fully understood. Circular RNAs (circRNAs), as a novel regulatory molecule, have been found to be closely involved in various key biological processes in CRC. CircRNAs also have been shown to encode proteins, which could offer new possibilities for therapeutic applications. This ability to produce tumor-specific proteins makes circRNA-based vaccines a potentially valuable approach for targeted cancer treatment. In this review, we summarize recent findings on the various roles of circRNAs in CRC and explore their potential in the development of protein-encoding circRNA vaccines for CRC therapy.

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.

Emerging role and clinical applications of circular RNAs in human diseases

Circular RNAs (circRNAs) are a large family of non-coding RNAs characterized by a single-stranded, covalently closed structure, predominantly synthesized through a back-splicing mechanism. While thousands of circRNAs have been identified, only a few have been functionally characterized. Although circRNAs are less abundant than other RNA types, they exhibit exceptional stability due to their covalently closed structure and demonstrate high cell and tissue specificity. CircRNAs play a critical role in maintaining cellular homeostasis by influencing gene transcription, translation, and post-translation processes, modulating the immune system, and interacting with mRNA, miRNA, and proteins. Abnormal circRNA expression has been associated with a wide range of human diseases and various infections. Due to their remarkable stability in body fluids and tissues, emerging research suggests that circRNAs could serve as diagnostic and therapeutic biomarkers for these diseases. This review focuses on the emerging role of circRNAs in various human diseases, exploring their biogenesis, molecular functions, and potential clinical applications as diagnostic and therapeutic biomarkers with current evidence, challenges, and future perspectives. The key theme highlights the significance of circRNAs in regulating gene expression, their involvement in diseases like cancer, neurodegenerative disorders, cardiovascular diseases, and diabetes, and their potential use in translational medicine for developing novel therapeutic strategies. We also discuss recent clinical trials involving circRNAs. Thus, this review is important for both basic researchers and clinical scientists, as it provides updated insights into the role of circRNAs in human diseases, aiding further exploration and advancements in the field.

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.

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.

Functions and application of circRNAs in vascular aging and aging-related vascular diseases

Circular RNAs (circRNAs), constituting a novel class of endogenous non-coding RNAs generated through the reverse splicing of mRNA precursors, possess the capacity to regulate gene transcription and translation. Recently, the pivotal role of circRNAs in controlling vascular aging, as well as the pathogenesis and progression of aging-related vascular diseases, has garnered substantial attention. Vascular aging plays a crucial role in the increased morbidity and mortality of the elderly. Endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) are crucial components of the intima and media layers of the vascular wall, respectively, and are closely involved in the mechanisms underlying vascular aging and aging-related vascular diseases. The review aims to provide a comprehensive exploration of the connection between circRNAs and vascular aging, as well as aging-related vascular diseases. Besides, circRNAs, as potential diagnostic markers or therapeutic targets for vascular aging and aging-related vascular diseases, will be discussed thoroughly, along with the challenges and limitations of their clinical application. Investigating the role and molecular mechanisms of circRNAs in vascular aging and aging-related vascular diseases will provide a novel insight into early diagnosis and therapy, and even effective prognosis assessment of these conditions.

Roles of circRNAs in viral pathogenesis

Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed circular structure, lacking 5'-caps or 3'-poly(A) tails. They are relatively conserved, highly stable, and often exhibit tissue- or cell-specific production in eukaryotic cells. Based on the advances in sequencing technologies and bioinformatics, multiple reports have suggested that viruses and other microorganisms may encode circRNA-like molecules, providing new insights into the physiological and pathological roles of circRNAs. The innate immune system functions as the body's primary defense mechanism against viral infections. It detects pathogen-associated molecular patterns (PAMPs) and activates signaling pathways to suppress viral replication and limit their spread. CircRNAs are involved in regulation of the host innate immune signaling pathways and play essential roles in viral pathogenesis. It has been shown that circRNAs can regulate gene expression by acting as miRNA sponges or protein sponges, or encoding small proteins in specific cases. For example, previous studies have revealed that circRNAs participate in the host antiviral immune response through the competitive endogenous RNA (ceRNA) network by acting as miRNA sponges. This review highlights research progress in the regulation and functions of host- and virus-encoded circRNAs in host-virus interactions, as well as their potential as diagnostic biomarkers and therapeutic targets in clinical applications.

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.

