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

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.

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

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

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

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

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

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

CircTTC13 promotes sorafenib resistance in hepatocellular carcinoma through the inhibition of ferroptosis by targeting the miR-513a-5p/SLC7A11 axis

The high mortality rate from hepatocellular carcinoma (HCC) is due primarily to challenges in early diagnosis and the development of drug resistance in advanced stages. Many first-line chemotherapeutic drugs induce ferroptosis, a form of programmed cell death dependent on ferrous iron-mediated oxidative stress, suggesting that drug resistance and ensuing tumor progression may in part stem from reduced ferroptosis. Since circular RNAs (circRNAs) have been shown to influence tumor development, we examined whether specific circRNAs may regulate drug-induced ferroptosis in HCC. Through circRNA sequencing, we identified a novel hsa_circ_0000195 (circTTC13) that is overexpressed in HCC tissues. This overexpression is linked to higher tumor grade, more advanced tumor stage, decreased ferroptosis, and poorer overall survival. Overexpression of CircTTC13 in HCC cell lines and explant tumors was associated with increased proliferation rates, enhanced metastatic capacity, and resistance to sorafenib, while also inhibiting ferroptosis. Conversely, circTTC13 silencing reduced malignant characteristics and promoted ferroptosis. In silico analysis, luciferase assays, and fluorescence in situ hybridization collectively demonstrated that circTTC13 directly targets and reduces miR-513a-5p expression, which in turn leads to the upregulation of the negative ferroptosis regulator SLC7A11. Moreover, the inhibition of SLC7A11 mirrored the effect of circTTC13 knockdown, whereas ferroptosis inhibition mimicked the effect of circTTC13 overexpression. Both circTTC13 and SLC7A11 were highly expressed in drug-resistant HCC cells, and circTTC13 silencing induced ferroptosis and reversed sorafenib resistance in explant tumors. These findings identify circTTC13 as a critical driver of HCC progression and resistance to drug-induced ferroptosis via upregulation of SLC7A11. The cicTTC13/miR-513a-5p/SLC7A11 axis represents a potential therapeutic target for HCC.

NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation

RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures. NuFold is a deep neural network trained end-to-end for the output structure from the input sequence. NuFold incorporates a nucleobase center representation, which enables flexible conformation of ribose rings. Benchmark study showed that NuFold clearly outperformed energy-based methods and demonstrated comparable results with existing state-of-the-art deep-learning-based methods. NuFold exhibited a particular advantage in building correct local geometries of RNA. Analyses of individual components in the NuFold pipeline indicated that the performance improved by utilizing metagenome sequences for multiple sequence alignment and increasing the number of recycling. NuFold is also capable of predicting multimer complex structures of RNA by linking the input sequences.

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

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

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

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

Circular RNA Formation and Degradation Are Not Directed by Universal Pathways

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

CircCCT2/miR-146a-5p/IRAK1 axis promotes the development of head and neck squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC), a highly invasive malignancy with a poor prognosis, is one of the most common cancers globally. Circular RNAs (circRNAs) have become key regulators of human malignancies, but further studies are necessary to fully understand their functions and possible causes in HNSCC.

METHODS

CircCCT2 expression levels in HNSCC tissues and cells were measured via qPCR. CircCCT2 was characterized by Sanger sequencing, qRT-PCR, RNase R & Actinomycin D treatment, nucleoplasmic separation and FISH experiments. CCK-8 and colony formation assays were performed to determine cell proliferation, and Transwell assays were used to determine migration and invasion. A xenograft tumor model was used to study the influence of circCCT2 on HNSCC in vivo. Dual-luciferase gene reporter, RIP, western blotting, and rescue experiments, were used to explore target-binding relationships and regulatory mechanisms.

RESULTS

CircCCT2 was significantly upregulated in HNSCC tissues and cells. High circCCT2 levels were associated with advanced T stage, N stage, clinical stage and poor prognosis. Functionally, we verified that circCCT2 promotes HNSCC development in vitro and in vivo. Mechanistically, functioning as a competitive endogenous RNA (ceRNA) or miRNA sponge, circCCT2 binds directly to miR-146a-5p and increases interleukin-1 receptor-associated kinase 1 (IRAK1) levels, which enhances the malignant development of HNSCC by driving epithelial-mesenchymal transition (EMT).

CONCLUSION

CircCCT2 promotes HNSCC development through the miR-146a-5p/IRAK1 axis, revealing that circCCT2 is a potential biomarker and target for HNSCC.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Hither-CMI: Prediction of circRNA-miRNA Interactions Based on a Hybrid Multimodal Network and Higher-Order Neighborhood Information via a Graph Convolutional Network

Numerous studies show that circular RNA (circRNA) functions as a sponge for microRNA (miRNA), significantly regulating gene expression by interacting with miRNA, which in turn affects the progression of human diseases. Traditional experimental approaches for investigating circRNA-miRNA interactions (CMI) are both time-consuming and costly, making computational methods a valuable alternative. Hence, we propose a computational model for predicting CMI, leveraging a hybrid multimodal network and higher-order neighborhood information (Hither-CMI). Specifically, Hither-CMI employs Multiple Kernel Learning (MKL) to integrate sequence, structure, and expression similarity networks of circRNA and miRNA, resulting in a hybrid multimodal network. Next, an enhanced Graph Convolutional Network (GCN) is utilized to combine the circRNA-miRNA hybrid multimodal network with the CMI association network, producing a hybrid higher-order embedding representation. Finally, the XGBoost classifier is applied for training and prediction. The Hither-CMI model achieved a predicted AUC value of 0.9134. In case studies, 25 out of the top 30 predicted CMI were confirmed by recent literature. These extensive experimental results further validate the effectiveness of Hither-CMI in predicting potential CMI, making it a promising prescreening tool for further biological research.

