Circular RNAs (circRNAs) represent a class of widespread and diverse covalently closed circular endogenous RNAs that play critical roles in regulating gene expression in mammals. However, the roles and regulatory mechanisms of circRNAs during influenza A virus (IAV) infection remain largely unexplored. In this study, we screened the circRNA transcription profiles of WSN-infected cells to identify circRNAs involved in viral replication and identified a novel differentially expressed circular RNA, circMYO9A. Mechanistically, circMYO9A acts as a competing endogenous RNA (ceRNA) for SERPINE1/PAI-1 by sponging miR-6059-3p, thereby increasing SERPINE1/PAI-1 expression, which restricts IAV haemagglutinin cleavage and subsequently reduces the infectivity of progeny viruses. Importantly, our findings demonstrate that circMYO9A significantly inhibits viral replication in the lungs of infected mice, potentially increasing their survival during IAV infection. These results demonstrate that circRNAs play crucial roles in inhibiting IAV replication and provide novel insights into potential therapeutic strategies involving circRNAs.

Circular RNAs (circRNAs) are a unique class of covalently closed single-stranded RNA molecules that play diverse roles in normal physiology and pathology. Among the major types of circRNA, exon-intron circRNA (EIciRNA) distinguishes itself by its sequence composition and nuclear localization. Recent RNA-seq technologies and computational methods have facilitated the detection and characterization of EIciRNAs, with features like circRNA intron retention (CIR) and tissue-specificity being characterized. EIciRNAs have been identified to exert their functions via mechanisms such as regulating gene transcription, and the physiological relevance of EIciRNAs has been reported. Within this review, we present a summary of the current understanding of EIciRNAs, delving into their identification and molecular functions. Additionally, we emphasize factors regulating EIciRNA biogenesis and the physiological roles of EIciRNAs based on recent research. We also discuss the future challenges in EIciRNA exploration, underscoring the potential for novel functions and functional mechanisms of EIciRNAs for further investigation.

Objectives. This study investigated the role and underlying regulatory mechanisms of circular RNA fibronectin type III domain containing 3B (circFNDC3B) in abdominal aortic aneurysm (AAA). Methods. The expression of circFNDC3B in AAA and normal tissues was assessed by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). To evaluate the biological functions of circFNDC3B, assays were employed including 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT), flow cytometry, and Caspase-3 activity assays. Additionally, RNA immunoprecipitation (RIP), dual-luciferase reporter assay, Western blotting, and rescue experiments were utilized to elucidate the molecular mechanism of circFNDC3B. Results. Our findings revealed a significant upregulation of circFNDC3B expression in AAA clinical specimens compared to normal tissues. Functionally, overexpression of circFNDC3B inhibited vascular smooth muscle cells (VSMCs) proliferation and induced apoptosis, contributing to AAA formation in the Ang II-induced AAA model. Mechanistically, circFNDC3B acted as a molecular sponge for miR-1270, leading to the upregulation of programmed cell death 10 (PDCD10). Decreased expression of PDCD10 abrogated the -promoting effects of circFNDC3B overexpression on AAA development. Conclusions. This study demonstrates that circFNDC3B promotes the progression of AAA by targeting the miR-1270/PDCD10 pathway. Our findings suggest that circFNDC3B as well as miR-1270/PDCD10 pathway may serve as a potential therapeutic target for AAA treatment.

Circular RNAs (circRNAs) are endogenous covalently closed non-coding RNAs with cell-/developmental-stage-/tissue-specific expression patterns, and they can act as the miRNA sponges and gene transcription regulatory factors to influence numerous biological processes. Herein, we develop a palindrome-crosslinked DNA nanoaggregate system to rapidly detect circRNA and precisely identify lung cancer. We utilize a self-assembled palindromic DNA nanosphere (DS) as the spatial-confinement scaffold to anchor hairpin probes (HP) for the formation of the hybrid assemblies (DSH). The presence of target circSATB2 can hybridize with the hairpin probe to expose the locked palindromic sequence, initiating the cross-linking of the palindromic ends to form a self-catenated structure through intermolecular hybridization. Then the hybridized palindromic ends serve as the self-primers to initiate extension reaction and eventually assemble into the net-like crosslinked DNA nanoaggregates, resulting in the recovery of Cy5 signals. Taking advantage of the excellent antidegradation capability and superior kinetic behavior of DSH nanostructure, high amplification efficiency of Klenow Fragment polymerase (KF)-mediated extension reaction, and signal enhancement induced by the DNA nanoaggregates, this nanosystem enables mix-and-read detection of circSATB2 within 30 min under isothermal conditions (37 °C) with a limit detection of 77.56 fM. Moreover, it is capable of measuring intracellular circSATB2 with single-cell sensitivity, exploring its biological functions, and precisely identifying different stages (I/II/III) and subtypes (IA1/IA2/IA3/IB) of lung cancers, holding great potential in early screening of lung cancers.

