The Biogenesis, Functions, and Challenges of Circular RNAs

Role of non-coding RNAs in the pathogenesis of viral myocarditis

Viral myocarditis (VMC) is a common inflammatory disease of the myocardium that is characterized mainly by inflammatory cell infiltration and cardiomyocyte necrosis. Coxsackievirus B3 (CVB3) is a common cause of VMC, although major progress has been made in the treatment of VMC, the long-term prognosis is still not ideal and further research is needed. Non-coding RNAs (ncRNAs) are RNA molecules without coding functions and include microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), which play extensive regulatory roles in gene expression; however, their mechanisms of action in CVB3-induced VMC remain incompletely understood. Here, we review the currently known roles of various ncRNAs in CVB3-induced VMC models, with a focus on cell death, inflammation and viral replication, with the aim of providing a reference for their therapeutic or vaccine development for the treatment of VMC.

Exploring the complex dimensions of Alzheimer's disease: The promising role of circular RNAs and their potential contributions

Circular RNAs (circRNAs) are multifunctional molecules that regulate gene expression at transcriptional and post-transcriptional levels. They are generated through the back-splicing of mRNA precursors and exhibit tissue-specific expression patterns. CircRNAs highly conserved among various species, exhibit significant abundance and dynamic expression within the nervous system, especially at synaptic sites. Research has shown varied distributions of circRNAs across different organs, including the brain, heart, liver, and lungs, with pronounced enrichment in the nervous system. Neurological disorders lead to alterations in gene expression, transcript profiles, and modifications of non-coding RNAs, including circRNAs. Alzheimer's disease is marked by the accumulation of amyloid-beta (Aβ) plaques and the presence of phosphorylated tau (P-tau) neurofibrillary tangles, both of which are key histological features that contribute to the pathophysiology of the disease. Notably, circRNAs cross the blood-brain barrier (BBB), presenting promising avenues for therapeutic interventions in neurological conditions like Alzheimer's disease (AD) due to their stability and the specificity of their expression in various tissues, circular RNAs are increasingly recognized as promising candidates for therapeutic intervention.

Expanded insights into the mechanisms of RNA-binding protein regulation of circRNA generation and function in cancer biology and therapy

RNA-binding proteins (RBPs) regulate the generation of circular RNAs (circRNAs) by participating in the reverse splicing of circRNA and thereby influencing circRNA function in cells and diseases, including cancer. Increasing evidence has demonstrated that the circRNA-RBP network plays a complex and multifaceted role in tumor progression. Thus, a better understanding of this network may provide new insights for the discovery of cancer drugs. In this review, we discuss the characteristics of RBPs and circRNAs and how the circRNA-RBP network regulates tumor cell phenotypes such as proliferation, metastasis, apoptosis, metabolism, immunity, drug resistance, and the tumor environment. Moreover, we investigate the factors that influence circRNA-RBP interactions and the regulation of downstream pathways related to tumor development, such as the tumor microenvironment and N6-methyladenosine modification. Furthermore, we discuss new ideas for targeting circRNA-RBP interactions using various RNA technologies.

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.

The function of circular RNAs in regulating Wnt/β-catenin signaling: An innovative therapeutic strategy for breast and gynecological cancers

Breast cancer (BC) and gynecological malignancies, including cervical, ovarian, and uterine cancers, are significant global health challenges due to their high prevalence, complex nature, and elevated mortality rates. Dysregulation of the Wnt/β-catenin signaling pathway is a common feature in gynecological malignancies, contributing to cancer cell growth, progression, migration, and metastasis. Recent studies have highlighted the pivotal role of non-coding RNAs (ncRNAs), particularly circular RNAs (circRNAs), in modulating the Wnt/β-catenin signaling pathway. Acting as sponges for microRNAs (miRNAs), circRNAs regulate key oncogenic and tumor-suppressive processes by influencing Wnt-related components. This research explores the role of circRNAs in breast and gynecological malignancies, focusing on their regulatory effects on the Wnt/β-catenin pathway. The findings reveal that circRNAs modulate critical cellular processes such as proliferation, apoptosis, autophagy, and metastasis, with potential implications for therapeutic interventions. Targeting circRNA-mediated dysregulation of Wnt signaling could offer novel strategies for improving diagnostic precision, treatment efficacy, and survival outcomes in breast and gynecological cancers.

