circRNA Biogenesis Competes with Pre-mRNA Splicing

Nuclear circGUSBP1 promotes cancer stemness via transcriptional coordination with OCT4

AIMS

Endometrial cancer (ECa) is a prevalent gynecological malignancy, with treatment often hindered by metastasis and recurrence driven by cancer stem-like cells. While circular RNAs (circRNAs) are well known for their cytoplasmic roles as microRNA sponges, their nuclear functions remain largely unexplored. This study investigates nuclear circRNAs and their roles in regulating cancer stem-like properties in ECa.

MATERIALS AND METHODS

Nuclear RNA sequencing data were analyzed to identify nuclear-enriched circRNAs. The subcellular localization of circGUSBP1 and circZNF680 was assessed via nuclear-cytoplasmic fractionation and RT-qPCR. The functional impact of circGUSBP1 was evaluated using tumorsphere formation, migration, and cisplatin sensitivity assays. Transcriptomic profiling and survival analysis were conducted using circGUSBP1-knockdown ECa cells and The Cancer Genome Atlas (TCGA) dataset.

KEY FINDINGS

CircGUSBP1 exhibited a high circular-to-linear transcript ratio and was preferentially nuclear, independent of intron retention. Its expression correlated with NANOG and OCT4 upregulation. Overexpression of circGUSBP1 enhanced tumorsphere formation, whereas circGUSBP1-knockdown (KD) reduced tumorsphere formation, impaired migration, and increased cisplatin sensitivity. Transcriptomic analysis revealed downregulation of stemness-related genes, supporting its role as a transcriptional co-activator. Notably, 230 circGUSBP1-regulated genes were co-targeted by OCT4, including SUPT16H and SUV39H2, chromatin remodelers linked to poor prognosis in ECa patients. Higher GUSBP1 expression, but not GUSB, correlated with worse survival outcomes in TCGA data.

SIGNIFICANCE

These findings identify circGUSBP1 as a nuclear regulator of cancer stemness. Through circGUSBP1/OCT4 co-regulation of chromatin modulators, circGUSBP1 promotes aggressive tumor behavior, highlighting its potential as a therapeutic target.

The role of circRNA in insulin resistance and its progression induced by adipose inflammation

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.

miR-660: A novel regulator in human cancer pathogenesis and therapeutic implications

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.

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 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.

Lighting up three-dimensional nanolantern for circular RNA imaging and precise gene therapy

Circular RNAs (circRNAs) are a category of endogenous single-stranded RNAs with covalently closed head-to-tail topology, and they play a crucial part in regulating gene expression at post-transcriptional and transcriptional levels. Herein, we construct a three-dimensional nanolantern for circRNA imaging and precise gene therapy. This assay involves an integrated multi-functionalized lantern-shaped probe. By rationally engineering four vertexes and six edges of DNA dimensional architecture, the integrated nanolantern probe functions not only as a delivery machine for reactants but also as a scaffold for catalytic hybridization reactions. The presence of circCDYL initiates the entropy-driven strand displacement assembly of nanolantern monomer to generate long nanolantern concatemers while releasing small interfering RNAs (siRNAs) for target-stimulated on-site and on-demand gene therapy. Compared with canonical linear probe-based catalytic circuit, this method exhibits significantly improved fluorescence stability and gene therapy efficiency due to the inherent resistance of DNA rigid structure to enzymic digestion. This strategy enables one-step detection of circCDYL with a limit of detection (LOD) of 28.2 aM, and accurate quantification of circCDYL expressions in breast cancer patients and healthy individuals. Importantly, this catalytic circuit can achieve tumor-specific gene silencing with minimal off-target toxicity, holding great potential in tumor diagnosis and precise medicine.

A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression

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.

The role of circular RNAs in regulating cytokine signaling in cancer

Dysregulation of cytokine signaling is central to the development and progression of cancer. Cytokines are not only involved in promoting cancer development but also regulate anti-tumor immune responses. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules lacking free ends, which have emerged as critical regulators of cytokine signaling. Transcriptional and post-transcriptional regulation of cytokine signaling by circRNAs contributes to cancer pathogenesis. Here, we discuss the emerging role of circRNAs in modulating cytokine signaling pathways that regulate cancer development. In particular, we examine the role of circRNAs in TGF-β, IL-6, IL-10, TNF-α, VEGF, FGF, PDGF, and chemokine signaling in cancer.

Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis

BACKGROUND

Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood.

RESULTS

In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation.

CONCLUSIONS

In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia.

Impacts of Circular RNAs on the Osteogenic Differentiation of Dental Stem Cells

Dental stem cells are widely viewed as good options for bone regeneration because of their ease of acquisition, innate ability to renew themselves, and ability to differentiate into different types of cells. However, the process of osteogenic differentiation of dental stem cells is orchestrated by an intricate system of regulatory mechanisms. Recent studies have demonstrated the critical impacts of circular RNAs (circRNAs) on osteogenic differentiation of dental stem cells. Exploring the roles and regulatory pathways of circRNAs in dental stem cells could identify novel targets and approaches for utilizing dental stem cell therapy in clinical settings. This review provides a comprehensive overview of the functions and mechanisms of circRNAs, with a particular focus on their expression patterns and regulatory roles in osteogenic differentiation of various dental stem cell types. Furthermore, this review discusses current research challenges in this field and proposes future directions for advancing our understanding of circRNA-mediated regulation in dental stem cell biology.

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.