Myeloid ecotropic virus insertion site 1 (MEIS1) is a transcription factor involved in a myriad of functions such as hematopoiesis, cardiac regeneration, cell cycle progression, and limb and organ development. Its functional versatility extends beyond developmental biology, as aberrant MEIS1 expression has been implicated in various pathological contexts like carcinogenesis, cardiomyopathies, and neurodegenerative disorders. Recent advances in the field have uncovered novel layers of MEIS1 regulation, focusing on post-transcriptional and translational mechanisms, which collectively fine-tune its activity, stability, and subcellular localization. These include chromatin remodeling, epigenetic modifications in the enhancer and promoter regions, and protein modifications like phosphorylation and ubiquitination. The sophisticated regulation of MEIS1 including its interplay with non-coding RNAs (ncRNAs), either being an upstream or downstream of ncRNAs, equally represents an important regulatory mechanism orchestrating MEIS1 expression and function. This review explores the multifaceted roles of MEIS1, emphasizing its dynamic regulatory networks and their implications in physiological and pathological conditions. It also provides forward-thinking guidance on the utilization of MEIS1 in targeted therapies across various clinical settings, highlighting its potential as a key regulatory factor in disease modulation and therapeutic innovation.

Progestin and adipoQ receptor family member 4 (PAQR4) gene is a recently discovered seven-transmembrane protein-coding gene that belongs to the PAQR family. An increasing amount of evidence suggests that PAQR4 is upregulated in multiple tumors and participates in tumor progression and chemotherapy resistance via different signaling pathways; PAQR4 regulates cellular ceramide homeostasis by influencing sphingolipid metabolism and glycerol metabolism, and plays a significant role in adipose tissue remodeling. Meanwhile, it is known that the differential expression of PAQR4 is associated with the occurrence of various diseases and is a potential biomarker and therapeutic target. This article conducts a systematic review of the subcellular localization of PAQR4, its topological structure characteristics, and its functions in cancer occurrence, metabolic diseases, and fertility, and provides clues for the future research and translational application of PAQR4.

CircRNAs refer to a type of closed circular non-coding RNA without a 5' cap or a 3' poly (A) structure. They are largely distributed in the cytoplasm or localized in exosomes and cannot be easily degraded by RNA exonuclease activity. Their stable expression is broadly observed across eukaryotic species. Insulin resistance (IR) refers to the inability of insulin to exert its normal biological function, as manifested by the impairment of glucose utilization in peripheral tissues (e.g., muscle and fat tissues). IR is a key factor in the pathogenesis of Type 2 diabetes (T2D) and is closely associated with obesity. Recent studies have shown that certain circRNAs play critical roles in obesity-induced diabetes by regulating IR and participating in inflammatory processes. CircRNAs, with their multiple microRNA (miRNA) binding sites, act as miRNA sponges to eliminate the inhibitory actions of miRNAs and up-regulate the expression of target genes. CircRNAs play a significant role in regulating obesity-induced diabetes through their interactions with disease-related miRNAs. In the present study, we explored the biological characteristics of circRNAs and extensively discussed the role of circRNAs in the development of inflammation and IR in adipocytes, highlighting their potential as therapeutic targets for obesity-induced diabetes. Specific circRNAs (e.g., circARF3 and circ-ZNF609) have been identified as key players in modulating IR and inflammatory responses in adipose tissue. CircRNAs are emerging as important regulators of IR and inflammation in adipocytes, with significant potential for therapeutic intervention in obesity-induced diabetes. Further research is needed to elucidate the mechanisms underlying their actions and to explore strategies for targeting circRNAs in clinical applications.

MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression. Among these, miR-660, located on chromosome Xp11.23, is increasingly studied for its role in cancer due to its abnormal expression in various biological contexts. It is regulated by 8 competing endogenous RNAs (ceRNAs), which adds complexity to its function. miR- 660 targets 19 genes involved in 6 pathways such as PI3K/AKT/mTOR, STAT3, Wnt/β-catenin, p53, NF‑κB, and RAS, influencing cell cycle, proliferation, apoptosis, and invasion/migration. It also plays a role in resistance to chemotherapies like cisplatin, gemcitabine, and sorafenib in lung adenocarcinoma (LUAD), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC), thus highlighting its clinical importance. Additionally, leveraging liposomes as nanocarriers presents a promising avenue for enhancing cancer drug delivery. Our comprehensive study not only elucidates the aberrant expression patterns, biological functions, and regulatory networks of miR-660 and its ceRNAs but also delves into the intricate signaling pathways implicated. We envisage that our findings will furnish a robust framework and serve as a seminal reference for future investigations of miR-660, fostering advancements in cancer research and potentially catalyzing breakthroughs in cancer diagnosis and treatment paradigms.

The transcription factor YY1 is significantly upregulated in M2 macrophages, which can facilitate the malignant progression of multiple cancers. However, the precise mechanisms underlying the influence of YY1-high M2 macrophages on prostate cancer (PCa) progression remain elusive. Therefore, this study aims to elucidate the specific mechanisms by which YY1-high M2 macrophages influence PCa progression. Cell proliferation was assessed through colony formation and CCK8 assays. To evaluate cell invasion and migration, Transwell and wound healing assays were utilized. We investigated the effects of exosomes derived from M2 macrophages overexpressing YY1 on PCa cells. Subsequently, circRNA microarrays and qRT-PCR identified a high level of hsa-circ-0000326 in exosomes. Nucleoplasmic isolation, luciferase reporter, RNA-pulldown assays elucidated the functions and downstream targets (miR-338-3p and AR) of hsa-circ-0000326. Chromatin immunoprecipitation sequencing, chromatin conformation capture, qRT-PCR, western blotting, and agarose-electrophoresis assays examined YY1's role in transcribing the hsa-circ-0000326 maternal gene MALAT1 as well as its modulation of QKI expression. Our results demonstrated that the secretion of exosomes enriched with hsa-circ-0000326 by YY1-overexpressing M2 macrophages contributes to PCa metastasis. Hsa-circ-0000326 functions as a competitive endogenous RNA against miR-338-3p to promote androgen receptor levels in PCa cells. Mechanistic investigations revealed that YY1 binds to the super-enhancer region of MALAT1 enhancing transcriptional activity for this gene. Simultaneously, YY1 upregulates QKI expression, facilitating splicing events leading to the formation of hsa-circ-0000326. Inhibiting exosomal hsa-circ-0000326 presents a potential therapeutic approach for treating metastatic PCa.