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.

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

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

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

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

Global research landscape and emerging trends of non-coding RNAs in prostate cancer: a bibliometric analysis

Background

Prostate cancer (PC) is the most frequently diagnosed cancer in men and continues to be a major cause of cancer-related mortality worldwide. In recent years, non-coding RNAs (ncRNAs) have emerged as a significant focus in molecular biology research, playing a pivotal role in the development and progression of PC. This study employed bibliometric analysis to explore the global outputs, research hotspots, and future trends in ncRNA-related PC research over the past 20 years.

Methods

Publications on PC-related ncRNAs from 2004 to 2023 were retrieved from Web of Science Core Collection. The co-operation network of countries, institutions, and authors on this topic was analyzed using CiteSpace (version 6.2. R6). In addition, co-occurrence analysis of keywords and co-citation analysis of references were performed using CiteSpace, and emergent detection was also performed.

Results

A total of 2,951 articles on PC-related ncRNAs were finally included in this study for analysis. China contributed the largest number of publications, while the United States was the most influential country in this field, with collaborative ties to 26 other countries. Fudan University was identified as the most active institution in this field. Rajvir Dahiya was the most prolific and influential author. Within the co-citation network, clusters labeled "EVs," "circRNA," and "ceRNA" represented current research directions. The cluster labeled "gene" dominated the co-occurrence keywords. "circRNA" showed the highest burst strength among keywords, with "circRNA," "EVs" and "exosome" maintaining sustained burst strength, suggesting these are the emerging research frontiers in this field.

Conclusion

Investigating ncRNAs as pivotal research subjects in PC is essential for addressing the public health impact of the disease and advancing innovative diagnostic and targeted therapeutic strategies. This study provides a comprehensive bibliometric analysis of research related to PC-associated ncRNAs, delivering a scientific perspective and identifying potential research directions for scholars in this field.

Translation of circular RNAs

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

Circular RNAs: key players in tumor immune evasion

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

Identification and Analysis of Circular RNAs in Mammary Gland from Yaks Between Lactation and Dry Period

Lactation is a complex physiological process regulated by numerous genes and factors. Circular RNA (circRNA), a non-coding RNA, acts as a molecular sponge that sequesters microRNAs (miRNAs) to regulate target gene expression. Although circRNA has been linked to mammary gland lactation, its specific role in yaks remains underexplored. This study employed circular RNA sequencing (circRNA-seq) to examine the differential expression of circRNAs in yak mammary tissues during lactation and the dry period. Additionally, an enrichment analysis of the differentially expressed circRNAs (DECs) was performed. A competing endogenous RNA (ceRNA) network was then constructed to explore the potential of their roles in lactation and mammary gland development. We detected 18,905 circRNAs in yak mammary tissue, among which 302 showed differential expression. The host genes of these DECs were enriched in functions and pathways associated with yak milk synthesis and composition. Through the construction of a ceRNA network and the enrichment analysis of associated mRNAs, this study identified ceRNAs potentially involved in regulating lactation and mammary gland development. In conclusion, circRNAs in yak mammary tissues were identified and analyzed across lactation and dry periods, establishing a ceRNA network related to lactation regulation. These findings provide novel insights into the regulatory mechanisms governing lactation in yaks (Bos grunniens).

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

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

Emerging roles of circular RNAs on the regulation of production traits in chicken

Chickens are vital agricultural animals that supply a significant portion of the protein consumed by humans. In society today, enhancing the productive performance of chickens in a safe and efficient manner has become a central focus of research. This performance is determined by various production traits that are primarily influenced by multiple factors, including epigenetics-a critical aspect of gene regulation. Circular RNAs (circRNAs), a unique class of non-coding RNAs, have emerged as key epigenetic regulators. Recent studies have demonstrated that circRNAs are extensively engaged in numerous production traits, which include skeletal muscle formation, fat deposition, ovarian follicle development, liver function, bone development, immunity, and resistance to environmental stress. These processes play crucial roles in determining the overall productivity of chickens. Given the significance of circRNAs in these various traits, this article provides a comprehensive review of the functional circRNAs associated with different traits in chickens, serving as a valuable theoretical reference for future research. Further investigation into the role of circRNAs may reveal novel insights into the molecular mechanisms underlying key economic traits in chickens and pave the way for innovative strategies in molecular breeding aimed at enhancing chicken productive performance.

Silencing circLDLRAD3 Inhibits Lung Cancer Progression by Regulating the miR-497-5p/PFKP Axis

PURPOSE

Lung cancer is one of the leading causes of death worldwide. Recent studies have shown that circular RNAs are dysregulated in a variety of cancers, but the mechanism in lung cancer is still indistinct. In our work, we explored the action mechanism of circLDLRAD3 in lung cancer.

METHODS

The abundance of circLDLRAD3, microRNA-497-5p (miR-497-5p) and platelet-type PFK (PFKP) was measured by real-time quantitative polymerase chain reaction (RT-qPCR) in lung cancer. Meanwhile, the level of PFKP was quantified by western blot. Cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU) assay, transwell assay, wound healing assay, flow cytometry, western blot, immunohistochemical (IHC) assay and glycolysis metabolism analysis were performed for functional analyses. Furthermore, the interplay between miR-497-5p and circLDLRAD3 or FKPF was detected by the dual-luciferase reporter and RNA Immunoprecipitation (RIP) assays. Eventually, the in vivo experiments were applied to measure the role of circLDLRAD3.