Comprehensive Analysis of circRNA Expression and circRNA-miRNA-mRNA Networks in the Ventral Hippocampus of the Rat: Impact of Chronic Stress and Biological Sex

This study provides new insights into how sex and chronic stress influence circRNA expression in the rat ventral hippocampus, a region critical for emotional processing. We identified 206 sex-biased circRNAs and 194 stress-responsive circRNAs, highlighting distinct expression profiles. Parental genes of male circRNAs were primarily enriched in synaptic transmission pathways, while those of female circRNAs were associated with axon guidance, emphasizing sex-specific molecular differences. Chronic stress also triggered miRNA changes unique to each sex, revealing divergent regulatory mechanisms. The identified circRNA-miRNA-mRNA axes, modulated under stress, appear to regulate the translation of numerous potential mRNA targets. In males, stress positively regulated neuroprotective pathways, suggesting a compensatory response to mitigate stress-induced damage. In contrast, females exhibited a broader translational network that favored mRNA expression without distinct pathway-specific actions. However, the smaller repressed network in females─characterized by a higher circRNA-to-miRNA and mRNA ratio─may indicate a more selective and targeted regulatory mechanism, with many interactions linked to anti-inflammatory processes. Coexpression analysis revealed two male-specific modules with altered activity under stress. These were associated with processes such as reticulum stress and actin dynamics, the latter linked to dendritic spine loss and depressive-like behaviors, extensively documented in chronically stressed male rats. Conversely, females displayed an activated stress-responsive module, promoting axon guidance and long-term potentiation, which may contribute to improved cognitive outcomes. Among the identified circRNAs, rno-Gabrg3_0001 emerged as stress-sensitive in males. This circRNA exhibited predicted miRNA binding sites and interactions with proteins involved in vesicle trafficking, forming part of a highly active module enriched in genes related to ion transport and membrane protein localization. Overall, these findings uncover sex-dependent regulatory mechanisms driving transcriptomic changes under chronic stress, deepening our understanding of ventral hippocampal molecular functions. Investigating these regulatory networks, which differentially affect the male and female ventral hippocampus, could inform the development of sex-specific therapeutic strategies for stress-related disorders.

circRNA/TLR interaction: key players in immune regulation and autoimmune diseases

Circular RNAs are a class of non-coding RNAs with covalently closed loops. They have been revealed to regulate immune responses by affecting gene expression. Although initially considered splicing byproducts, new studies have indicated their role in transcriptional and post-transcriptional control, especially with TLRs. TLRs start inflammatory signaling and let the innate immune system recognize PAMPs. circRNAs interact context-dependently with TLR pathways to influence immune homeostasis and inflammation in either pathogenic or protective roles. In autoimmune diseases, dysregulated circRNA expression can aggravate immune responses and damage tissue. CircRNAs can interact with RNA-binding proteins, function as molecular sponges for miRNAs, and change inflammatory pathways like the NF-κB signaling cascade, influencing immune responses. They control adaptive immunity, function of antigen-presenting cells, and cytokine generation. The stability and presence of circRNAs in many body fluids make them therapeutic targets and biomarkers for inflammatory and autoimmune diseases. The several immune control roles of circRNA-TLR interactions are discussed in this review, as well as their consequences for immunologically mediated disease diagnosis and treatment.

The Functional Diversity of Chromatin-Associated RNA Binding Proteins in Transcriptional and Post-Transcriptional Regulation

RNA-binding proteins (RBPs) are a diverse class of proteins that interact with their target RNA molecules to regulate gene expression at the transcriptional and post-transcriptional levels. RBPs contribute to almost all aspects of RNA processing with sequence-specific, structure-specific, and nonspecific binding modes. Advances in our understanding of the mechanisms of RBP-mediated regulatory networks consisting of DNAs, RNAs, and protein complexes and the association between these networks and human diseases have been made very recently. Here, we discuss the "unconventional" functions of RBPs in transcriptional regulation by focusing on the cutting-edge investigations of chromatin-associated RBPs (ChRBPs). We briefly introduce examples of how ChRBPs influence the genomic features and molecular structures at the level of transcription. In addition, we focus on the post-transcriptional functions of various RBPs that regulate the biogenesis, transportation, stability control, and translation ability of circular RNA molecules (circRNAs). Lastly, we raise several questions about the clinical significance and potential therapeutic utility of disease-relevant RBPs.

TransRM: Weakly supervised learning of translation-enhancing N6-methyladenosine (m6A) in circular RNAs

As our understanding of Circular RNAs (circRNAs) continues to expand, accumulating evidence has demonstrated that circRNAs can interact with microRNAs and RNA-binding proteins to modulate gene expression. More importantly, a subset of circRNAs has been reported to possess coding potential, enabling them to translate into functional proteins. Recent studies also indicate that the N6-methyladenosine (m6A)-modified start codon may function as an Internal Ribosome Entry Site (IRES), influencing the translation of circRNAs. Therefore, elucidating how m6A regulates circRNA translation potential could significantly advance circRNA research, including the development of circRNA-based vaccines. However, to our knowledge, there are currently no computational tools specifically designed for this purpose. To bridge this gap, we have developed the first computational model, termed TransRM, to predict the impact of base-resolution m6A sites on circRNA translation. Our model employs weakly supervised learning with two convolution layers. These layers extract RNA modification features, and a bidirectional gated recurrent unit predicts the contribution of each RNA modification to circRNA translation. Subsequently, the RNA modification features are then integrated with their contribution to assess the probability of circRNA translation using a random forest algorithm. TransRM has demonstrated efficiency in identifying translation-enhancing m6A sites, with an AUROC of 0.9188 and an AUPRC of 0.9371, respectively. We hope that our newly proposed model could help to broaden our understanding of circRNA regulation at the epitranscriptome layer, particularly in identifying translated circRNAs, thereby contributing to the development of more effective circular RNA-based therapeutics.

Circular RNA discovery with emerging sequencing and deep learning technologies

Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disease pathogenesis. However, their low expression levels and high sequence similarity to linear RNAs present substantial challenges for circRNA detection and characterization. Recent advances in long-read and single-cell RNA sequencing technologies, coupled with sophisticated deep learning-based algorithms, have revolutionized the investigation of circRNAs at unprecedented resolution and scale. This Review summarizes recent breakthroughs in circRNA discovery, characterization and functional analysis algorithms. We also discuss the challenges associated with integrating large-scale circRNA sequencing data and explore the potential future development of artificial intelligence (AI)-driven algorithms to unlock the full potential of circRNA research in biomedical applications.