This study investigated the role of integrin-linked kinase (ILK) in neuronal apoptosis induced by cerebral ischemia‒reperfusion injury (CIRI) and its interaction with a circRNA (0000964) and miR-758-3p. Using in vivo and in vitro rat models, we clarified how ILK regulates neuronal apoptosis during CIRI. Our findings revealed that ILK expression is upregulated in response to CIRI and is modulated by the circRNA (0000964)/miR-758-3p axis. This study provides new insights into the molecular mechanisms of CIRI and suggests potential therapeutic targets to reduce neuronal apoptosis. A CIRI rat model was created through middle cerebral artery occlusion (MCAO). After miR-758-3p overexpression, neurological deficits, CIRI volume, and the expression levels of circRNAs (0000964) and ILK were evaluated. Neurons were subjected to oxygen‒glucose deprivation (OGD) to simulate in vitro CIRI, and the same molecules were analyzed. MCAO-induced CIRI downregulated a circRNA (0000964) and upregulated ILK and miR-758-3p. Similarly, in vitro OGD-induced apoptosis downregulated a circRNA (0000964) and upregulated ILK and miR-758-3p. Further analysis confirmed that a circRNA (0000964) negatively regulates miR-758-3p, which in turn negatively regulates ILK. This axis controls ILK and Caspase-3 expression, influencing neuronal apoptosis. ILK has been identified as a key regulator of neuronal apoptosis in CIRI. The circRNA (0000964)/miR-758-3p axis modulates ILK, impacting neuronal survival. This molecular network offers new insights into CIRI pathophysiology and highlights possible therapeutic approaches.

Non-coding RNA (ncRNA) and competing endogenous RNA (ceRNA) network play vital roles in gene expression regulation, but their involvement in sex determination and differentiation remains unclear in molluscs. In this study, a comprehensive transcriptomic analysis was performed to investigate ncRNAs and ceRNA network in female and male gonads of Crassostrea gigas. Differential expression analysis identified 3496 mRNAs, 582 lncRNAs, 184 miRNAs, and 644 circRNAs with sex-biased expression. Functional enrichment analyses highlighted key pathways such as the cell cycle, oocyte meiosis, energy metabolism, and lipid metabolism, underscoring their involvement in sex determination and differentiation. A ceRNA network was constructed involving 398 lncRNAs, 119 circRNAs, 140 miRNAs, and 720 mRNAs. Hub genes, such as Fem1c, Spef1, Dgkq, Ppp1ca, Nkd1, Morn3, Dpf2, and Gabarap were identified, with pronounced sex-biased expression and localization in specific gonadal cell types, as revealed by bulk and single-nucleus RNA-seq analysis. These genes are associated with critical processes, including follicle development, spermatogenesis, and hormonal regulation. Collectively, these findings provide novel insights into the ceRNA-mediated regulatory mechanisms underlying sex determination and differentiation in C. gigas, contributing to a deeper understanding of molluscan reproductive biology.

MicroRNAs (miRNAs) are small non-coding RNAs that act as critical regulators of gene expression by repressing mRNA translation. The role of miRNAs in cell physiology spans from cell cycle control to cell proliferation and differentiation, both during development and in adult tissues. Accordingly, dysregulated expression of miRNAs has been reported in several diseases, including cancer, where miRNAs can act as oncogenes or oncosuppressors. Of note, miRNA signatures are also under investigation for classification, diagnosis, and prognosis of cancer patients. Brain tumours are primarily associated with poor prognosis and high mortality, highlighting an urgent need for novel diagnostic, prognostic, and therapeutic tools. Among miRNAs investigated in brain tumours, miR-326 has been shown to act as a tumour suppressor in adult and paediatric brain cancers. In this review, we describe the role of miR-326 in malignant as well as benign cancers originating from brain tissue. In addition, since miR-326 expression can be regulated by other non-coding RNA species, adding a further layer of regulation in the cancer-promoting axis, we discuss this miRNA's role in targeted therapy for brain cancers.

Acute lung injury (ALI) is a serious disease with sudden onset, rapid progression, poor treatment response and high mortality. Acid-sensitive ion channels (ASICs) are a type of cation channel activated by extracellular acidification and are involved in the pathogenesis of inflammatory and immune diseases. Our previous research revealed that ASIC1a promotes ALI, but the specific mechanism is unclear. Circular RNAs (circRNAs) are a large class of noncoding RNAs that play important roles in the pathological processes of many diseases. However, their role in lipopolysaccharide (LPS)-induced ALI and their correlation with the ASIC1a channel remain unclear. In this study, via high-throughput sequencing, we investigated the effect of ASIC1a on circRNA expression. We focused on circRNA18-658 and its downstream signaling pathway in rat models of ALI. Our results revealed that ASIC1a promotes ALI through the circRNA18-658/miR-127-5p/TRIM72 axis, providing new targets and ideas for the study of the mechanism of ALI and the development of new drugs.