RESULT

The levels of circLDLRAD3 and PFKP were increased. Silencing circLDLRAD3 inhibited cell viability, proliferation, migration, invasion and glycolysis metabolism and promoted cell apoptosis in lung cancer cells. In mechanism, circLDLRAD3 regulated PFKP level as a miR-497-5p sponge. MiR-497-5p suppressed the progression of lung cancer by inhibiting PFKP. In addition, circLDLRAD3 knockdown also inhibited tumor growth in vivo.

CONCLUSION

CircLDLRAD3 promoted the development of lung cancer through increasing PFKP expression by regulating miR-497-5p, which also provided a potential targeted therapy for lung cancer treatment.

Revealing the Complex Interaction of Noncoding RNAs, Sirtuin Family, and Mitochondrial Function

Mitochondria are key organelles that perform and coordinate various metabolic processes in the cell, and their homeostasis is essential for the maintenance of eukaryotic life. To maintain mitochondrial homeostasis and cellular health, close communication between noncoding RNAs (ncRNAs) and proteins is required. For example, there are numerous crosstalk between ncRNAs and the sirtuin (SIRT1-7) family, which is a group of nicotinamide adenine dinucleotides (NAD(+))-dependent Type III deacetylases. NcRNAs are involved in the regulation of gene expression of sirtuin family members, and deacetylation of sirtuin family members can also influence the generation of ncRNAs. This review focuses on the relationship between the two mentioned above and summarizes the impact of their interactions on mitochondrial metabolism, oxidative stress, mitochondrial apoptotic pathways, mitochondrial biogenesis, mitochondrial dynamics, and other mitochondria-related pathophysiological processes. Finally, the review also describes targeted and appropriate treatment strategies. In conclusion, we provide an overview of the ncRNA-sirtuins/mitochondria relationship that could provide a reference for related research in the mitochondrial field and help the future development of new biomedical applications in this area.

Exosomal noncoding RNA (ncRNA) in breast cancer pathogenesis and therapy; two sides of the same coin

Over the past few years, breast cancer has become the most prevalent type of cancer globally, with the primary cause of death from the disease being metastatic cancer. This has led to the development of early detection techniques, mainly using non-invasive biomarkers in a range of body fluids. Exosomes are unique extracellular vesicles (EVs) transmitting cellular signals over great distances via various cargo. They are readily apparent in physiological fluids due to release by breast cancer cells or breast cancer-tumor microenvironment (TME) cells. In light of this, numerous biological and functional facets of human tumours, such as breast cancer, are intimately associated with exosomal noncoding RNAs (ncRNAs), containing miRNAs (microRNAs), lncRNAs (long noncoding RNAs), and circRNAs (circular RNAs). Exosomal ncRNAs serve a critical role in various steps of breast cancer development, enabling the exchange of genetic information between cancer cells and other cells (e.g., immune cells), thus regulating tumour angiogenesis, growth, metastasis, immune responses and drug resistance. They interact with multiple regulatory complexes with dissimilar enzymatic actions, which, in turn, modify the chromatin sceneries, including nucleosome modifications, DNA methylation, and histone modifications. Herein, we look into the exosomes' underlying regulatory mechanisms in breast cancer. Furthermore, we inspect the existing understanding of the functions of exosomal miRNAs, lncRNAs, and circRNAs in breast cancer to authenticate their possible significance in identifying biomarkers, deciphering their role in immune escape and drug resistance, and finally, analyzing treatment practices.

Circular RNA regulatory role in pathological cardiac remodelling

Cardiac remodelling involves structural, cellular and molecular alterations in the heart after injury, resulting in progressive loss of heart function and ultimately leading to heart failure. Circular RNAs (circRNAs) are a recently rediscovered class of non-coding RNAs that play regulatory roles in the pathogenesis of cardiovascular diseases, including heart failure. Thus, a more comprehensive understanding of the role of circRNAs in the processes governing cardiac remodelling may set the ground for the development of circRNA-based diagnostic and therapeutic strategies. In this review, the current knowledge about circRNA origin, conservation, characteristics and function is summarized. Bioinformatics and wet-lab methods used in circRNA research are discussed. The regulatory function of circRNAs in cardiac remodelling mechanisms such as cell death, cardiomyocyte hypertrophy, inflammation, fibrosis and metabolism is highlighted. Finally, key challenges and opportunities in circRNA research are discussed, and orientations for future work to address the pharmacological potential of circRNAs in heart failure are proposed. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.

Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination

Aberrant gene expression lies at the heart of many pathologies. This review will point out how 3' end processing, the final mRNA-maturation step in the transcription cycle, is surprisingly prone to regulated as well as stochastic variations with a wide range of consequences. Whereas smaller variations contribute to the plasticity of gene expression, larger alternations to 3' end processing and coupled transcription termination can lead to pathological consequences. These can be caused by the local mutation of one gene or affect larger numbers of genes systematically, if aspects of the mechanisms of 3' end processing and transcription termination are altered.

The Emerging Roles of CircPVT1 in Cancer Progression

CircRNA is stable due to its ring structure and is abundant in humans, which not only exists in various tissues and biofluids steadily but also plays a significant role in the physiology and pathology of human beings. CircPVT1, an endogenous circRNA, has recently been identified from the PVT1 gene located in the cancer risk region 8q24. CircPVT1 is reported to be highly expressed in many different tumors, where it affects tumor cell proliferation, apoptosis, invasion, and migration. We summarize the biosynthesis and biological functions of circPVT1 and analyze the relationship between circPVT1 and tumors as well as its significance to tumors. Further, it's noteworthy for the diagnosis, treatment, and prognosis of cancer patients. Therefore, circPVT1 is likely to become an innovative tumor marker.