RBM24-mediated biogenesis of circ23679 protects cardiomyocytes against apoptosis via sponging miR-15b-5p

Circular RNAs (circRNAs) have emerged as significant members of gene regulatory networks and play important roles in normal heart biology and cardiac diseases. RNA binding proteins (RBPs) are key regulatory factors in circRNA formation; however, the mechanisms by which RBP regulate circRNA production remain unclear. RNA binding motif protein 24 (RBM24) is essential for alternative splicing of genes related to cardiac function, and its loss leads to dilated cardiomyopathy and heart failure. In this study, we performed circRNA profiling on hearts from wild-type and Rbm24 knockout mice, identifying the differential expression of circRNAs. We demonstrated that RBM24 could directly bind to pre-mRNA, facilitating the inclusion of specific exons to provide a substrate for circ23679 production. Moreover, RBM24-regulated circRNA production depended on its phosphorylation status. Further, we showed that RBM24-mediated circ23679 acted as a sponge of miR-15b-5p, and a deficient in circ23679-mediated 'sponging events' could drive cardiac apoptosis. Conversely, circ23679 overexpression inhibited cardiac apoptosis and alleviated the disease phenotype in mouse models of heart failure. Thus, our study not only proposes a novel model in which RBPs provide the substrate for circRNA formation but also reveals that RBM24-dependent circRNA production is a crucial post-transcriptional regulatory circuit in cardiac pathogenesis.

Comprehensive analysis of non-coding RNAs in the ovaries of high and low egg production hens

Egg production performance a critical economic trait in the poultry industry. The regulatory mechanisms underlying egg production performance mediated by non-coding RNAs remain to be characterized. To systematically investigate ovarian lncRNAs, circRNAs, and miRNAs associated with laying efficiency, we conducted comparative transcriptomic analyses using RNA sequencing (RNA-seq) of ovarian tissues from phenotypically divergent groups - high egg production (HEP) and low egg production (LEP) hens. In our study, we identified 675 lncRNAs, 140 circRNAs, and 10 miRNAs that were significantly differentially expressed (DE) between HEP and LEP. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that target genes of DE lncRNAs, DE miRNAs, and the source genes of DE circRNAs are involved in the MAPK signaling pathway, endocytosis, notch signaling pathway, among others. Furthermore, we identified five miRNA-mRNA interactions related to egg production including gga-miR-449c-3p, and five genes (GLI2, TAC1, EML6, THOC3, MMP9). These findings establish the first comprehensive ncRNA interactome driving ovarian efficiency, offering both biomarkers for breeding selection and mechanistic targets for reproductive enhancement.

Quaking-cZFP609 Axis Remedies Aberrant Plasticity of Vascular Smooth Muscle Cells via Mediating Platelet-Derived Growth Factor Receptor β Degradation

Vascular smooth muscle cell (VSMC) plasticity is crucial for the repair after vascular injury. However, the high plasticity of VSMCs may make them transform into pathogenic phenotypes. Here, we show that VSMCs overexpressing Sirtuin 1 (SIRT1) exhibit a reduced phenotypic plasticity in the context of platelet-derived growth factor (PDGF)-BB treatment. SIRT1 activated Quaking (QKI)-cZFP609 axis is involved in the plasticity regulation in the VSMCs. Mechanically, SIRT1 deacetylates K133 and K134 of QKI and mediates its activation. Activated QKI binds the QKI response elements located in the upstream and downstream of the cZFP609-forming exons in ZFP609 pre-mRNA to mediate cZFP609 production. Furthermore, the acetylation of QKI is increased by inhibiting SIRT1 with the selective and potent inhibitor EX527 or deletion of SIRT1, accompanied with parallel decrease in cZFP609 formation. Final, we identify that cZFP609 directs PDGF receptor (PDGFR)β sorting into endosomal/lysosomal pathway and degradation by bridging PDGFRβ and Rab7, resulted in attenuating Raf-MEK-ERK cascade activation downstream of PDGFRβ signaling. Overexpression of cZFP609 remedies aberrant plasticity and overproliferation of VSMCs, and ameliorates neointimal formation. Together, these results highlight that modulating the QKI-cZFP609 axis may help propel repair without stenosis as a therapeutic strategy in vascular injury.

ADAR1-HNRNPL-Mediated CircCANX Decline Promotes Autophagy in Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a characteristic chronic airway inflammatory disease that worsens over time, however, there are currently limited clinical therapeutics to suspend its progression. Circular RNAs (circRNAs), which have emerged as functional regulators in various diseases, including COPD, may server as new pharmacological targets in COPD. Here, it is identified a nuclear circRNA, circCANX, that is preferentially decreased in COPD. The linear splicing of CANX pre-mRNA, enhanced by the ADAR1-HNRNPL interaction, is responsible for the circCANX decline. Clinically, the higher circCANX expression is associated with a worse lung function index of FEV1/FVC among patients with COPD. CircCANX suppresses autophagy and stress granule (SG) formation to strengthen inflammation of COPD in vivo and in vitro. Mechanistically, circCANX recruits the tumor suppressor protein P53 (P53) mRNA and RNA helicase upstream frameshift 1 (UPF1) to form a ternary complex, which mediates P53 mRNA degradation through nonsense-mediated mRNA decay (NMD) process. Together, this study reveals an important circCANX-mediated regulatory mechanism in COPD, and provides new insights into the potential of circRNA-based drug and biomarker development for COPD.

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.

Dysregulated circular RNAs in rheumatoid arthritis: Cellular roles and clinical prospects

Rheumatoid arthritis (RA) is still a healthcare challenge, although current therapeutic strategies have substantially improved its clinical outcomes. The development of novel biomarkers and treatments can increase the likelihood of identification and disease remission in RA patients, especially for patients with seronegative RA and difficult-to-treat RA (D2T RA). Circular RNAs (circRNAs), a novel non-coding RNA species, have been reported to play crucial roles in various biological process of RA. The mechanistic functions of the dysregulated circRNAs in RA are primarily associated with miRNA sponging and regulating transcription. CircRNAs acting as miRNA sponges are further summarized by cell types, including fibroblast-like synoviocytes (FLSs), lymphocytes, macrophages, chondrocytes, and mesenchymal stem cells (MSCs)-/plasma-secreted exosomes. Besides, a description of dysregulated circRNAs in blood, synovial tissue and cartilage tissue suggests their diagnostic potential for RA. In addition, some directions for future research are provided to open the possibility that dysregulated cell- and tissue- specific circRNAs constituting a fresh reservoir of therapeutic targets, and biomarkers for diagnosis, predicting response to therapy, drug selection or patient stratification for RA.