Increasing evidences have indicated that circular RNAs play a crucial role in the onset and progression of various diseases. However, exploring potential disease-associated circRNAs using conventional experimental techniques remains both time-intensive and costly. Recently, various computational approaches have been developed to detect the circRNA-disease associations. Nevertheless, due to the sparsity of the data and the inefficient utilization of similarity representation, it is still a challenge to effectively detect unknown circRNA-disease associations using multisource data. In this work, we propose an innovative computational framework, MVGNCDA, which merges a multi-view graph convolutional network (GCN) and biased random walk-based network embeddings to evaluate potential circRNA-disease associations from multisource data. First, we calculate disease semantic similarity, circRNA functional similarity, and their Gaussian interaction profile (GIP) kernel and cosine similarity. MVGNCDA utilizes multi-view GCNs to extract local node embeddings of diseases and circRNAs in the context of multisource information. Then, we construct a heterogeneous network utilizing integrated similarity and verified circRNA-disease associations, which is subsequently used to learn global node embeddings. Furthermore, the final fused local and global node embeddings are decoded to evaluate the circRNA-disease associations using a bilinear decoder. The fivefold cross-validation results demonstrate that MVGNCDA outperforms existing methods across five public datasets. Moreover, case study also confirms that MVGNCDA is capable of efficiently identifying unknown circRNA-disease associations.

Cervical cancer (CC) and ovarian cancer (OC) are among the most common gynecological cancers with significant mortality in women, and their incidence is increasing. In addition to the prominent role of the malignant aspect of these cancers in cancer-related women deaths, chemotherapy drug resistance is a major factor that contributes to their mortality and presents a clinical obstacle. Although the exact mechanisms behind the chemoresistance in these cancers has not been revealed, accumulating evidence points to the dysregulation of non-coding RNAs (ncRNAs), particularly long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), as key contributors. These ncRNAs perform the roles of regulators of signaling pathways linked to tumor formation and chemoresistance. Strong data from various recent studies have uncovered that the main mechanism of these ncRNAs in the induction of chemoresistance of CC and OC is done through a dysregulated miRNA sponge activity as competing endogenous RNA (ceRNA) in the competing endogenous RNA networks (ceRNETs), where a miRNA regulating a messenger RNA (mRNA) is trapped, thereby removing its inhibitory effect on the desired mRNA. Understanding these mechanisms is essential to enhancing treatment outcomes and managing the problem of drug resistance. This review provides a comprehensive overview of lncRNA- and circRNA-mediated ceRNETs as the core process of chemoresistance against the commonly used chemotherapeutics, including cisplatin, paclitaxel, oxaliplatin, carboplatin, and docetaxel in CC and OC. Furthermore, we highlight the clinical potential of these ncRNAs serving as diagnostic indicators of chemotherapy responses and therapeutic targets.

Esophageal squamous cell carcinoma (ESCC) is a major contributor to cancer-related deaths, driven by its invasive and metastatic nature. Circular RNAs (circRNAs) are increasingly recognized as regulators of cancer progression, primarily through miRNA sponging and interactions with RNA-binding proteins. Their dysregulation has been linked to the development of in various cancers. The present study aimed to investigate the potential involvement of circSLC22A3 in the pathogenesis of ESCC.

CircSLC22A3 expression in ESCC tissues and cells was analyzed using transcriptome sequencing and RT-qPCR. Its circular structure was validated through Sanger sequencing, agarose gel electrophoresis, RNase R digestion, and random priming assays. Subcellular localization was determined by nucleoplasmic separation and fluorescence in situ hybridization (FISH). Clinical correlations were assessed via tissue microarrays. Functional roles of circSLC22A3 in ESCC progression were investigated through in vitro and in vivo assays. Downstream miR-19b-3p and target gene TRAK2 were screened by bioinformatics analysis and RT-qPCR, with binding confirmed via luciferase reporter assays. RNA pulldown combined with RNA immunoprecipitation (RIP) identified IGF2BP1 as a circSLC22A3-interacting protein. RNA-seq and RT-qPCR revealed ACSBG1 as a key downstream effector. IGF2BP1-mediated m6A modification of ACSBG1 was mapped by MeRIP-seq and RIP, with mRNA stability assessed via Actinomycin D assay. ACSBG1 expression and biological function in ESCC were confirmed by immunohistochemistry, RT-qPCR, and functional assays.

Significant downregulation of circSLC22A3 was observed in both ESCC tissues and cell lines. Overexpression of circSLC22A3 significantly reduced ESCC cells' migration and invasion capabilities. Mechanistic investigation revealed that circSLC22A3 played a pivotal role in the invasion and metastasis of esophageal cancer through distinct pathways. On one hand, circSLC22A3 functioned as a miR-19b-3p sponge to augment trafficking kinesin protein 2 (TRAK2) expression, while, on the other hand, circSLC22A3 formed a protein-RNA complex with IGF2BP1, resulting in the degradation of acyl-CoA synthetase bubblegum family member 1 (ACSBG1) mRNA through the recognition of m6A modification, thereby suppressing invasion and metastasis of ESCC.

The present study identified circSLC22A3 as a new tumor suppressor that inhibited ESCC progression through both the circSLC22A3/ miR-19b-3p/ TRAK2 and circSLC22A3/ IGF2BP1/ ACSBG1 axes.