Circular RNAs: key players in tumor immune evasion

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

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

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

Functional characterization of a novel protein-coding circular RNA, circRNA_1193, from the mAAP gene in silkworm and its role in antiviral defense against BmCPV

A novel circular RNA, circRNA_1193, which originates from the membrane alanyl aminopeptidase-like gene in silkworms, was explored for its potential function and regulatory mechanism. We validated the presence of circRNA_1193 in Bombyx mori cytoplasmic polyhedrosis virus (BmCPV)-infected silkworm ovary cell line (BmN) cells through a combination of reverse transcription polymerase chain reaction, Northern blotting, and in situ hybridization. CircRNA_1193 exhibited tissue-specific expression, being highly enriched in the midgut and Malpighian tubules, and displayed a specific response to BmCPV infection, but not to Bombyx mori nucleopolyhedrovirus or lipopolysaccharide. Functional analyses revealed that the overexpression of circRNA_1193 suppressed BmCPV replication, whereas its knockdown increased viral replication. Bioinformatic analyses revealed potential internal ribosome entry sites, m6A methylation sites, and open reading frames (ORFs) within circRNA_1193, suggesting its potential coding capacity. We confirmed the translation of the ORF by constructing a DsRed reporter vector and demonstrating DsRed expression in transfected cells. Furthermore, a mutation of the start codon within circRNA_1193 abolished its antiviral activity, highlighting the crucial role of the translated protein, which is 35 kDa and is designated as VSP35. Furthermore, our data suggest that the formation of circRNA_1193 relies on reverse complementary flanking sequences. These findings unveil a novel protein-coding circular RNA in silkworms that plays a critical role in antiviral defense.

IMPORTANCE

This study identified a novel circular RNA, circRNA_1193, in the silkworm Bombyx mori, and revealed its critical role in antiviral defense against Bombyx mori cytoplasmic polyhedrosis virus (BmCPV). We demonstrated that circRNA_1193 exhibits tissue-specific expression, is upregulated in response to BmCPV infection, and possesses antiviral activity. Importantly, we show that circRNA_1193 encodes the viral protein VSP35, which is essential for its antiviral function. These findings provide new insights into the complex regulatory mechanisms of circular RNAs in antiviral immunity and underscore the potential of circular RNAs as therapeutic targets in viral diseases. The identification of a protein-coding circular RNA with antiviral activity in B. mori has broader implications for understanding the evolution and diversity of host defense mechanisms against viruses.

Tumor cell-intrinsic circular RNA circFNDC3B attenuates CD8+ T cells infiltration in non-small cell lung cancer

Tumor-infiltrating CD8+ T cells are critical for anti-tumor immunity and positively associated with patient survival. However, the mechanisms governing CD8+ T cell infiltration remain incompletely elucidated, particularly those involving circular RNAs (circRNAs). In this study, we characterized circRNA expression profiles in four paired normal and tumor tissues of non-small-cell lung cancer (NSCLC) and identified that circFNDC3B, a circular transcript derived from exons 2 and 3 of the fibronectin type III domain containing 3B (FNDC3B) gene, as significantly upregulated in NSCLC tissues. Mechanistic investigations revealed that circFNDC3B directly binds to transcription factor II-I (TFII-I), forming an RNA-protein complex that competitively disrupts the interaction between TFII-I and STAT1. This sequestration abrogates the transcriptional activation of CXCL10 and CXCL11, two critical chemokines governing CD8+ T cell chemoattraction. Consequently, reduced CXCL10/11 expression significantly impairs CD8+ T cell infiltration into the tumor microenvironment. Consistently, the murine ortholog circFndc3b expression exhibits an inverse correlation with CD8+ T cell infiltration in tumors. Our study uncovers a crucial circRNA-mediated regulatory axis wherein circFNDC3B impedes anti-tumor immunity by suppressing chemokine-dependent CD8+ T cell recruitment, positioning circFNDC3B as a potential therapeutic target to enhance CD8+ T cell-mediated anti-tumor responses in NSCLC.