Transcriptome-scale analysis of functional alternative back-splicing events in colorectal cancer

BACKGROUND

Circular RNAs (circRNAs) are a class of non-polyadenylated RNAs generated from back-splicing of genes. Multiple circRNAs can be generated at a single gene locus through alternative back-splicing events (ABS), sharing the same 5' or 3' back-splice site. To date, how prevalent ABS events are and how they are participated in carcinogenesis of human colorectal cancer (CRC) remains unexplored.

METHODS

To explore the functional roles of ABS events in CRC carcinogenesis, we analyzed ribosomal RNA-depleted transcriptome sequencing data of 176 CRC samples and characterized the landscape of ABS events in CRC. CRC cancer-related ABS events were identified by comparing paired CRC tumor tissues and adjacent normal tissues. Then, univariate and multivariate Cox regression was used to find prognostic ABS events. Moreover, in vitro and in vivo assays were used to exploring the functional roles of circXPO1-1 and circXPO1-2 in CRC.

RESULTS

We totally identified 19,611 high confidence circRNAs in CRC, among which 17,874 (91·1%) of circRNAs were found recurrently. The number of ABS circRNAs accounted for 68.8% of all identified high confidence circRNAs, which suggested that ABS events are prevalent in CRC transcriptome. Particularly, 552 ABS circRNAs were found to be aberrantly expressed between paired CRC tumor tissues and adjacent normal tissues, and their parent genes are closely associated with cancer-related hallmarks. In addition, 13 differential ABS circRNAs were identified to be associated with CRC patient survival and could act as independent prognostic indicators. Furthermore, we identified two ABS circRNAs of XPO1 gene (circXPO1-1 and circXPO1-2). The result showed that overexpression of circXPO1-2 inhibited CRC cell proliferation, migration, and invasion in vitro and in vivo, whereas circXPO1-1 is not, indicating that the circularization isoforms of XPO1 gene have different functions in CRC.

CONCLUSIONS

In conclusion, our work provides the landscape of ABS events in CRC transcriptome and the close association of ABS circRNAs with tumorigenesis offers a new set of targets with potential clinical benefit.

QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis

Colorectal cancer (CRC) is the third most common cancer and remains a significant challenge due to high rates of drug resistance and limited therapeutic options. Circular RNAs (circRNAs) are increasingly recognized for their roles in CRC initiation, progression, and drug resistance. However, no circRNA-based therapies have yet entered clinical development, underscoring the need for comprehensive detection and mechanistic studies of circRNAs in CRC. Here, we identified and characterized a circular RNA, circ_0001766 (hsa_circ_0001766), through microarray analysis of CRC tissues. Our results showed that circ_0001766 is downregulated in CRC tissues and closely associated with patient survival and metastasis. Functional experiments demonstrated that circ_0001766 inhibits CRC cell proliferation, migration and invasion both in-vitro and in-vivo. Mechanistically, hypoxia downregulates Quaking (QKI), an RNA-binding protein essential for the biogenesis of circ_0001766 by binding to introns 1 and 3 of PDIA4 pre-mRNA. Reduced QKI expression under hypoxic conditions leads to decreased circ_0001766 levels in CRC. Circ_0001766 acts as a competitive endogenous RNA, sponging miR-1203 to prevent the degradation of PPP1R3C mRNA. Loss of circ_0001766 results in decreased PPP1R3C expression, leading to the activation of mTOR signaling and increased phosphorylation of Myc, which promotes CRC progression and rapamycin resistance. Our study reveals that overexpression of circ_0001766 or PPP1R3C in CRC cells inhibits the mTOR and Myc pathway, thereby resensitizing cells to rapamycin. The combination of circ_0001766 or PPP1R3C with rapamycin markedly inhibits CRC cell proliferation and induces apoptosis by reducing rapamycin-induced Myc phosphorylation. In summary, our study elucidates a critical circ_0001766/miR-1203/PPP1R3C axis that modulates CRC progression and rapamycin resistance. Our findings highlight circ_0001766 as a promising therapeutic target in CRC, providing a new avenue for enhancing the efficacy of existing treatments and overcoming drug resistance.

Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators

Circular RNAs (circRNAs) increase in the brain with age across various animal systems. To elucidate the reasons behind this phenomenon, we profile circRNAs from fly heads at six time points throughout their lifespan. Our results reveal a linear increase in circRNA levels with age, independent of changes in mRNA levels, overall transcription, intron retention, or host gene splicing, demonstrating that the age-related accumulation is due to high stability rather than increased biogenesis. This remarkable stability suggests that circRNAs can serve as markers of environmental experience. Indeed, flies exposed to a 10-day regimen at 29°C exhibit higher levels of specific circRNAs even 6 weeks after returning to standard conditions, indicating that circRNAs can reveal past environmental stimuli. Moreover, half-life measurements show circRNA stability exceeding 20 days, with some displaying virtually no degradation. These findings underscore the remarkable stability of circRNAs in vivo and their potential as markers for stress and life experiences.

Genome wide analysis of allele-specific circular RNAs in mammals and their role in cell proliferation

Circular RNAs (circRNAs) are a large class of widely expressed RNAs with covalently closed continuous structures. However, it is currently unknown if circRNAs shows allele-specific expression, as are the consequences of genetic variation on their circularization efficiency and subsequent biological function. Here, we propose a novel pipeline, ASE-circRNA, to accurately quantify both circRNA and their related linear RNA for each allele, and then assess the allele-specificity of the expression of a circular RNA. We identified and analyzed allele-specific circRNAs from human tissue, as well as brains from reciprocal crosses between pairs of highly divergent strains of both mice and pigs by next generation sequencing. Droplet digital PCR (ddPCR) was used to confirm the circularization efficiency measured by next generation sequencing. We found that variation in intron sequences affect the circularization efficiency of circRNAs. Furthermore, we demonstrate that a circRNA, circHK1, regulates the expression of POLR2A to influence the rate of cell proliferation. Our study provides new insight into the molecular mechanisms impacted by variation in genome sequence in the origin of human disease and phenotype.