Circular RNAs (circRNAs) are key regulators of reproductive biology. However, limited information is available regarding circRNA expression profiles in seminal plasma samples from individuals with male infertility. The present study aimed to identify circRNAs associated with infertility in seminal plasma samples and to clarify their potential as biomarkers, as well as the possible molecular mechanisms underlying their functions. Next-generation RNA sequencing was conducted to analyze circRNA profiles in seminal plasma from healthy controls, oligoasthenospermia (OAZ) patients, and non-obstructive azoospermia (NOA) patients. Bioinformatics analysis revealed that 637 circRNAs were differentially expressed between OAZ and control subjects, as well as 272 circRNAs that were differentially expressed between NOA and control subjects. The expression of key circRNAs ( hsa-SAP130_0002, hsa-TRPC1_0001, hsa-FBRS_0001, hsa-ACACA_0025, hsa-UTRN_0042, and hsa-ZNF532_0023) was then validated by qPCR, and their diagnostic accuracy for infertility was confirmed through ROC curve analysis. Additionally, possible circRNA-miRNA-mRNA regulatory networks were developed for these candidate biomarkers. Collectively, this study identifies a novel set of circRNAs with potential as diagnostic biomarkers for male infertility and provides molecular insights that may facilitate both diagnostic and therapeutic efforts.

Endocrine resistance is a leading cause of relapse in patients with estrogen receptor (ER)-positive breast cancer (ER+ BC), with tamoxifen resistance being the most prevalent form. circTNK2, a circular RNA, is overexpressed in tamoxifen-resistant BC tissues and is correlated with poor prognosis. circTNK2 encodes a novel 487-amino acid protein, termed C-TNK2-487aa, which inhibits the recruitment of natural killer (NK) cells into BC tumors. Mechanistically, C-TNK2-487aa interacts with STAT3 and promotes STAT3 phosphorylation (p-STAT3) in ER+ BC cells. The increased p-STAT3 competes with STAT1 binding, inhibiting the formation of STAT1 homodimers that induces CXCL10 expression, ultimately leading to immune evasion. Additionally, circTNK2 RNA binds to SRSF1 and promotes tamoxifen resistance and BC tumorigenicity by activating AKT-mTOR signaling. Delivery of BC-targeting ZIF-8 nanoparticles loaded with circTNK2 antisense oligonucleotides (ASOs) and a CXCL10-encoding plasmid DNA markedly suppresses the growth of BC tumor xenografts, restores tamoxifen sensitivity, and increases CD56+ NK cell infiltration into BC tumors. Our data describe a critical role of the circTNK2-encoded peptide and its RNA in ER+ BC resistance to tamoxifen and immune evasion, providing a therapeutic vulnerability in treating tamoxifen-resistant breast cancer.

We demonstrate non-immunogenic circRNA as a tool for targeted gene regulation in plants, where it acts in an isoform- and sequence-specific manner, enabling future agronomic applications. Circular RNAs (circRNAs) are single-stranded RNA molecules characterized by their covalently closed structure and are emerging as key regulators of cellular processes in mammals, including gene expression, protein function and immune responses. Recent evidence suggests that circRNAs also play significant roles in plants, influencing development, nutrition, biotic stress resistance, and abiotic stress tolerance. However, the potential of circRNAs to modulate target protein abundance in plants remains largely unexplored. In this study, we investigated the potential of designer circRNAs to modulate target protein abundance in plants using Arabidopsis protoplasts as a model system. We show that PEG-mediated transfection with a 50-nt circRNAGFP containing a 30-nt GFP-antisense sequence results in a dose- and sequence-dependent reduction of GFP reporter target protein abundance. Notably, a single-stranded open isoform of circRNAGFP had little effect on protein abundance, indicating the importance of the closed circular structure. Additionally, circRNAGFP also reduced GFP abundance in Arabidopsis mutants defective in RNA interference (RNAi), suggesting that circRNA activity is independent of the RNAi pathway. We also show that circRNA, unlike dsRNA, does not induce pattern-triggered immunity (PTI) in plants. Findings of this proof-of-principle study together are crucial first steps in understanding the potential of circRNAs as versatile tools for modulating gene expression and offer exciting prospects for their application in agronomy, particularly for enhancing crop traits through metabolic pathway manipulation.

Diabetic cardiomyopathy (DCM) is a myocardial structural and functional abnormality directly caused by diabetes and is a principal factor in the development of cardiovascular complications in patients with diabetes. The study aims to investigate the role of circOGDH in the development of DCM and elucidate its precise underlying mechanisms. We established two well-characterised diabetic mouse models, C57BL/6J and db/db, and assessed cardiac function by serum lactate dehydrogenase activity assay and echocardiography, as well as quantitative histological analyses of the extent of myocardial fibrosis in combination with HE staining and Masson trichrome staining. The results demonstrated that there was a significant upregulation of circOGDH expression levels in myocardial tissues of mice in a diabetic state, accompanied by increased expression of key effector proteins of PANoptosis. It is noteworthy that the knockdown of circOGDH led to a substantial enhancement in cardiac function indices, a reduction in the area of myocardial fibrosis, and the effective inhibition of the PANoptosis process in myocardial tissues. In the H9c2 cells model, silencing of circOGDH also exhibited significant protective effects, including increased cell survival, reduced levels of oxidative stress, decreased apoptosis, and suppressed expression of PANoptosis-related proteins. Subsequent employing RNA pull-down, RNA immunoprecipitation and co-immunoprecipitation experimental methods have elucidated, for the first time, the molecular mechanism by which circOGDH specifically targets and regulates RIPK3 through the HMGB1 signalling pathway. The present study definitively demonstrated that up-regulation of circOGDH expression in a diabetic state could exacerbate pathological damage in diabetic cardiomyopathy by activating the HMGB1/RIPK3 signalling pathway.