Circ_0003314 Combines with the miR-26b-5p/IL1RAP Axis to Inhibit HTR-8/SVneo Cell Proliferation, Migration, Invasion and Tube Formation and Promote Apoptosis

Preeclampsia (PE) is a pregnancy-related syndrome that can lead to a variety of pathophysiological processes, such as impaired implantation. The pathogenesis of PE involves circular RNA (circRNA). The study aims to determine the role of a novel circRNA, circ_0003314, in trophoblast cell phenotypes. Circ_0003314, microRNA-26b-5p (miR-26b-5p) and IL-1 receptor accessory protein (IL1RAP) expression were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was investigated by MTT assay and 5-Ethynyl-2'-deoxyuridine assay. Cell migration and invasion were investigated by transwell assay. Cell apoptotic rate and angiogenesis were investigated by flow cytometry analysis and tube formation assay, respectively. Protein expression was detected by western blotting. The binding relationship between miR-26b-5p and circ_0003314 or IL1RAP was identified using dual-luciferase reporter assay and RNA pull-down assay. Circ_0003314 and IL1RAP expression were significantly increased, while miR-26b-5p was decreased in placental tissues of PE patients. Circ_0003314 overexpression inhibited trophoblast cell proliferation, migration, invasion and angiogenesis and induced cell apoptosis. Additionally, circ_0003314 acted as a sponge for miR-26b-5p, and miR-26b-5p bound to IL1RAP. Introduction of miR-26b-5p or silencing of IL1RAP attenuated the effects of circ_0003314 overexpression on trophoblast cell phenotypes. Further, circ_0003314 induced IL1RAP expression through miR-26b-5p in trophoblast cells. Circ_0003314 regulated trophoblast cell phenotypes by increasing IL1RAP expression through binding to miR-26b-5p.

Cellular functions and biomedical applications of circular RNAs

Circular RNAs (circRNAs) have emerged as a large class of stable and conserved RNAs that are derived primarily from back-splicing of pre-mRNAs and expressed in a cell- and tissue-specific fashion. Recent studies have indicated that a subset of circRNAs may undergo translation through cap-independent pathways mediated by internal ribosome entry sites (IRESs), m6A modifications, or IRES-like short elements. Considering the stability and low immunogenicity of circRNAs, in vitro transcribed circRNAs hold great promise in biomedical applications. In this review, we briefly discuss the noncoding and coding functions of circRNAs in cells, as well as the methods for the in vitro synthesis of circRNAs and current advances in the applications of circRNAs in biomedicine.

Validation and in silico function prediction of circtial1 as a novel marker of abnormal lung development in nitrofen-induced congenital diaphragmatic hernia (CDH)

PURPOSE

Circular RNAs (circRNAs) are stable, non-coding RNAs with tissue- and developmental-specific expression making them suitable biomarkers for congenital anomalies. Current circRNA discovery pipelines have focused on human and mouse. We aim to bridge this gap by combining bioinformatics resources and used circtial1 as a model candidate in the nitrofen rat model of congenital diaphragmatic hernia (CDH).

METHODS

Circtial1 backsplice junction sequences from a microarray were used to predict mature circRNA sequences and downstream pathways by miRNA interactions using CRAFT and circAtlas. We validated circtial1 expression using conventional PCR, amplicon sequencing, RT-Qpcr, and Basescope™ in situ hybridization.

RESULTS

Expression of parental gene tial1 was decreased in nitrofen-induced lungs at embryonic day (E)15 (p = 0.004) and E21 (p = 0.008), while at E18, there was no significant difference (p = 0.65). At E21, circtial1 expression did not differ between CDH and control lungs (p = 0.07); however, there was a decreased expression in male pups (p = 0.0167). In situ hybridization confirmed low circtial1 expression. CircRNA::miRNA::mRNA interactions revealed pathway enrichment for inflammation/infection and neuron function/development.

CONCLUSION

For the first time, we report circRNA profiling in nitrofen-induced CDH with a sex-specific expression of circtial1. Current bioinformatics tools have significant challenges, but can guide hypothesis formation on their biological role.

Exosomes containing circSCP2 in colorectal cancer promote metastasis via sponging miR-92a-1-5p and interacting with PTBP1 to stabilize IGF2BP1

Exosomes have emerged as significant biomarkers for multiple diseases, including cancers. Circular RNAs (circRNAs), abundant in exosomes, are involved in regulating cancer development. However, the regulatory function and the underlying molecular mechanism of hsa_circ_0006906 (circSCP2) in colorectal cancer (CRC) metastasis remain unclear. A competing endogenous RNA microarray was used to analyze circRNA expression in serum exosomes in patients with CRC at early and late stages. circSCP2 expression was evaluated using qRT-PCR. The biological functions of circSCP2 in CRC were assessed through in vitro and in vivo experiments. The molecular mechanism of circSCP2 was explored using western blotting, RNA pulldown, RNA immunoprecipitation, luciferase assays, and relative rescue experiments. circSCP2 expression was significantly elevated in CRC tissues, with higher levels in serum exosomes correlating with advanced TNM stages. circSCP2 knockdown inhibited CRC cell proliferation, migration, invasion, and metastasis in vitro and in vivo. Mechanistically, circSCP2 sponged miR-92a-1-5p to increase insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) expression. Additionally, circSCP2 directly bound to and stabilized polypyrimidine tract binding protein 1 (PTBP1) by inhibiting protein ubiquitination, resulting in IGF2BP1 mRNA stabilization and enhanced CRC migration and invasion. Our findings demonstrate that circSCP2 regulates the miR-92a-1-5p/IGF2BP1 pathway, promotes PTBP1/IGF2BP1 interaction, and accelerates CRC progression. Exosomal circSCP2 is a promising circulating biomarker for CRC prognosis and needs further therapeutic investigation.