Degradation of circular RNA by the ribonuclease DIS3

Features of circular RNAs (circRNAs) produced by back-splicing of eukaryotic exon(s) make them resistant to degradation by linear RNA decay machineries. Thus, a general circRNA degradation pathway under normal conditions has remained largely elusive. Here, we report that the endonucleolytic enzyme DIS3 is responsible for the degradation of circRNAs. Depletion of DIS3 leads to the upregulation of more than 60% of circRNAs with little effect on their linear cognates. Such DIS3-mediated circRNA degradation is conserved, occurs in the cytoplasm, and relies on DIS3's endonucleolytic activity but is independent of the RNA exosome complex. Sequence enrichment analyses suggest that DIS3 prefers to degrade circRNAs containing U-rich motifs. Correspondingly, synthesized RNA circles with or without U-rich motifs exhibit decreased or increased stabilities, respectively. Together, these findings suggest a general regulation of circRNA turnover by DIS3.

The regulatory role of the circELMOD3-associated ceRNA network in the progression and prognosis of hepatocellular carcinoma

Background

Our previously research has validated the effect of circELMOD3 on HCC tumor inhibition. However, further investigations are warranted to investigate the prognostic significance of circELMOD3 in HCC and its regulation via the competitive endogenous RNA (ceRNA) network.

Methods

The gene expression profiles and clinical information were obtained from The Cancer Genome Atlas (TCGA-LIHC) and International Cancer Genome Consortium (ICGC). Base on the circMine, miRWalk and TargetScan database, we constructed circELMOD3-miRNA-mRNA network. Univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis was used to constructed the prognostic model. Additionally, Gene set enrichment analysis (GSEA) was conducted for the prognostic-related genes. Finally, the expression levels of genes and proteins were respectively assessed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting.

Results

We constructed a ceRNA network comprising circELMOD3, 5 miRNAs, and 274 mRNAs. From this ceRNA network, we identified four prognostication-relation genes to develop a survival prediction model. In the TCGA-LIHC training set, the area under the curve (AUC) values for one-, three- and five-years of survival were 0.734, 0.718 and 0.707, respectively, then we validated the prognostic model in International Cancer Genome Consortium database. Gene set enrichment analysis displayed that these four prognostic genes were primary enriched pathways related to cell cycle regulation. Our finding demonstrated that circELMOD3 could affect the relative expression levels of N-cadherin, E-cadherin, CDK4, CDK6 and CyclinD1 proteins.

Conclusion

we constructed a novel ceRNA network based on circELMOD3, to comprehensively characterizing the prognosis of HCC, providing valuable insights for the therapy and prognosis of HCC.

Chronic hypoxia-induced upregulation of hsa_circ_0005255 attenuates myocardial injury via targeting hsa-miR-3916/FTO/m6A axis

Chronic hypoxia initiates compensatory mechanisms to protect the heart. Circular RNAs (circRNAs), a recently identified class of non-coding RNAs, represent a significant portion of mammalian transcriptome. We aimed to explore the underlying mechanisms of circRNA involvement in chronic hypoxia-related cardiovascular diseases. In the presents study, we firstly observed hsa_circ_0005255 was elevated in myocardial samples collected from patients with cyanotic heart disease through using circRNA array sequencing, which was confirmed both in vivo and in vitro. The upregulation of hsa_circ_0005255 reduced the levels of N6-methyladenosine (m6A) modification and protected cardiomyocytes from chronic hypoxia induced injury. Fat mass and obesity-associated protein (FTO), the classic regulator of methylation, was proved to be regulated by hsa_circ_0005255. Further research verified the direct target interactions of hsa_circ_0005255/hsa-miR-3916 and hsa-miR-3916/FTO. Our findings suggested hsa_circ_0005255 played pivotal protective role in cardiomyocytes via hsa-miR-3916/FTO/m6A axis. We also showed that silencing hsa_circ_0005255 increased myocardial apoptosis and worsened ischemia/reperfusion (I/R) injury in vivo. In addition, the expression of hsa_circ_0005255 in clinical myocardial samples showed a significant negative correlation with myocardial enzyme levels and early clinical outcomes. This study elucidates a novel mechanism that hsa_circ_0005255/hsa-miR-3916/FTO-m6A axis is involved in myocardial adaptation to chronic hypoxia, representing a promising therapeutic target for cardiovascular diseases.

Research progress on circular RNA in the regulation of drug resistance in genitourinary cancers

In recent years, significant progress has been made in the management of genitourinary cancers, primarily due to advancements in surgical techniques, the emergence of targeted therapy and immunotherapy, and the refinement of chemotherapy agents. However, despite the expanding arsenal of treatment modalities, some patients still face challenges associated with drug resistance, which hinders efforts to improve survival rates. Circular RNAs (circRNAs) are covalently closed RNA molecules with a stable structure and a unique ability to form reverse splicing loops. Increasing evidence suggests that abnormal expression of circRNAs is significantly correlated with the occurrence of genitourinay cancers, indicating their potentials as diagnostic and prognostic biomarkers, as well as new targets for treatment. Although research on circRNAs in genitourinary cancers has progressed, it is still in the preliminary stage. This review summarizes the properties and functions of circRNAs, focusing on their molecular and cellular mechanisms involved in mediating cancer-related drug resistance in the genitourinary system, including autophagy, epithelial-mesenchymal transition, and glycolysis, etc. The clinical potential of circRNAs in regulating drug resistance is also carefully discussed.