Circular RNAs (circRNAs) play critical roles in the occurrence of gastric cancer (GC). However, the roles of proteins encoded by circRNAs in GC remain largely unknown. This study aimed to investigate the role of ZNF131-354aa in GC. circZNF131 overexpression plasmids and short hairpin RNAs were used to overexpress and silence circZNF131 expression levels, respectively. Mass spectrometry, co-immunoprecipitation, and Western blotting were used to identify the circZNF131-encoded protein, named ZNF131-354aa. Chromatin immunoprecipitation assay was used to examine the DNA-binding activity of ZNF131-354aa. A subcutaneous tumor model was established in nude mice to examine the effects of ZNF131-354aa on GC growth. Overexpression of circZNF131 was found to inhibit the proliferation, migration and invasion of GC cells, while knockdown of circZNF131 had the opposite effect. Furthermore, immunoprecipitation and mass spectrometry verified that circZNF131 encoded a 40.5 kDa protein, ZNF131-354aa. ZNF131-354aa was shown to inhibit GC progression. ZNF131-354aa was found to be degraded by tripartite motif-containing 28 (TRIM28)-mediated ubiquitination. Moreover, ZNF131-354aa was found to promote E-cadherin and phosphatase and tensin homolog (PTEN) expression by interacting with the intron of the C-terminal binding protein 2 (CTBP2) gene and repressing its expression. In conclusion, ZNF131-354aa acts as a tumor suppressor in GC by inhibiting CTBP2 transcription.

Circular RNAs (circRNAs) are essential regulators of cellular processes, but are challenging to study using traditional methods. Overexpression approaches, such as the use of linearized plasmids and viral vectors, often result in high rates of false-positive clones, where cells retain selection markers without expressing the target circRNA. This study addresses this limitation by developing a dual-selection circRNA system designed to enhance the accuracy and reliability of circRNA overexpression. Our system integrates a fluorescent reporter gene upstream of the circRNA expression cassette, under a shared promoter, and a downstream antibiotic resistance marker, allowing for both antibiotic selection and flow cytometric cell-sorting to identify and enrich cells with genuine circRNA expression. We successfully incorporated this system into an inducible lentiviral vector for controlled overexpression in various cell types. The dual-selection circRNA system offers a significant advance for circRNA research and studies of other RNA species where accurate and reliable overexpression is essential.

Circular RNAs (circRNAs) have been reported to be associated with the progression of various tumors including colorectal cancer (CRC). However, the role and underlying mechanism of hsa_circ_0087862 in CRC remains unclear. Hsa_circ_0087862 expression in CRC tissues was analyzed using two GEO datasets (GSE138589 and GSE126094). Expression of hsa_circ_0087862, miR-149-5p and tumor necrosis factor receptor-associated factor 6 (TRAF6) in CRC cells was detected. The subcellular distribution of hsa_circ_0087862 was analyzed using a Cytoplasmic & Nuclear RNA Purification Kit. The function of hsa_circ_0087862 in CRC cells was detected using CCK-8, Transwell invasion assay, flow cytometry analysis, and Caspase-3 activity assay. The relationships between hsa_circ_0087862, miR-149-5p and TRAF6 were detected using luciferase reporter assay, RIP, or biotinylated RNA pull-down assay. Hsa_circ_0087862 was upregulated in CRC tissues and cells. Hsa_circ_0087862 is resistant to RNase R digestion and predominantly localized in the cytoplasm. Interference with hsa_circ_0087862 inhibited the malignant phenotypes of CRC cells by reducing cell proliferation and invasive abilities and triggering apoptosis. Hsa_circ_0087862 silencing inhibited TRAF6 expression by sponging miR-149-5p in CRC cells. Inhibition of miR-149-5p attenuated the effects of hsa_circ_0087862 on the malignant phenotypes of CRC cells. TRAF6 overexpression abolished the effects of miR-149-5p on cell growth, invasion and apoptosis in CRC cells. In conclusion, hsa_circ_0087862 silencing inhibited the malignant behaviors of CRC cells through inhibiting TRAF6 expression by sponging miR-149-5p.

Dysregulation of circRNA expression is associated with increased metastasis and an adverse prognosis in non-small cell lung cancer (NSCLC). Herein, this study assessed the role and regulatory mechanism of circPVT1 in NSCLC development.

CircPVT1 expression was determined using qPCR. Functional assays, including cell proliferation, colony formation, and ferroptosis-related measurements (ROS, MDA, SOD, GSH and Fe2+ levels), were conducted following circPVT1 knockdown. The interactions between RNA and protein were determined through RIP, dual-luciferase reporter and fluorescence in situ hybridization. Actinomycin D assay was employed to test circPVT1 stability. Additionally, tumor progression in vivo was evaluated in xenograft models with U2AF65 knockdown.

CircPVT1 was significantly elevated in NSCLC samples, correlating with worse clinical outcomes. Its knockdown resulted in diminished cell proliferation and increased ferroptosis. Mechanically, circPVT1 sponges miR-338-3p, facilitating GPX4 expression, which enhanced cell proliferation. U2AF65 bound to and stabilized circPVT1, promoting cell proliferation. In animal models, U2AF65 knockdown suppressed tumor progression by regulating the circPVT1/miR-338-3p/GPX4 signaling pathway.

U2AF65 stabilizes circPVT1 to promote NSCLC advancement through miR-338-3p suppression and GPX4 upregulation. Thus, circPVT1 and U2AF65 may be potential therapeutic targets in NSCLC.