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.

Circ-PSMB1 knockdown inhibits the pyroptosis of ox-LDL treated human aortic cells via the miR-624-3p/ASC axis

BACKGROUND

Atherosclerosis (AS) is a cardiovascular disease that is caused by a variety of factors, including hypertension, diabetes, hyperlipidaemia and smoking. Circular RNAs (circRNAs) have been reported to participate in the progression of AS. Here, we investigated the mechanism by which circ-proteasome 20 S subunit beta 1 (PSMB1) participates in AS.

METHODS

HAECs were stimulated with oxidized low-density lipoprotein (ox-LDL) to establish a model of AS in vitro. Cell viability was investigated with MTT assays. Western blotting and qRT‒PCR were used to measure relative protein and mRNA expression. Cell pyroptosis was analysed by flow cytometry. Lactate dehydrogenase (LDH) levels were measured with a commercial kit.

RESULTS

We found that circ-PSMB1 and apoptosis-associated speck-like protein containing a CARD (ASC) were overexpressed and miR-624-3p was expressed at low levels in HAECs treated with ox-LDL. Circ-PSMB1 silencing enhanced cell viability and decreased pyroptosis, as shown by the downregulation of IL-1β and IL-18 mRNA expression as well as NOD-like receptor thermal protein domain associated protein 3 (NLRP3) and GasderminD-N (GSDMD-N) protein expression. In addition, the miR-624-3p inhibitor neutralized the effects of si-circ-PSMB1, and ASC overexpression neutralized the effects of the miR-624-3p mimic in ox-LDL-treated HAECs.

CONCLUSION

This research demonstrated that circ-PSMB1 might participate in AS development through regulating the pyroptosis of HAECs via the miR-624-3p/ASC axis.

PDGF-BB promotes oral submucosal fibrosis by driving phenotypic transformation and autophagy in oral mucosal fibroblasts through downregulation of circHIPK3

Circular RNA HIPK3 (circHIPK3), known to regulate cell proliferation, migration, transformation, and autophagy in various fibrotic conditions. However, its role has not been studied in oral submucous fibrosis (OSF). Therefore, we conducted this study to explore whether platelet-derived growth factor-BB (PDGF-BB) induces human oral submucous fibroblasts (hOMF) proliferation, migration, transformation, and autophagy through circHIPK3 regulation. Treatment of hOMFs with PDGF-BB significantly increased circHIPK3 expression, promoting proliferation, migration, and autophagy. While inhibiting circHIPK3 mitigated these effects, confirming its role in PDGF-BB-mediated pathways. These findings reveal that PDGF-BB regulates hOMFs via circHIPK3, contributing to OSF pathogenesis and offering potential therapeutic targets. The molecular characteristics of circHIPK3 in fibroblasts (FBs) were identified by Agarose Gel Electrophoresis, Sanger Sequencing and Actinomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the expression of target molecules. The proliferation and migration capacity of FBs in oral mucosa were detected by the CCK8 and Cell Scratch Assay. Protein molecules interacting with circHIPK3 and downstream signaling pathways were screened by RNA pull down and mass spectrometry. Data are available via ProteomeXchange with identifier PXD062842. Firstly, the ring structure of circHIPK3 is verified. The expression level of circHIPK3 in OSF tissues and hOMFs was significantly decreased, while the expression level of circHIPK3 was significantly increased after inhibition of platelet-derived growth factor receptor beta‌‌ (PDGFR-β) by Imatinib (IMA). Subsequently, it was confirmed that the overexpression of circHIPK3 could effectively inhibit the proliferation, migration, transformation and autophagy of PDGF-BB-induced hOMFs. Finally, the mechanism study showed that circHIPK3 could inhibit the proliferation, migration, transformation and autophagy of hOMFs by regulating Y-box binding protein 1 (YBX1) protein and extracellular regulated protein kinases (ERK), phosphatidylinositol 3-kinase (PI3K) and p38 mitogen-activated protein kinase (p38 MAPK) signaling pathways. PDGF-BB downregulates circHIPK3 expression and induces proliferation, migration, transformation, and autophagy of oral mucosal FBs via the circHIPK3/YBX1 axis and the circHIPK3/ERK, PI3K, p38 MAPK axis.