CircRNA-mTOR Promotes Hepatocellular Carcinoma Progression and Lenvatinib Resistance Through the PSIP1/c-Myc Axis

Circular RNAs (circRNAs) are crucial regulators of targeted drug resistance in hepatocellular carcinoma (HCC). However, the specific mechanisms underlying resistance that significantly hampers the effectiveness of HCC treatments remain unclear. Here, it is found that circRNA-mTOR is highly expressed in HCC and strongly correlated with patient prognosis. Furthermore, circRNA-mTOR enhances the stemness of HCC cells, thereby promoting the progression of HCC and contributing to lenvatinib resistance. Mechanistically, circRNA-mTOR promotes the nuclear translocation of the RNA-binding protein (RBP) PC4 and SRSF1 interacting protein 1 (PSIP1) through specific binding. The enhancement of HCC cell stemness by circRNA-mTOR occurs via the PSIP1/c-Myc signaling pathway, ultimately driving HCC progression and lenvatinib resistance. This study highlights the important role of circRNA-mTOR in HCC progression and the maintenance of lenvatinib resistance and underscores its potential as a biomarker for the diagnosis and prognosis of HCC. In conclusion, this study provides an experimental foundation for targeted drug therapy in HCC and offers novel insights, perspectives, and methodologies for understanding the development and occurrence of this disease. These findings are significant for the development of new diagnostic and therapeutic markers for HCC, with the ultimate goal of reducing drug resistance.

Identification of circular RNAs as biomarkers for pupal age estimation and postmortem interval in forensically important Sarcophaga peregrina (Diptera: Sarcophagidae)

Accurate estimation of the pupal age in necrophagous flies is vital for determining the postmortem interval (PMI) in forensic entomology. Differential expression of genes (DEGs) exhibits temporal fluctuations across the developmental stages of these flies. This study evaluates circular RNAs (circRNAs) as novel molecular markers and develops a model for predicting pupal development time based on circRNA expression. Transcriptomic analysis of Sarcophaga peregrina pupae at various stages identified four circRNAs (circRNA_0037, circRNA_0531, circRNA_3373, circRNA_2847) showing significant expression differences. Using real-time quantitative PCR and regression analysis, we constructed a model to estimate development time, which accurately predicts intra-puparial periods. Additionally, we examined circRNA degradation patterns in pupae under lethal conditions and identified a clear degradation trend in circRNA_2847, suggesting its potential use for estimating the PMI. This study introduces new molecular markers and insights for estimating necrophagous fly pupal age.

Frequent dysregulation of multiple circular RNA isoforms with diverse regulatory mechanisms in cancer - Insights from circFNDC3B and beyond: Why unique circular RNA identifiers matter

Circular RNAs (circRNAs) are post-transcriptional regulators generated through backsplicing of pre-mRNAs, primarily comprising exons of host genes. A single host gene may produce multiple circRNA isoforms with distinct structures and sequences. Dysregulated circRNA expression has been implicated in tumorigenesis. This review aims to investigate the selection and regulatory roles of circRNA isoforms in cancer using the extensively studied hsa_circFNDC3B and thirteen other circRNAs as study models. Interrogation of literature and databases, particularly the circBase, confirms that host genes generate a plethora of circRNA isoforms; however, only a small subset of isoforms is validated as dysregulated in tumor tissues. Notably, two or more isoforms of the same circRNA are frequently dysregulated in cancer. Structurally, short isoforms retaining 5'-proximal exons are preferentially selected, but for long host genes, circRNAs may arise from mid- or 3'-regions. We identify dysregulation of seven circFNDC3B isoforms across twelve cancer types and multi-isoforms in nine of the other thirteen circRNAs also in multiple cancers. MicroRNA sponging appears to be the major regulatory mechanism, but possible biased study designs raise concerns. Using circFNDC3B and circZFR as examples, we show inconsistency and inadequacy in circRNA nomenclature in different databases and the literature, underscoring the urgent need for a universally accepted standardized central circRNA database. As an interim measure, we propose guidelines for circRNA nomenclature in journal publications. Our findings caution against indiscriminate clinical use of specific circRNA isoforms as biomarkers or therapeutic targets without further validation.

Decoding the complex journeys of RNAs along neurons

Neurons are highly polarized, specialized cells that must overcome immense challenges to ensure the health and survival of the organism in which they reside. They can spread over meters and persist for decades yet communicate at sub-millisecond and millimeter scales. Thus, neurons require extreme levels of spatial-temporal control. Neurons employ molecular motors to transport coding and noncoding RNAs to distal synapses. Intracellular trafficking of RNAs enables neurons to locally regulate protein synthesis and synaptic activity. The way in which RNAs get loaded onto molecular motors and transported to their target locations, particularly following synaptic plasticity, is explored below.

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.

Quaking RNA-Binding protein (QKI) mediates circular RNA biogenesis in Litopenaeus vannamei during WSSV infection

The Quaking RNA-binding protein (QKI), a member of the STAR family, is considered critical in the formation of circular RNAs (circRNAs), as it aids in catalyzing a back-splicing phenomenon by interacting with RNA precursors. CircRNAs have progressively been revealed to play central roles in the regulation of various biological processes, such as antiviral defense mechanisms. This study identifies a QKI in L. vannamei, referred to as LvQKI, comprised of conserved STAR and KH RNA-binding domains. Analysis through tissue-specific expression using qRT-PCR has revealed a high expression level of LvQKI in the gill - one of the primary regions heavily populated by the white spot syndrome virus (WSSV) - and its activation was triggered during WSSV infection. From an RNA interference-mediated suppression targeting LvQKI, a decrease and increase in survival rates and WSSV copy number were observed, respectively. Notably, circRNA levels were significantly lowered in LvQKI-silenced shrimp, whereas linear RNAs remained stable. Conversely, administration of recombinant LvQKI (rLvQKI) protein before a WSSV challenge not only enhanced survival rates but also reduced viral load, wherein both circRNAs and linear RNAs underwent up-regulation in rLvQKI-treated shrimp. Our results introduce LvQKI as a crucial factor in circRNA biogenesis and immune defense in shrimp, emphasizing the interplay between LvQKI's and circRNAs' roles in fighting viral invasion.

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.