The exploration of associations between circular RNAs (circRNAs) and diseases contributes to a deeper understanding of the pathogenesis of diseases. Many computational methods have been proposed for circRNA-disease associations identification. However, these methods still exhibit some limitations such as ignoring the effect of noise. In this paper, we proposed a new knowledge graph attribute mining attention network (KAATCDA) to predict circRNA-disease associations based on knowledge graph attribute network (KGA) and attribute mining attention network (AMA). Firstly, KGA is used to learn the feature representation of diseases. Then, the features of circRNAs are obtained using AMA, which are similar to disease feature representations. Finally, the scores of circRNA-disease associations are predicted based on circRNA feature representation and disease feature representation. Experiments of five-fold cross-validation on two datasets demonstrate that KAATCDA outperforms other state-of-the-art methods. In addition, the case study shows our method can effectively predict unknown circRNA-disease associations.

Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. Its role in the transdifferentiation of prostate and lung adenocarcinoma into neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC) remains unexplored. Here, we identified circRMST as an exceptionally abundant circRNA predominantly expressed in NEPC and SCLC, with strong conservation between humans and mice. Functional studies using shRNA, siRNA, CRISPR-Cas13, and Cas9 consistently demonstrate that circRMST is essential for tumor growth and the expression of ASCL1, a master regulator of neuroendocrine fate. Genetic knockout of Rmst in NEPC genetic engineered mouse models prevents neuroendocrine transdifferentiation, maintaining tumors in an adenocarcinoma state. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, collectively leading to the loss of ASCL1 transcription.

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.

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.

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.

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.

Background: Aberrant expression of microRNAs in neoplastic lesions may serve as potential personalized therapeutic targets. To inhibit oncogenic microRNAs (oncomiRs) expression and restore tumor suppressor proteins, linear miRNA sponges have been developed, leading to several drugs in clinical trials. Despite their efficacy, chemically synthesized miRNA inhibitors face challenges with sustained inhibition and high production costs, hindering widespread clinical adoption. Additionally, single-stranded circular RNAs (circRNAs) act as miRNA sponges, enhancing protein expression and demonstrating stability and therapeutic potential in cancer treatment. Our approach involves the use of synthetic single-stranded circular nucleic acids, including circDNA and circRNA, to selectively target and inhibit a variety of aberrantly overexpressed oncomiRs in tumors. The objective of this strategy is to restore the expression levels of multiple tumor suppressor factors and to suppress the malignant progression of tumors. Methods: Our methodology comprises a two-step process. First, we identified tumor suppressor genes (TSGs) with abnormally low expression in hepatocellular carcinoma (HCC) tumor cells by transcriptomic analysis and targeted the upstream cancer miRNA clusters of these TSGs. Second, we designed and validated a fully complementary circDNA or circRNA construct, ligated by T4 DNA ligase or T4 RNA ligase, respectively, that specifically targets the sponge oncomiRs both in vitro and in vivo to inhibit the malignant progression of HCC. Results: CircNAs demonstrated superior, long-lasting therapeutic efficacy against HCC compared to inhibitors. Furthermore, we compared the immune effects in vivo of three different nucleic acid adsorption carriers, including commercial miRNA inhibitor, circDNA, and circRNA. We found that the miRNA inhibitor activates a more robust inflammatory response compared to circDNA and circRNA. Conclusions: These findings underscore the substantial therapeutic potential of circDNA in tumorigenesis and provide novel insights for the formulation of personalized treatment plans for malignant tumors, such as HCC.

miRNA arm switching is a pivotal regulatory mechanism that allows organisms to fine-tune gene expression by selectively utilizing either the 5p or 3p strand of a miRNA duplex. This process, conserved across species, facilitates adaptive responses to developmental cues, environmental changes, and disease states. By dynamically altering strand selection, arm switching reshapes gene regulatory networks, contributing to phenotypic diversity and evolutionary innovation. Despite its growing recognition, the mechanisms driving arm switching-such as thermodynamic properties and enzyme-mediated processing-remain incompletely understood. This review synthesizes current findings, highlighting arm switching as a highly conserved mechanism with profound implications for the evolution of regulatory networks. We explore how this phenomenon expands miRNA functionality, drives phenotypic plasticity, and co-evolves with miRNA gene duplications to fuel the diversification of biological functions across taxa.

This study aimed to investigate the functional roles and molecular regulatory mechanisms of circular RNAs in the development of glioblastoma multiforme. Differentially expressed circular RNAs were identified by integrating RNA sequencing data and circular RNA microarray data from the Gene Expression Omnibus database. CircAtlas and CircInteractome databases were used to predict microRNAs (miRNAs) interacting with these circular RNAs. Survival analysis of the miRNAs was performed using data from the Chinese Glioma Genome Atlas. The miRTarBase database was used to predict miRNA target genes, followed by the construction of a circular RNA-miRNA-messenger RNA regulatory network specific to glioblastoma multiforme. Functional enrichment analysis was carried out using the DAVID website, and protein-protein interaction networks were created using the Search Tool for the Retrieval of Interacting Genes/Proteins website and Cytoscape. Hub genes were identified, and their expression and prognostic relevance in glioblastoma multiforme were further examined. Four differentially expressed circRNAs and 10 associated miRNAs related to glioblastoma multiforme prognosis were identified. Functional enrichment showed the miRNAs target genes were mainly involved in apoptosis, cell cycle regulation and enriched in cancer-related pathways like mitogen-activated protein kinase and PI3K-Akt. Through the circRNA-miRNA-messenger RNA regulatory network and survival analysis, 3 core genes (core hub genes: catenin beta 1, BCL2, nuclear factor kappa B subunit 1) were identified as significantly downregulated in glioblastoma multiforme and associated with patient survival. This study highlights the potential regulatory roles of circular RNAs in glioblastoma multiforme pathogenesis and their involvement in key molecular pathways. The findings offer a theoretical foundation for understanding glioblastoma multiforme development and may facilitate the identification of novel biomarkers for this aggressive cancer.