The Diagnostic Value of circFBXW7, circABCB10, and circ0103552 Levels in Breast Cancer

Despite advances in cancer treatment, breast cancer (BC) remains one of the most common cancers affecting women worldwide. This study aimed to determine serum circFBXW7, circABCB10, and circ0103552 levels and compare BC patients and healthy controls to investigate their roles in the molecular mechanism of BC and the significance of these circRNAs in BC diagnosis. The study group consisted of 92 patients with BC and 31 healthy controls. Total RNA was isolated from serum samples. Following total RNA, complementary DNA was synthesized from this material. Following complementary DNA analysis, the circRNA levels were analyzed by the qRT-PCR method. Expression levels were evaluated in ΔCt values. High ΔCt values of circFBXW7 and circ0103552 and low ΔCt values of circABCB10 were correlated with BC diagnosis (circFBXW7, p = 0.043, r = 0.183, circ0103552, p < 0.001, r = 0.321, circABCB10, p = 0.001, r = -0.291). According to Fold Change (FC) values, circFBXW7 (FC = 0.30) and circ0103552 (FC = 0.26) showed low expression in the patient group compared to the control group, while circABCB10 (FC = 11.09) showed high expression (p < 0.05, for all comparisons). We think that our study is one of the rare studies investigating the relationship between BC and serum circRNA levels. This study concludes that the significant downregulation of circFBXW7 and circ0103552 and the upregulation of circABCB10 are directly related to the diagnosis of BC and can be used for diagnosis, but further studies are needed to elucidate the molecular mechanism of the relationship between circRNAs and BC.

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

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

Characterisation of the genetic diversity of citrus viroid VII using amplicon sequencing

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term 'quasispecies' to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (> 10% sample) variants. The composition of variants differed in samples from different plants and among tissue types of a single plant. Single-nucleotide polymorphisms (SNPs), mostly in the form of substitutions, were the primary source of variation; in this study, SNPs were observed in approximately 10% of the viroid genome. The results of the three experiments indicate that CVd-VII follows the quasispecies model as reported for other viroids and that variability occurs in viroid populations in different tissue types and host species.

Circular RNAs in Viral Infection and Antiviral Treatment

Circular RNAs (circRNAs) are a class of noncoding RNAs that lack the 5'-cap structure and the 3' poly(A) tail. Their distinguishing feature is that the 3' and 5' ends are covalently linked to form a closed circular structure. CircRNAs have a longer half-life and stronger ribonuclease resistance compared with linear RNA. Viral infections lead to the production of circRNA molecules through the transcription and splicing mechanisms of host cells. circRNAs are produced from the transcription and splicing of the viral genome or from the splicing reactions of the host cell gene. They participate in regulating the replication of many viruses, including coronaviruses, human herpesviruses, human immunodeficiency virus, and cytomegalovirus. CircRNAs regulate the infection process by modulating circRNA expression in host cells and affect cellular biological processes. Some circRNAs have been proposed as diagnostic markers for viral infections. In this review, we discussed the properties of virus-derived circRNAs, the biological functions of diverse viruses-derived and host circRNAs during viral infections, and the critical role of circRNAs in the host's antiviral immune defense. Extensive research on the applications of circRNAs can help us better understand gene regulatory networks and disease mechanisms.

CircRNAs and miRNAs: Key Player Duo in Breast Cancer Dynamics and Biomarkers for Breast Cancer Early Detection and Prevention

Breast cancer (BC) remains a significant global health issue, necessitating advanced molecular approaches for early detection and prevention. This review delves into the roles of microRNAs (miRNAs) and circular RNAs (circRNAs) in BC, highlighting their potential as non-invasive biomarkers. Utilizing in silico tools and databases, we propose a novel methodology to establish mRNA/circRNA/miRNA axes possibly indicative of early detection and possible prevention. We propose that during early tumor initiation, some changes in oncogene or tumor suppressor gene expression (mRNA) are mirrored by alterations in corresponding circRNAs and reciprocal changes in sponged miRNAs affecting tumorigenesis pathways. We used two Gene Expression Omnibus (GEO) datasets and identified five mRNA/circRNA/miRNA axes as early possible tumor initiation biomarkers. We further validated the proposed axes through a Kaplan-Meier (KM) plot and enrichment analysis of miRNA expression using patient data. Evaluating coupled differential expression of circRNAs and miRNAs in body fluids or exosomes provides greater confidence than assessing either, with more axes providing even greater confidence. The proposed methodology not only improves early BC detection reliability but also has applications for other cancers, enhancing preventive measures.

Liquid biopsy in cancer current: status, challenges and future prospects

Cancer has a high mortality rate across the globe, and tissue biopsy remains the gold standard for tumor diagnosis due to its high level of laboratory standardization, good consistency of results, relatively stable samples, and high accuracy of results. However, there are still many limitations and drawbacks in the application of tissue biopsy in tumor. The emergence of liquid biopsy provides new ideas for early diagnosis and prognosis of tumor. Compared with tissue biopsy, liquid biopsy has many advantages in the diagnosis and treatment of various types of cancer, including non-invasive, quickly and so on. Currently, the application of liquid biopsy in tumor detection has received widely attention. It is now undergoing rapid progress, and it holds significant potential for future applications. Around now, liquid biopsies encompass several components such as circulating tumor cells, circulating tumor DNA, exosomes, microRNA, circulating RNA, tumor platelets, and tumor endothelial cells. In addition, advances in the identification of liquid biopsy indicators have significantly enhanced the possibility of utilizing liquid biopsies in clinical settings. In this review, we will discuss the application, advantages and challenges of liquid biopsy in some common tumors from the perspective of diverse systems of tumors, and look forward to its future development prospects in the field of cancer diagnosis and treatment.