CircFBLN2 regulates duck myoblast proliferation and differentiation through miR-22-5p and MEF2C interaction

The growth and development of duck skeletal muscle significantly affect duck meat production, making it essential to understand the molecular mechanisms underlying these processes. Circular RNAs (circRNAs) and microRNAs (miRNAs) are identified in many species and play essential roles in the regulation of myogenic processes; however, research on circRNAs and miRNAs involved in the duck skeletal muscle development is limited. In prior whole-transcriptome RNA sequencing study, we identified differential expression of miR-22-5p and the novel circular RNA circFBLN2, which arises from the second exon of the FBLN2 gene, in duck primary myoblasts (DPMs). In this study, we confirmed the circular structure of circFBLN2 and explored its expression patterns and functional implications in myogenesis. To elucidate the function of circFBLN2 in the myogenic processes of duck, we conducted experiments involving both the silencing and overexpression of circFBLN2 in DPMs. Our findings indicated that circFBLN2 inhibits DPM proliferation while promoting their differentiation. Conversely, when miR-22-5p was silenced and overexpressed, it exhibited opposing effects by promoting the proliferation of DPMs and inhibiting their differentiation. These results suggest a complex dynamic interplay between circFBLN2 and miR-22-5p in the regulation of DPMs proliferation and differentiation. Additionally, our results revealed that both circFBLN2 and myocyte enhancer factor 2 C (MEF2C) act as sponges for miR-22-5p, as demonstrated by binding predictions and dual-luciferase reporter assays. These results offer novel perspectives on the regulatory pathways underlying the duck embryonic skeletal muscle development, underscoring the pivotal function of circFBLN2 in the regulation of miR-22-5p expression. This research deepens our comprehension of the molecular underpinnings of avian myogenesis, potentially paving the way for more effective approaches to bolster growth and development of livestock.

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.

Transcriptome reveals the roles and potential mechanisms of CeRNA in the regulation of salivary gland development in the tick Rhipicephalus haemaphysaloides

Introduction

The salivary glands of female ticks rapidly degenerate after feeding. The mechanism involves programmed cell death mediated by an ecdysteroid receptor. A competing endogenous RNA (ceRNA) network has been established using miRNA and the competitive binding of three types of RNA (lncRNA, circRNA, and mRNA), that were demonstrated to be involved in the regulation of biological processes. However, the comprehensive expression profile and competing endogenous RNA (ceRNA) regulatory network between mRNAs and ncRNAs involved in salivary gland development remain unclear.

Methods

In the current study, we employed whole-transcriptome sequencing (RNA sequencing) at various stages of feeding to identify differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs. The ceRNA networks combining lncRNAs, circRNAs, miRNAs, and mRNAs were predicted and constructed based on the miRanda and TargetScan databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for target mRNAs with significantly different expression levels.