Global dysregulation of circular RNAs in frontal cortex and whole blood from DM1 and DM2

Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular disorders associated with expansions of microsatellites, respectively, in DMPK and CNBP. Their pathogenesis is linked to the global aberrant alternative splicing (AAS) of many genes and marks mostly muscular and neuronal tissues, while blood is the least affected. Recent data in DM1 skeletal muscles indicated that abnormalities in RNA metabolism also include global upregulation of circular RNAs (circRNAs). CircRNAs are a heterogeneous group considered splicing errors and by-products of canonical splicing. To elucidate whether circRNA dysregulation is an inherent feature of the myotonic environment, we perform their analysis in the frontal cortex and whole blood of DM1 and DM2 patients. We find a global elevation of circRNAs in both tissues, and its magnitude is neither correlated with the differences in their parental gene expression nor is associated with AAS published earlier. Aberrantly spliced cassette exons of linear transcripts affected in DM1 and DM2 are not among the circularized exons, which unique genomic features prerequisite back-splicing. However, the blueprint of the AAS of linear RNAs is found in a variety of circRNA isoforms. The heterogeneity of circRNAs also originates from the utilization of exonic and intronic cryptic donors/acceptors in back splice junctions, and intron-containing circRNAs are more characteristic of the blood. Overall, this study reveals circRNA dysregulation in various tissues from DM1 and DM2; however, their levels do not correlate with the AAS in linear RNAs, suggesting a potential independent regulatory mechanism underlying circRNA upregulation in myotonic dystrophy.

The diagnostic and therapeutic potential of multiple myeloma-associated circular RNAs

Circular RNA (circRNA) was first discovered in viruses in 1974; they are primarily formed through back splicing, where a downstream splice donor is joined to an upstream splice acceptor, resulting in a closed circRNA transcript. Under normal conditions, most circRNAs are stably expressed; however, in pathological conditions, circRNAs can play critical roles in the disease process of multiple myeloma (MM) through mechanisms such as competing endogenous RNAs (ceRNAs), regulation of transcription and splicing, affecting protein expression and localization, and even direct encoding of peptides. In recent years, there has been increasing interest in the role of circRNAs in MM and their regulatory functions during the disease process. Numerous studies have revealed that circRNAs are involved in the pathogenesis and prognosis of MM, aiding in the identification of reliable prognostic markers and potential therapeutic targets. Therefore, this review summarizes the structural characteristics of circRNAs, and their regulatory roles in MM, and introduces the latest advancements in understanding the novel functions of circRNAs in MM.

Circular RNA NXN (circNXN) promotes diabetic retinopathy by regulating the miR-338-3p/FGFR1 axis

Diabetic retinopathy (DR) is the leading manifestation of diabetic microangiopathy. However, effective biomarkers and therapies are lacking. Circular RNAs (circRNAs) have been implicated in various diseases including DR. However, the role of circRNAs in DR remains elusive. In the present study, circNXN was upregulated in high glucose (HG)-treated human retinal microvascular endothelial cells (hRMECs). circNXN knockdown inhibited the proliferation, migration, and angiogenesis of hRMECs and promoted apoptosis. In addition, circNXN acted as a sponge for miR-338-3p to facilitate the FGFR1 (fibroblast growth factor receptor 1) expression. Furthermore, rescue assays revealed that the reduced promoting effect on hRMECs induced by the knockdown of circNXN could be reversed by a miR-338-3p inhibitor in HG-treated hRMECs. Additionally, in a DR rat model, circNXN downregulation ameliorated retinal vasculature changes. Our findings reveal a new therapeutic strategy for DR that may provide a new approach to clinical DR therapy.

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.

CircZmMED16 delays plant flowering by negatively regulating starch content through its binding to ZmAPS1

Circular RNAs (circRNAs), a type of head-to-tail closed RNA molecules, have been implicated in various aspects of plant development and stress responses through transcriptome sequencing; however, the precise functional roles of circRNAs in plants remain poorly understood. In this study, we identified a highly expressed circular RNA, circZmMED16, derived from exon 8 of the mediator complex subunit 16 (ZmMED16) across different maize (Zea mays L.) inbred lines using circRNA-seq analysis. This circRNA is predominantly expressed in maize tassels and functions in the cytoplasm. Overexpression of circZmMED16 resulted in increased expression of ZmMED16/AtMED16 and delayed flowering in both maize and Arabidopsis thaliana, compared with that in wild-type plants. In contrast, overexpression of the parent gene ZmMED16 did not alter the flowering time of transgenic plants in Arabidopsis, suggesting that circZmMED16 plays a specific role in regulating flowering, distinct from that of linear ZmMED16. To further understand the mechanisms underlying the regulation of flowering time by circZmMED16, we performed RNA pull-down, dual-luciferase, RNA interference (RNAi), and ribonuclease protection assays (RPA). These results indicate that circZmMED16 interacts with small subunit 1 of ADP-glucose pyrophosphorylase (APS1) mRNA in both maize and Arabidopsis. The knockdown of circZmMED16 increased the expression of ZmAPS1, whereas the overexpression of circZmMED16 led to the downregulation of ZmAPS1 RNA and protein. By affecting ZmAPS1 expression, circZmMED16 reduced ADP-glucose pyrophosphorylase (AGPase) activity and led to delayed flowering. These results revealed a novel regulatory mechanism for circRNAs in flowering time and shed light on their functional and regulatory roles in plants.

Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses

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

hsa_circ_0004846 enhances the malignant phenotype of papillary thyroid carcinoma cells via the miR‑142‑3p/PELI1 axis

Circular RNAs (circRNAs) are closely associated with human tumorigenesis; however, whether hsa_circ_0004846 serves a role in the progression of papillary thyroid carcinoma (PTC) remains unclear. Therefore, the present study aimed to investigate the effect of hsa_circ_0004846 on PTC. The results demonstrated that circ_0004846 was abnormally upregulated in PTC tissues and thyroid cancer cell lines (BCPAP, TPC-1 and IHH-4). Furthermore, hsa_circ_0004846-overexpressing or -depleted PTC cell lines (TPC-1 and IHH-4) were constructed using a lentiviral vector system. Notably, hsa_circ_0004846 overexpression markedly promoted cell proliferation, migration and invasion, as evidenced by activation of the PI3K/AKT pathway and the upregulation of vimentin, a class-III intermediate filament, which acts by regulating cell attachment and migration. However, hsa_circ_0004846 knockdown displayed the opposite effects. Mechanistically, the regulatory association among hsa_circ_0004846, microRNA (miR)-142-3p and Pellino E3 ubiquitin protein ligase 1 (PELI1) was validated using a dual-luciferase reporter assay. Specifically, the results demonstrated that hsa_circ_0004846 could sponge miR-142-3p, and the expression levels of miR-142-3p were negatively associated with those of hsa_circ_0004846. In addition, PELI1, a cancer-related E3 ubiquitin ligase, was identified as a downstream target of the hsa_circ_0004846/miR-142-3p axis in PTC. Therefore, PELI1 silencing could reverse the hsa_circ_0004846-induced malignant phenotype of PTC cells. Taken together, the results of the current study highlighted the effect of the hsa_circ_0004846/miR-142-3p/PELI1 regulatory network on PTC progression, thus providing a promising target for PTC treatment.

A functional screen uncovers circular RNAs regulating excitatory synaptogenesis in hippocampal neurons

Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogate their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identify seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, promotes the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown results in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p. Overexpression of circRERE stabilizes miR-128-3p and rescues exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a means to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.

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.

Estrogen-induced circFAM171A1 regulates sheep myoblast proliferation through the oar-miR-485-5p/MAPK15/MAPK pathway

Estrogen is an important hormone that affects muscle development in female animals. Previous studies have shown that estrogen can protect muscle cells from apoptosis by inhibiting the MAPK signaling pathway. However, the molecular mechanisms by which estrogen-induced MAPK signaling regulates myoblast growth and development remain unclear. In this study, RNA-seq was performed on ovariectomized small-tailed Han (OR-STH) sheep and sham surgery small-tailed Han (STH) sheep to analyze the effects of estrogen on muscle growth and development in female animals. There were 8721 differentially expressed circRNAs (DECs), 143 differentially expressed miRNAs (DEMs) and 2238 differentially expressed mRNAs (DEGs) in the longissimus dorsi between the OR-STH and STH groups. Bioinformatics analysis revealed that the differentially expressed gene MAPK15 was significantly enriched in the MAPK signaling pathway, which is important for muscle development. Therefore, we constructed the ceRNA network circFAM171A1/oar-miR-485-5p/MAPK15 and explored its effect on muscle growth and development. The results of the molecular mechanism experiments indicated that circFAM171A1 can sponge oar-miR-485-5p to regulate MAPK15. The addition of the exogenous hormone estradiol (E2) to sheep myoblasts could induce circFAM171A1, regulate the expression of oar-miR-485-5p and MAPK15, and promote the proliferation of sheep myoblasts. The results showed that MAPK15 and circFAM171A1 significantly promoted the proliferation of myoblasts and inhibited the apoptosis of myoblasts in sheep, whereas oar-miR-485-5p inhibited the expression of MAPK15 and circFAM171A1, inhibited myoblast proliferation and promoted apoptosis. Furthermore, circFAM171A1 attenuated the inhibitory effect of oar-miR-485-5p on myoblasts. In summary, estrogen induced the expression of circFAM171A1 in sheep myoblasts, and circFAM171A1 can act as a sponge for oar-miR-485-5p to promote the expression of the target gene MAPK15 and ultimately regulate the proliferation of sheep myoblasts. This study provides new insights into the molecular mechanism of estrogen regulation of muscle growth and development in female animals.

Discovery of circular transcripts of the human BCL2-like 12 (BCL2L12) apoptosis-related gene, using targeted nanopore sequencing, provides new insights into circular RNA biology

Circular RNAs (circRNAs) constitute an RNA type formed by back-splicing. BCL2-like 12 (BCL2L12) is an apoptosis-related gene comprising 7 exons. In this study, we used targeted nanopore sequencing to identify circular BCL2L12 transcripts in human colorectal cancer cells and investigated the effect of circRNA silencing on mRNA expression of the parental gene. In brief, nanopore sequencing following nested PCR amplification of cDNAs of BCL2L12 circRNAs from 7 colorectal cancer cell lines unraveled 46 BCL2L12 circRNAs, most of which described for the first time. Interestingly, 40 novel circRNAs are likely to form via back-splicing between non-canonical back-splice sites residing in highly similar regions of the primary transcripts. All back-splice junctions were validated using next-generation sequencing (NGS) after circRNA enrichment. Surprisingly, 2 novel circRNAs also comprised a poly(A) tract after BCL2L12 exon 7; this poly(A) tract was back-spliced to exon 1, in both cases. Furthermore, the selective silencing of a BCL2L12 circRNA resulted in a subsequent decrease of BCL2L12 mRNA levels in HCT 116 cells, thus providing evidence of parental gene expression regulation by circRNAs. In conclusion, our study led to the discovery of many circular transcripts from a single human gene and provided new insights into circRNA biogenesis and mode of action.

Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA

Lately, important advancements in visualizing RNAs in fixed and live cells have been achieved. Although mRNA imaging techniques are well-established, the development of effective methods for studying noncoding RNAs (ncRNAs) in living cells is still challenging but necessary, as they show a variety of functions and intracellular localizations, including participation in highly dynamic processes like phase transition, which is still poorly studied in vivo. Addressing this issue, we tagged two exemplary ncRNAs with the fluorescent RNA (fRNA) Pepper. Specifically, we showed that circ-HDGFRP3 interacts with p-bodies and is recruited in pathological FUS aggregates in a dynamic fashion, and we super-resolved its distribution in such condensates via structured illumination microscopy. Moreover, we tracked the long noncoding RNA (lncRNA) nHOTAIRM1, a motor neuron-specific constituent of stress granules, monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNA development progresses, our work demonstrates an effective use of Pepper for monitoring complex processes, such as phase transition, in living cells through the visualization of circular RNAs (circRNAs) and lncRNAs with super-resolution power.