Crosstalk between circular RNAs and the STAT3 signaling pathway in human cancer

Circular RNAs (circRNAs) are endogenous covalently closed single-stranded RNAs produced by reverse splicing of pre-mRNA. Emerging evidence suggests that circRNAs contribute to cancer progression by modulating the oncogenic STAT3 signaling pathway, which plays key roles in human malignancies. STAT3 signaling-related circRNAs expression appears to be extensively dysregulated in diverse cancer types, where they function either as tumor suppressors or oncogenes. However, the biological effects of STAT3 signaling-related circRNAs and their associations with cancer have not been systematically studied before. Given this, shedding light on the interaction between circRNAs and STAT3 signaling pathway in human malignancies may provide several novel insights into cancer therapy. In this review, we provide a comprehensive introduction to the molecular mechanisms by which circRNAs regulate STAT3 signaling in cancer progression, and the crosstalk between STAT3 signaling-related circRNAs and other signaling pathways. We also further discuss the role of the circRNA/STAT3 axis in cancer chemotherapy sensitivity.

Hsa_circRNA_000166 accelerates breast cancer progression via the regulation of the miR-326/ELK1 and miR-330-5p/ELK1 axes

PURPOSES

To probe the expression, clinical significance, roles, and molecular mechanisms of circRNA_000166 in breast cancer (BC).

METHODS

Clinical tissue samples were gathered from 84 BC patients who underwent surgery at the Affiliated Hospital of Chengde Medical College. Clinical data were obtained from medical records and postoperative follow-up. Expression levels of circRNA_000166, miR-326, miR-330-5p, and ELK1 mRNA in BC tissues and cells were measured by qRT-PCR, and ELK1 protein levels were assessed by WB. Pearson's correlation analysis evaluated the interrelationships between these RNAs in clinical samples. Luciferase reporter assays verified the interactions between miR-326/miR-330-5p and circRNA_000166, as well as between miR-326/miR-330-5p and ELK1. Cell proliferation, migration, and apoptosis were examined using CCK-8, colony formation, transwell, and flow cytometry assays, respectively.

RESULTS

CircRNA_000166 was highly expressed in BC tissues and inversely correlated with miR-326/miR-330-5p levels but positively with ELK1 mRNA levels. ELK1 mRNA also inversely associated with miR-326/miR-330-5p levels in BC tissues. Importantly, our findings demonstrated that circRNA_000166 targets miR-326 and miR-330-5p, while ELK1 is the target of miR-326 and miR-330-5p in BC cells. CircRNA_000166 levels positively correlated with tumour size, TNM stage, histological grade, and lymph node metastasis, and negatively associated with postoperative progression-free survival (PFS) and overall survival (OS) in BC patients. CircRNA_000166 was also highly expressed in BC cells, and knockdown of circRNA_000166 reduced proliferation and migration, and increased apoptosis via miR-326/ELK1 and miR-330-5p/ELK1 pathways in vitro.

CONCLUSION

CircRNA_000166 enhances BC progression through miR-326/ELK1 and miR-330-5p/ELK1 pathways and shows potential as a biomarker for BC diagnosis and treatment.

CircPWWP2A promotes renal interstitial fibrosis through modulating miR-182/ROCK1 axis

Renal fibrosis is a long-term and progressively worsening condition that impacts kidney function during aging and in the context of chronic kidney disease (CKD). CKD and renal fibrosis affect approximately 10% of the global population and are prevalent in about half of individuals over the age of 70. Despite ongoing research, the mechanisms underlying renal fibrosis are still not well understood, and there is currently a lack of effective treatments available. In the present study, we demonstrated a significant increase of circPWWP2A in renal tubular cells both in vivo and in vitro models of renal fibrosis. Suppressing circPWWP2A has the potential to reduce mitochondrial dysfunction and the production of mitochondrial reactive oxygen species (mtROS), ultimately leading to the inhibition of renal fibrosis. Whereas, supplementation of circPWWP2A led to more serve mitochondrial dysfunction, mtROS production and renal fibrosis. Mechanistically, we found the expression of circPWWP2A was negatively correlated with the expression of miR-182. And we further confirmed miR-182 was the direct target of circPWWP2A by dual-luciferase reporter assay and RIP assay. Then, we found miR-182 suppressed the expression of ROCK1 in both in vitro and in vivo models of renal fibrosis. Luciferase microRNA target reporter assay further indicated ROCK1 as a direct target of miR-182. Knockdown of ROCK1 inhibits renal fibrosis and mitochondrial dysfunction, suggesting ROCK1 not only served as an injurious role in mitochondrial homeostasis but also a pro-fibrotic factor in CKD. Taking together, our findings suggest that circPWWP2A may promote renal interstitial fibrosis by modulating miR-182/ROCK1-mediated mitochondrial dysfunction.

Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging

Aging presents a significant challenge to health and social care systems due to the increasing proportion of the elderly population. The identification of reliable biomarkers to assess the progression of aging remains an unresolved question. Circular RNAs (circRNAs) are single-stranded covalently closed RNAs. They have been found to regulate various biological processes. CircRNAs are present in human biological fluids, are relatively stable, and accumulate with age, making them promising as biomarkers of aging. Current information on the expression of circRNAs in aging was analyzed using scientific databases. In this review, we have identified key stages in the study of circRNAs during aging and summarized the current understanding of their biogenesis. By focusing on the role of circRNAs in processes that contribute to aging - such as genomic stability, metabolism, cell death, and signaling pathways - we hypothesize that circRNAs may drive the aging process through their age-related accumulation and resultant deregulation. Examples of age-related differential expression of circRNAs in various species, including humans, are provided. This review highlights the importance of finding novel epigenetic biomarkers of aging, beyond the already identified molecules (circFOXO3, circRNA100783, circPVT1), and highlights circRNAs as a potential therapeutic target for the treatment of age-associated diseases.