Results

We identified several pathways related to organ growth and development: Insulin secretion, the Hippo signaling pathway, the Pl3K-Akt signaling pathway, the FoxO signaling pathway, and the Ferroptosis pathway in the lncRNA-miRNA-mRNA network, and Steroid biosynthesis, Cholesterol metabolism, the FoxO signaling pathway, and the Ferroptosis pathway in the circRNA-miRNA-mRNA network, each of which involved insulin and ecdysteroid regulation.

Discussion

Our findings have advanced our understanding of the underlying mechanisms of salivary gland development and degeneration.

Liquid Biopsy in Pituitary Neuroendocrine Tumors-Potential Biomarkers for Diagnosis, Prognosis, and Therapy

Pituitary neuroendocrine tumors (PitNETs) are slow-growing neoplasms with various clinical presentations, often leading to diagnostic challenges. While neuroimaging assessment and histopathological evaluation remain the gold standard for diagnosis, emerging research highlights the potential of liquid biopsy, mainly through the analysis of circulating non-coding RNAs (ncRNAs), as a promising diagnostic and prognostic tool. Recent studies have demonstrated distinct expression profiles in different types and subtypes of tumors, with implications in assessing tumor aggressiveness and predicting treatment response. The current article summarizes data about potential biofluid markers implicated in PitNET development, mainly circulating tumor DNA (ctDNA), cell-free RNAs (cfRNA), circulating tumor cells (CTCs), and exosomes. Many studies on genetic and molecular markers in PitNET tissue samples provide exciting information about tumor biology, but to date, specific studies on liquid biopsy biomarkers are still few. Over the past years, a certain understanding of the mechanisms involved in pituitary tumorigenesis has been gained, including the landscape of genomic alterations, changes in epigenetic profile, crucial molecules involved in specific signaling pathways, and non-coding RNA molecules with critical roles in malignant transformation. Genetic and molecular characterization of the PitNETs could help distinguish between functional and non-functional PitNETs, different types and subtypes of pituitary tumors, and invasive and non-invasive forms. Further studies are required to identify and validate innovative biomarkers or therapeutic targets for treating PitNET. Integrating liquid biopsy into clinical workflows could revolutionize the management of pituitary adenomas, enabling more personalized and less invasive diagnostic and therapeutic strategies.

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.

The role of circular RNA in immune response to tuberculosis and its potential as a biomarker and therapeutic target

Circular RNA (circRNA) is a new type of non-coding RNA that has gained significant attention in recent years, especially in tuberculosis research. Tuberculosis poses a major global public health threat. Its complex pathological mechanisms and worsening drug resistance urgently necessitate new research breakthroughs. The role of circRNA in mycobacterium tuberculosis infection is being gradually revealed, highlighting its importance in regulating gene expression, immune response, and inflammation. Additionally, researchers are interested in circRNA because of its potential for early tuberculosis diagnosis and its role as a biomarker. This article systematically analyzes existing literature to provide new insights into early tuberculosis diagnosis and personalized treatment. We also emphasize the need for future research to enhance the application of circRNA in tuberculosis prevention and control.

Alternative splicing in autism spectrum disorder: Recent insights from mechanisms to therapy

Alternative splicing (AS) is a vital and highly dynamic RNA regulatory mechanism that allows a single gene to generate multiple mRNA and protein isoforms. Dysregulation of AS has been identified as a key contributor to the pathogenesis of autism spectrum disorders (ASD). A comprehensive understanding of aberrant splicing mechanisms and their functional consequences in ASD can help uncover the molecular basis of the disorder and facilitate the development of therapeutic strategies. This review focuses on the major aberrant splicing events and key splicing regulators associated with ASD, highlighting their roles in linking defective splicing to ASD pathogenesis. In addition, a discussion of how emerging technologies, such as long-read sequencing, single-cell sequencing, spatial transcriptomics and CRISPR-Cas systems are offering novel insights into the role and mechanisms of AS in ASD is presented. Finally, the RNA splicing-based therapeutic strategies are evaluated, emphasizing their potential to address unmet clinical needs in ASD treatment.