Prebiotic RNA self-assembling and the origin of life: Mechanistic and molecular modeling rationale for explaining the prebiotic origin and replication of RNA

In recent years, a great interest has been focused on the prebiotic origin of nucleic acids and life on Earth. An attractive idea is that life was initially based on an autocatalytic and autoreplicative RNA (the RNA-world). RNA duplexes are right-handed helical chains with antiparallel orientation, but the rationale for these features is not yet known. An antiparallel (inverted) stacking of purine nucleosides was reported in crystallographic studies. Molecular modeling also supports the inverted orientation of nucleosides. This preferential stacking can also appear when nucleosides are included in a montmorillonite clay matrix. Free-energy values and geometrical parameters show that D-ribose chirality is preferred for the formation of right-handed RNA molecules. Thus, a "zipper" model with antiparallel and auto-intercalated nucleosides linked by phosphate groups can be proposed to form single RNA chains. Unstacking with strand separation and base pairing by H-bonding, results in shortening and inclination of ribose-phosphate chains, leading to right-handed helicity and antiparallel duplexes. Incorporation of complementary precursors on the major groove template by a self-assembly mechanism provides a prebiotic (non-enzymatic) "tetris" replication model by formation of a transient RNA tetrad and tetraplex. Original hairpin motifs appear as simple building units that form typical RNA structures such as hammerheads, cloverleaves and dumbbells. They occur today in the circular viroids and virusoids, as well as in highly branched and complex rRNA molecules.

Circular RNAs as key regulators in cancer hallmarks: New progress and therapeutic opportunities

Circular RNAs (circRNAs) have emerged as critical regulators in cancer biology, contributing to various cancer hallmarks, including cell proliferation, apoptosis, metastasis, and drug resistance. Defined by their covalently closed loop structure, circRNAs possess unique characteristics like high stability, abundance, and tissue-specific expression. These non-coding RNAs function through mechanisms such as miRNA sponging, interactions with RNA-binding proteins (RBPs), and modulating transcription and splicing. Advances in RNA sequencing and bioinformatics tools have enabled the identification and functional annotation of circRNAs across different cancer types. Clinically, circRNAs demonstrate high specificity and sensitivity in samples, offering potential as diagnostic and prognostic biomarkers. Additionally, therapeutic strategies involving circRNA mimics, inhibitors, and delivery systems are under investigation. However, their precise mechanisms remain unclear, and more clinical evidence is needed regarding their roles in cancer hallmarks. Understanding circRNAs will pave the way for novel diagnostic and therapeutic approaches, potentially improving patient outcomes.

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.

CircArid4b: A novel circular RNA regulating antibacterial response during hypoxic stress via apoptosis in yellow catfish (Pelteobagrus fulvidraco)

The intricate interaction among host, pathogen, and environment significantly influences aquatic health, yet the influence of hypoxic stress combined with bacterial infection on host response is understudied. Circular RNAs with stable closed-loop structures have emerged as important regulators in immunity, yet remain ill-defined in fish. In this study, we systematically explored the circRNA response in yellow catfish subjected to combined hypoxia-bacterial infection (HB) stress. Following HB stress, H&E and TUNEL staining identified heightened hepatocyte apoptosis, intracellular vacuolation, and inflammatory tissue damage. RT-qPCR elucidated that differentially expressed genes stimulated by HB synergistically enhanced apoptosis and inflammatory responses. Importantly, we systematically evaluated differentially expressed circRNAs (DEcirs) in yellow catfish under hypoxia with and without Aeromonas veronii infection and identified a novel HB-specific DEcir, designated as circArid4b, whose parental gene Arid4b is highly associated with apoptosis. Experiments confirmed the circular structure of circArid4b and revealed that under HB stimulation, specific knockdown of circArid4b inhibited the expression of Arid4b, while concurrent alterations in multiple apoptosis- and inflammation-related genes synergistically indicated the promotion of apoptotic and inflammatory pathways. Notably, the downregulation of circArid4b expression significantly reduced the susceptibility to bacterial infection in yellow catfish during hypoxia. These results suggest that HB-induced suppression of circArid4b promotes cell apoptosis and inflammation by inhibiting its parental gene and thereby facilitating resistance to bacterial infection during hypoxia. Our study enriches the understanding of fish circRNA mechanisms and offers novel preventive and control strategies for bacterial infections in fish under hypoxic environments.

Prostate Cancer: De-regulated Circular RNAs With Efficacy in Preclinical In Vivo Models

Therapy resistance, including castration-resistance and metastasis, remains a major hurdle in the treatment of prostate cancer. In order to identify novel therapeutic targets and treatment modalities for prostate cancer, we conducted a comprehensive literature search on PubMed to identify de-regulated circular RNAs that influence treatment efficacy in preclinical prostate cancer-related in vivo models. Our analysis identified 49 circular RNAs associated with various processes, including treatment resistance, transmembrane and secreted proteins, transcription factors, signaling cascades, human antigen R, nuclear receptor binding, ubiquitination, metabolism, epigenetics and other target categories. The identified targets and circular RNAs can be further scrutinized through target validation approaches. Down-regulated circular RNAs are candidates for reconstitution therapy, while up-regulated RNAs can be inhibited using small interfering RNA (siRNA), antisense oligonucleotides (ASO) or clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR-CAS)-related approaches.