Imaging Techniques and Biochemical Biomarkers: New Insights into Diagnosis of Pancreatic Cancer

Pancreatic cancer (PaC) incidence is increasing, but our current screening and diagnostic strategies are not very effective. However, screening could be helpful in the case of PaC, as recent evidence shows that the disease progresses gradually. Unfortunately, there is no ideal screening method or program for detecting PaC in its early stages. Conventional imaging techniques, such as abdominal ultrasound, CT, MRI, and EUS, have not been successful in detecting early-stage PaC. On the other hand, biomarkers may be a more effective screening tool for PaC and have greater potential for further evaluation compared to imaging. Recent studies on biomarkers and artificial intelligence (AI)-enhanced imaging have shown promising results in the early diagnosis of PaC. In addition to proteins, non-coding RNAs are also being studied as potential biomarkers for PaC. This review consolidates the current literature on PaC screening modalities to provide an organized framework for future studies. While conventional imaging techniques have not been effective in detecting early-stage PaC, biomarkers and AI-enhanced imaging are promising avenues of research. Further studies on the use of biomarkers, particularly non-coding RNAs, in combination with imaging modalities may improve the accuracy of PaC screening and lead to earlier detection of this deadly disease.

The potential of circular RNAs as biomarkers and therapeutic targets for gastric cancer: A comprehensive review

BACKGROUND

Gastric cancer (GC) is a global health concern, contributing significantly to cancer-related mortality rates. Early detection is vital for improving patient outcomes. Recently, circular RNAs (circRNAs) have emerged as crucial players in the development and progression of various cancers, including GC.

AIM

This comprehensive review underscores the promising potential of circRNAs as innovative biomarkers for the early diagnosis of GC, as well as their possible utility as therapeutic targets for this life-threatening disease. Specifically, the review focuses on recent findings, mechanistic insights, and clinical applications of circRNAs in GC.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Dysregulation of circRNAs has been consistently observed in GC tissues, offering potential diagnostic value due to their stability in bodily fluids such as blood and urine. For instance, circPTPN22 and hsa_circ_000200. Furthermore, the expression levels of circRNAs such as circCUL2, hsa_circ_0000705 and circSHKBP1 have shown strong associations with critical clinical features of GC, including diagnosis, prognosis, tumor size, lymph node metastasis, tumor-node-metastasis (TNM) stage, and treatment response. Additionally, circRNAs such as circBGN, circLMO7, and circMAP7D1 have shown interactions with specific microRNAs (miRNAs), proteins, and other molecules that play key roles in development and progression of GC. This further highlighting their potential as therapeutic targets. Despite their potential, several challenges need to be addressed to effectively apply circRNAs as GC biomarkers. These include standardizing detection methods, establishing cutoff values for diagnostic accuracy, and validating findings in larger patient cohorts. Moreover, the functional mechanisms by which circRNAs contribute to GC pathogenesis and therapeutic resistance warrant further investigation. Advances in circRNAs research could provide valuable insights into the early detection and targeted treatment of GC, ultimately improving patient outcomes.

The role of circRNAs in resistance to doxorubicin

Doxorubicin is an anthracyline recognized as an antitumor antibiotic agent. It is widely used in the chemotherapeutic regimens in different types of cancers. Resistance to doxorubicin is a major clinical obstacle and main cause of failure in cancer chemotherapy. Among different mechanisms involved in this process, the role of epigenetic factors has been highlighted. Circular RNAs (circRNAs) have a prominent role in this process. Here, we summarize the recent findings on the role of circRNAs in doxorubicin resistance, particularly in breast cancer and osteosarcoma and underscore their clinical application as potential biomarkers and therapeutic targets in this field. Recognition of the underlying mechanism of circRNAs involvement in doxorubicin resistance will expand our understanding of chemoresistance establishment and may provide a prospect to develop circRNA-based predictive biomarkers of chemotherapy or therapeutic strategies for cancer patients.

Molecular Characteristics of Circ_002156 and Its Effects on Proliferation and Differentiation of Caprine Skeletal Muscle Satellite Cells

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) are responsible for the development of skeletal muscle. In our previous study, circ_002156 was found to be highly expressed in caprine Longissimus Dorsi muscle, but the regulatory role of the circular RNAs (circRNA) in goat SMSCs remains unclear. In this study, the authenticity of circ_002156 was validated, and its structurally characteristic and cellular localization as well as tissue expression of circ_002156 and its parent genes were investigated. Moreover, the effects of circ_002156 on the viability, proliferation, and differentiation of SMSCs were also studied. The circ_002156 is located on caprine chromosome 19 with a length of 36,478. The circRNA structurally originates from myosin heavy chain 2 (MYH2), MYH1, and MYH4 as well as intergenic sequences among the parent genes. RT-PCR and Sanger sequencing confirmed the authenticity of circ_002156. Most circ_002156 (55.5%) was expressed in the nuclei of SMSCs, while 44.5% of circ_002156 was located in the cytoplasm. The circ_002156 and its three parent genes had higher expression levels in the triceps brachii, quadriceps femoris, and longissimus dorsi muscle tissues than in the other five tissues. The expression of circ_002156 and its parent genes MYH1 and MYH4 reached the maximum on day 8 of differentiation, while MYH2 in expression reached the peak on day 4 after differentiation. The Pearson correlation coefficients revealed that circ_002156 had moderate or high positive correlations with the three parent genes in the expression of both quadriceps femoris muscle and SMSCs during different differentiation stages. The small interfering RNA circ_002156 (named si-circ_002156) remarkably increased the viability of the SMSCs. The si-circ_002156 also increased the number and parentage of Edu-labeled positive SMSCs as well as the expression levels of four cell proliferation marker genes. These suggest that circ_002156 inhibited the proliferation of SMSCs. Meanwhile, si-circ_002156 decreased the area of MyHC-labeled positive myotubes, the myotube fusion index, and myotube size as well as the expression of its three parent genes and four cell differentiation marker genes, suggesting a positive effect of circ_002156 on the differentiation of SMSCs. This study contributes to a better understanding of the roles of circ_002156 in the proliferation and differentiation of SMSCs.