Group IIC self-splicing intron-derived novel circular RNA vaccine elicits superior immune response against RSV

Introduction

The remarkable commercial success of mRNA vaccines against COVID-19 and tumors, along with their potential as therapeutic drugs, has significantly boosted enthusiasm for circular RNAs (circRNA) as a promising next-generation therapeutic platform. The development of novel circRNA cyclization technologies represents a significant leap forward in RNA engineering and therapeutic applications. Recent advancements in group I and IIB self-splicing intron-based ribozymes have enabled precise cyclization of RNA molecules. However, this approach faces significant limitations, including low cyclization efficiency and the requirement for additional additives, which restrict its broader application. Group IIC self-splicing introns represent the shortest known selfsplicing ribozymes and employ a splicing mechanism that is fundamentally distinct from that of group IIB self-splicing introns. However, the potential of group IIC self-splicing introns to carry exogenous sequences for the development of circular RNA-based platforms remains an open question and warrants further investigation.

Methods

Here, we demonstrate that group IIC self-splicing introns can efficiently circularize and express exogenous proteins of varying lengths, as evidenced by luciferase and GFP reporter systems. Leveraging structural biology-based design, we engineered the RSV pre-F protein and validated the potential of IIC self-splicing introns as a vaccine platform for preventing infectious diseases.

Results

In mouse models, the novel nucleic acid vaccine developed using IIC self-splicing introns elicited superior immunogenicity and in vivo protective efficacy compared to protein-adjuvant vaccines.

Discussion

The development of the novel circular RNA vaccine platform holds significant promise for advancing next-generation therapeutics for disease treatment and prevention.

Plasmodium Infection Modulates Host Inflammatory Response through circRNAs during the Intracellular Stage in Red Blood Cells

The integration of RNA- and DNA-based assays enables the investigation of disease dynamics, specifically assessing the role of asymptomatic or subclinical infections in malaria transmission. Circular RNAs (circRNAs), a distinct category of noncoding RNAs, are implicated in numerous pathogenic mechanisms. As of now, research has yet to explore circRNAs' function in malaria infection. The findings revealed that Plasmodium infection upregulated 60 circRNAs and downregulated 71 in BALB/c mice. We selected 11 differentially expressed (DE) circRNAs according to function prediction of target miRNA-mRNA and coding protein, and these were further confirmed by validation experiments. IRESfinder, GO, and KEGG evaluations indicated that 7 DE circRNAs possess protein-coding potential and are enriched in the MAPK signaling cascade. In P.y17XL-infected BALB/c mouse models, the findings substantiated that the dynamic characteristics of DE circRNAs correlated with inflammation, and the MAPK and NF-κB signaling cascades were activated, also contributing to the inflammatory reaction during malaria infection. This study establishes Plasmodium-induced circRNA expression as a novel mechanism by which the parasite modulates host immune signaling, advancing the understanding of Plasmodium-host cell interactions. In addition, 42 circRNAs were found in normal BALB/c mice, and 25 circRNAs were discovered in P.y17XL-infected BALB/c mice, excluding 1238 circRNAs shared by normal and P.y17XL-infected BALB/c mice. Plasmodium infection changes the expression profile of circRNAs in the host, and these altered circRNAs are involved in the inflammatory response during malaria infection. In addition, Plasmodium possibly regulates the reverse splicing of pre-mRNA or m6A modification of RNA, inducing the production of novel circRNAs in the host.

Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy

Pharmacogenomics is revolutionizing precision medicine by enabling tailored therapeutic strategies based on an individual genetic and molecular profile. Circular RNAs (circRNAs), a distinct subclass of endogenous non-coding RNAs, have recently emerged as key regulators of drug resistance, tumor progression, and therapeutic responses. Their covalently closed circular structure provides exceptional stability and resistance to exonuclease degradation, positioning them as reliable biomarkers and novel therapeutic targets in cancer management. This review provides a comprehensive analysis of the interplay between circRNAs and pharmacogenomics, focusing on their role in modulating drug metabolism, therapeutic efficacy, and toxicity profiles. We examine how circRNA-mediated regulatory networks influence chemotherapy resistance, alter targeted therapy responses, and impact immunotherapy outcomes. Additionally, we discuss emerging experimental tools and bioinformatics techniques for studying circRNAs, including multi-omics integration, machine learning-driven biomarker discovery, and high-throughput sequencing technologies. Beyond their diagnostic potential, circRNAs are being actively explored as therapeutic agents and drug delivery vehicles. Recent advancements in circRNA-based vaccines, engineered CAR-T cells, and synthetic circRNA therapeutics highlight their transformative potential in oncology. Furthermore, we address the challenges of standardization, reproducibility, and clinical translation, emphasizing the need for rigorous biomarker validation and regulatory frameworks to facilitate their integration into clinical practice. By incorporating circRNA profiling into pharmacogenomic strategies, this review underscores a paradigm shift toward highly personalized cancer therapies. circRNAs hold immense potential to overcome drug resistance, enhance treatment efficacy, and optimize patient outcomes, marking a significant advancement in precision oncology.

circSTIL mediates pirarubicin inhibiting the malignant phenotype of triple-negative breast cancer and acts as a biomarker in plasma exosomes

In clinical practice, pirarubicin (THP) is a widely used triple-negative breast cancer (TNBC) agent. It has been found that circular RNAs (circRNAs) are involved in cancer treatment and progression. However, the biological function of circRNAs in TNBC and the relationship between THP and circRNAs remain poorly studied. circSTIL (hsa_circ_0000069) was screened and validated by bioinformatics analysis, demonstrating that it was highly expressed in TNBC cell lines and plasma exosomes, and correlated with a poor prognosis of patients. The expression level of circSTIL in patients' plasma exosomes has potential diagnostic value in distinguishing TNBC from non-TNBC. In vitro studies confirmed that overexpression of circSTIL promotes the proliferation, migration, and invasion of MDA-MB-231 cells whereas silicification of circSTIL shows the reverse effect. Also, circSTIL mediates THP inhibiting the malignant phenotype of MDA-MB-231 cells. The above results suggested that circSTIL is a possible biomarker for the diagnosis, treatment, and prognosis of TNBC.

Comprehensive insights into circular RNAs, miRNAs, and lncRNAs as biomarkers in retinoblastoma

Retinoblastoma (RB) is a common and potentially lethal cancer that primarily affects young children worldwide, with survival rates significantly varying between high- and low-income countries. This review aims to identify essential diagnostic markers for early diagnosis by investigating the molecular pathways associated with RB. The prevalence of RB cases is notably concentrated in Asia and Africa, contributing to a global survival rate estimate of less than 30%. Current management strategies involve complex, individualized treatment plans that consider cultural nuances, genetic abnormalities, staging, and the availability of medical resources. Recent studies suggest that circular RNAs (circRNAs) may serve as predictive and diagnostic biomarkers in the etiology of RB. This review examines the roles of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circRNAs in RB, with the goal of improving survival rates, particularly in low- and middle-income countries. A deeper understanding of the molecular pathways of RB may facilitate the development of personalized treatment plans and targeted therapies. Elevated expression of circRNAs has been observed in most patient cases, and studies indicate that reducing specific circRNA production can inhibit tumor cell development and progression. Investigating the roles and mechanisms of circular RNAs in RB holds promise for future treatment approaches.

Targeting circFOXO3 to Modulate Integrin β6 Expression in Periodontitis: A Potential Therapeutic Approach

AIMS

Circular RNA forkhead box O3 (circFOXO3) is crucial in regulating inflammation in lung and heart injuries. However, its role in periodontitis remains unclear. We sought to elucidate the effects of circFOXO3 on periodontitis progression and related molecular mechanisms.