Circular RNAs (circRNAs) have been gradually revealed to regulate the progression of heart disease in depth, showing their clinical significance. However, a mass of cardiac circRNAs still has not been functionally characterized. We aimed to explore the potential candidates that are involved in pathological cardiac hypertrophy.

Public substantial RNA-sequencing data of cardiac circRNAs were utilized to search the cardiac hypertrophy-related circRNAs. Cardiomyocyte hypertrophy in vitro was induced by Ang II (angiotensin II) treatment. Mice were subjected to Ang II infusion to induce cardiac hypertrophy in vivo. Gain-of-function and loss-of-function assays were conducted to detect the effect of RNAs or proteins in cardiac hypertrophy.

A circRNA derived from the cdyl (chromodomain Y-like) gene was screened out and named circCDYL. Our results showed that the expression of circCDYL in primary rat cardiomyocytes was significantly induced by Ang II. Gain-of-function and loss-of-function assays demonstrated that circCDYL effectively promoted cardiomyocyte hypertrophy in vitro. CircCDYL could encode a ≈100-aa truncated CDYL peptide (tCDYL-100), whose sequence highly overlaps that of full-length CDYL. The translation of tCDYL-100 was activated by N6-methylation of circCDYL under prohypertrophic stimulation. tCDYL-100 fulfilled the prohypertrophic function of circCDYL. Mechanistically, tCDYL-100 competed with CDYL for binding REST (RE1-silencing transcription factor) and further disrupted the formation of REST-CDYL-EHMT2 (euchromatic histone-lysine N-methyltransferase 2) transcriptional repression complex, resulting in transcriptional activation of rhoa and nppb. Silence of circCDYL in mouse hearts could inhibit Ang II-induced cardiac hypertrophy, while forced expression of tCDYL-100 could cause cardiac hypertrophy.

In summary, our study uncovered an important circRNA-derived peptide and a regulatory mechanism on transcription mediated by N6-methyladenosine-circRNA-histone methylation in pathological cardiac hypertrophy.

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Among these, circular RNAs (circRNAs) represent a recently identified class of endogenous ncRNAs with a pivotal role in gene regulation, alongside short ncRNAs (e.g., microRNAs or miRNAs) and long non-coding RNAs (lncRNAs). CircRNAs are characterized by their single-stranded, covalently closed circular structure, which lacks polyadenylated tails and 5'-3' ends. This unique circular conformation makes them resistant to exonuclease degradation, rendering them more stable than linear RNAs, such as mRNAs in human blood cells, which highlights their potential as biomarkers. Both linear and circular RNAs are derived from pre-mRNA precursors. However, while linear RNAs are produced through conventional splicing, circRNAs are primarily formed through a process known as reverse splicing. CircRNAs can be categorized into five basic types: exon circRNAs, circular intronic RNAs, exon-intron circRNAs, intergenic circRNAs, and fusion circRNAs. These molecules have been shown to significantly influence key hallmarks of cancer, including sustained growth signaling, proliferation, angiogenesis, resistance to apoptosis, unlimited replicative potential, and metastasis. This article will delve into the biogenesis and functions of circRNAs, explore their roles in cancer, and discuss their potential applications as therapeutic options and diagnostic biomarkers.

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.

Noncoding RNAs (ncRNAs) are a class of RNA molecules with little or no protein-coding potential. Emerging evidence indicates that ncRNAs are frequently dysregulated and play pivotal roles in the pathogenesis of pancreatic cancer. Their aberrant expression can arise from chromosomal abnormalities, dysregulated transcriptional control, and epigenetic modifications. ncRNAs function as protein scaffolds or molecular decoys to modulate interactions between proteins and other biomolecules, thereby regulating gene expression and contributing to pancreatic cancer progression. In this review, we summarize the mechanisms underlying ncRNA dysregulation in pancreatic cancer, emphasize the biological significance of ncRNA-protein interactions, and highlight their clinical relevance. A deeper understanding of ncRNA-protein interactions is essential to elucidate molecular mechanisms and advance translational research in pancreatic cancer.

Despite mounting evidence linking circular RNAs (circRNAs) to various diseases, their specific role in liver damage triggered by obstructive sleep apnea (OSA) remains ambiguous. This study investigates alterations in circRNA expression patterns in a mouse model subjected to chronic intermittent hypoxia (CIH), aiming to elucidate the pathways that lead to liver damage associated with OSA. We established the CIH model and conducted circRNA microarray analysis on liver samples from both CIH and control groups. The findings were substantiated via qRT-PCR. Furthermore, a comprehensive circRNA-miRNA-mRNA (ceRNA) network was developed, followed by the analysis of GO and KEGG pathways to further elucidate the underlying biological processes. We identified 259 differentially expressed circRNAs, comprising 86 that were upregulated and 173 that were downregulated in CIH mice. The ceRNA analysis suggested that these circRNAs may modulate gene expression by sequestering miRNAs. Our findings highlight potential therapeutic targets for liver pathologies associated with OSA.

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.