Extracellular Vesicles from Human Induced Pluripotent Stem Cells Exhibit a Unique MicroRNA and CircRNA Signature

Extracellular vesicles (EV) have emerged as promising cell-free therapeutics in regenerative medicine. However, translating primary cell line-derived EV to clinical applications requires large-scale manufacturing and several challenges, such as replicative senescence, donor heterogeneity, and genetic instability. To address these limitations, we used a reprogramming approach to generate human induced pluripotent stem cells (hiPSC) from the young source of cord blood mesenchymal stem/stromal cells (CBMSC). Capitalizing on their inexhaustible supply potential, hiPSC offer an attractive EV reservoir. Our approach encompassed an exhaustive characterization of hiPSC-EV, aligning with the rigorous MISEV2023 guidelines. Analyses demonstrated physical features compatible with small EV (sEV) and established their identity and purity. Moreover, the sEV-shuttled non-coding (nc) RNA landscape, focusing on the microRNA and circular RNA cargo, completed the molecular signature. The kinetics of the hiPSC-sEV release and cell internalization assays unveiled robust EV production and consistent uptake by human neurons. Furthermore, hiPSC-sEV demonstrated ex vivo cell tissue-protective properties. Finally, via bioinformatics, the potential involvement of the ncRNA cargo in the hiPSC-sEV biological effects was explored. This study significantly advances the understanding of pluripotent stem cell-derived EV. We propose cord blood MSC-derived hiPSC as a promising source for potentially therapeutic sEV.

Noncoding RNA, friend or foe for nephrolithiasis?

Nephrolithiasis is one of the most common diseases in urology, characterized by notable incidence and recurrence rates, leading to significant morbidity and financial burden. Despite its prevalence, the precise mechanisms underlying stone formation remain incompletely understood, thus hindering significant advancements in kidney stone management over the past three decades. Investigating the pivotal biological molecules that govern stone formation has consistently been a challenging and high-priority task. A significant portion of mammalian genomes are transcribed into noncoding RNAs (ncRNAs), which have the ability to modulate gene expression and disease progression. They are thus emerging as a novel target class for diagnostics and pharmaceutical exploration. In recent years, the role of ncRNAs in stone formation has attracted burgeoning attention. They have been found to influence stone formation by regulating ion transportation, oxidative stress injury, inflammation, osteoblastic transformation, autophagy, and pyroptosis. These findings contributes new perspectives on the pathogenesis of nephrolithiasis. To enhance our understanding of the diagnostic and therapeutic potential of nephrolithiasis-associated ncRNAs, we summarized the expression profiles, biological functions, and clinical significance of these ncRNAs in the current review.

SGTCDA: Prediction of circRNA-drug sensitivity associations with interpretable graph transformers and effective assessment

CircRNAs are a type of circular non-coding RNA whose associations with drug sensitivities have been demonstrated in recent studies. Due to the high cost of biomedical experiments for detecting the associations between circRNAs and drug sensitivities, several computational methods have been developed. However, these methods were evaluated mainly based on 5- or tenfold cross-validation, which are often over-optimistic. Furthermore, there are technique issues with these models, such as over-smoothing and over-squashing. To address these issues, we propose a strategy to evaluate models based on independent test sets for association prediction-related studies. In the light of this effective assessment, we constructed a model, SGTCDA, by integrating structural deep network embedding (SDNE) and a graph transformer to predict the potential associations of circRNA-drug sensitivity, which can efficiently capture long-range dependencies and local structural information of nodes. Our results on the training sets and the independent test sets indicate that SGTCDA outperforms the other state-of-the-art models, demonstrating its capacity for accurate prediction of circRNA-drug sensitivity. Moreover, we leveraged EdgeSHAPer to explain the performance of the proposed SGTCDA model, which illustrates that the edges between drugs are more important than other edges for the performance of the model. The source code and dataset of SGTCDA are available at: https://github.com/hwxia/SGTCDA .

circARID1A Inhibits Tail Fat Cell Differentiation in Guangling Large-Tailed Sheep by Regulating the miR-493-3p/YTHDF2 Axis

The Guangling Large-Tailed sheep is renowned for its unique tail fat deposition, with a significant proportion of its total body fat being localized in the tail region. Fat deposition is a complex biological process regulated by various molecular mechanisms. Our previous studies have identified a large number of differentially expressed circular RNAs (circRNAs) in the tail adipose tissue of the Guangling Large-Tailed sheep. These circRNAs may play a pivotal role in the process of fat deposition. Given the potential regulatory functions of circRNAs in adipose metabolism, investigating their roles in tail fat deposition is of significant scientific importance. In this study, we identified novel circARID1A. Using various experimental methods, including lentivirus infection, RNase R treatment, actinomycin D assay, qPCR, western blotting, and dual-luciferase reporter assays, we determined that circARID1A inhibits the expression of miR-493-3p through competitive binding, thereby regulating adipocyte differentiation. Further research revealed that miR-493-3p promotes adipocyte differentiation by targeting YTH domain family 2 (YTHDF2), and this regulatory effect is also influenced by circARID1A. In conclusion, our findings suggest that circARID1A inhibits tail fat cell differentiation in the Guangling Large-Tailed sheep through the circARID1A/miR-493-3p/YTHDF2 axis, providing theoretical support for improving meat quality and fat deposition in sheep.