Fusion circRNA F-circEA1 facilitates EML4-ALK1 positive lung adenocarcinoma progression through the miR-4673/SMAD4/ADAR1 axis

Circular RNA (circRNA) can sponge miRNA participate in the tumorigenesis and progression of various cancers. We substantiate for the first time that the fusion circular RNA (F-circRNA) F-circEA1 is involved in driving the echinoderm microtubule associated-protein like 4-anaplastic lymphoma kinase variant 1-positive (EML4-ALK1) lung adenocarcinoma (LUAD) progression and the expression of the parental gene EML4-ALK1, molecular mechanisms of F-circEA1 in the EML4-ALK1 LUAD remain unknown. Bioinformatics analysis showed that only miR-4673 can bind to F-circEA1 and bind to EML4-ALK1 3'-UTR to regulate the expression of EML4-ALK1. Notably, high miR-4673 expression exerted an inhibitory impact on the invasion, migration, and proliferation of EML4-ALK1-positive LUAD cells, and partially reversed the invasion, migration, and proliferation of F-cirEA1. F-circEA1 can sponge miR-4673, enhanced the recombinant mothers against decapentaplegic homolog 4 (SMAD4) expression, which is a downstream target of miR-4673. As a transcription factor, SMAD4 exhibits the ability to directly associate with EML4-ALK1 and adenosinedeaminase RNA editingenzyme 1 (ADAR1) promoter regions. Interestingly, it was also observed that the RNA editing enzyme ADAR1 facilitated the expression of F-circEA1, but inhibited the expression of miR-4673. The interplay between F-circEA1, miR-4673, SMAD4, and ADAR1 forms a feedback pathway that aids in regulating the progression of EML4-ALK variant 1-positive LUAD. This novel finding offers promising therapeutic ideas for the EML4-ALK variant 1-positive lung adenocarcinoma.

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.

Extending scope and power of circular RNA research with circtools 2.0

Circular RNAs (circRNAs) play a pivotal role in gene regulation, acting as transcriptional modulators at various cellular levels and exhibit remarkable specificity across cell types and developmental stages. Detecting circRNAs from high-throughput RNA-seq data presents significant challenges, as it requires specialized tools to identify back-splice junctions (BSJ) in raw sequencing data. To address this need, we previously developed circtools, a robust and user-friendly software for circRNA detection, downstream analysis, and wet-lab integration. Building on this foundation, we now introduce circtools 2.0, a significantly enhanced framework designed to advance computational and support experimental analysis for circular RNA research. Novel key features of circtools 2.0 include: (1) an ensemble approach to circRNA detection with improved recall rates, (2) a module for automated design of circRNA padlock probes for the Xenium spatial trancriptomics platform, (3) circRNA conservation analysis across animal model species, and (4) support for the Oxford Nanopore sequencing platform for full-length circRNA detection.

Availability

circtools 2.0 is available at github.com/jakobilab/circtools and licensed under GPLv3.0.

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.

Emerging roles of non-coding RNAs in modulating the PI3K/Akt pathway in cancer

Cancer progression results from the dysregulation of molecular pathways, each with unique features that can either promote or inhibit tumor growth. The complexity of carcinogenesis makes it challenging for researchers to target all pathways in cancer therapy, emphasizing the importance of focusing on specific pathways for targeted treatment. One such pathway is the PI3K/Akt pathway, which is often overexpressed in cancer. As tumor cells progress, the expression of PI3K/Akt increases, further driving cancer advancement. This study aims to explore how ncRNAs regulate the expression of PI3K/Akt. NcRNAs are found in both the cytoplasm and nucleus, and their functions vary depending on their location. They can bind to the promoters of PI3K or Akt, either reducing or increasing their expression, thus influencing tumorigenesis. The ncRNA/PI3K/Akt axis plays a crucial role in determining cell proliferation, metastasis, epithelial-mesenchymal transition (EMT), and even chemoresistance and radioresistance in human cancers. Anti-tumor compounds can target ncRNAs to modulate the PI3K/Akt axis. Moreover, ncRNAs can regulate the PI3K/Akt pathway both directly and indirectly.

The role of circular RNAs in autoimmune diseases: Potential diagnostic biomarkers and therapeutic targets

With the emergence of high-quality sequencing technologies, further research on transcriptomes has become possible. Circular RNA (circRNA), a novel type of endogenous RNA molecule with a covalently closed circular structure through "back-splicing," is reported to be widely present in eukaryotic cells and participates mainly in regulating gene and protein expression in various ways. It is becoming a research hotspot in the non-coding RNA field. CircRNA shows close relation to several varieties of autoimmune diseases (AIDs) in both the physiological and pathological level and could potentially be used clinically in terms of diagnosis and treatment. Here, we focus on reviewing the importance of circRNA in various AIDs, with the aim of establishing new biomarkers and providing novel insights into understanding the role and functions of circRNA in AIDs. Specific signaling pathways of how circular RNAs are regulated in AIDs will also be illustrated in this review.