METHODS

Reverse-transcription quantitative polymerase chain reaction and fluorescence in situ hybridization were used to quantify and localize circFOXO3 expression. The mechanism by which circFOXO3 promotes inflammation in periodontitis was investigated using epithelial cells, human gingival epithelium and a rat model of ligature-induced periodontitis.

RESULTS

circFOXO3 expression was abnormally high in the gingival epithelial tissues of patients with periodontitis. Elevated circFOXO3 levels down-regulated microRNA (miR)-141-3p, leading to increased FOXO3 expression. FOXO3 interacted with JunB to form a transcriptional-repression complex that inhibited the integrin β6 (ITGβ6)-mediated activation of transforming growth factor β (TGF-β) in epithelial cells. Through the miR-141-3p/FOXO3/JunB axis, circFOXO3 suppressed TGF-β signalling, thereby exacerbating periodontal inflammation. Finally, circFOXO3 inhibition hindered disease progression and restored TGF-β activity in vivo via the FOXO3/JunB/ITGβ6 pathway.

CONCLUSION

Our study identified a novel mechanism by which circFOXO3 contributes to periodontal inflammation through a complex transcriptional regulatory network involving miR-141-3p, FOXO3, JunB and ITGβ6. These findings highlight potential therapeutic targets for the development of effective treatments for this debilitating disease.

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSION

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

Assessing transcriptomic signatures of aging: Testing an mRNA marker panel for forensic age estimation of blood samples

Estimating the age of an unknown perpetrator can be a valuable tool in narrowing down a group of suspects. Research efforts to estimate the age of a stain donor have mainly focused on epigenetic modifications, but there is evidence that RNA expression patterns, i.e. the composition of the transcriptome, change with increasing age, which could be a promising molecular alternative for age prediction. In a previous study, we identified a total of 508 mRNA markers with age related expression from two blood whole transcriptome sequencing data sets, using differential expression analysis with DESeq2 and marker selection with lasso regression. For this study, the selected markers from both approaches were combined into an RNA-specific targeted MPS assay for the Ion Torrent platform and evaluated with 100 EDTA blood samples from healthy donors (aged between 23 and 73 years). We compared three different normalization methods for the obtained sequencing data and investigated the performance of various regression techniques for age prediction. The model based on elastic net regression and dSVA-normalized data exhibited the most robust performance, achieving an MAE of 9.29 years and a correlation of 0.57 between the chronological and predicted age. Although the use of a targeted approach instead of RNA-Seq offers several advantages in a forensic setting, we observed a considerable amount of unwanted variation in the targeted sequencing data. We conclude that it is challenging to detect distinct signals associated with chronological age.

Treatment of Pathological Lymphangiogenesis via Circular RNA-Mediated Cholesterol Metabolism Remodeling

Purpose

Lymphangiogenesis plays important roles in the pathogenesis of human diseases, including inflammatory ocular diseases, metabolic diseases, and cancers, by affecting lipid metabolism and immune homeostasis. Despite growing evidence showing that circular RNAs (circRNAs) act as the regulators of inflammatory and metabolic pathways, their roles in lymphatic dysfunction remain unclear. This study aims to explore the involvement of circRNA-KIF6 (cKIF6) in pathological lymphangiogenesis and elucidate the underlying mechanism.

Methods

The cKIF6 expression was evaluated in mouse-sutured corneas and lymphatic endothelial cells (LECs) isolated from juvenile foreskin under inflammatory conditions. Functional assays, including viability, proliferation, migration, and tube formation, were conducted on LECs after cKIF6 silencing. Lymphangiogenesis was evaluated using mouse-sutured cornea and Matrigel plug models. Mechanistic studies explored the role of cKIF6 as a molecular sponge for miR-582 and its downstream effect on methylsterol monooxygenase 1 (MSMO1).

Results

The cKIF6 expression was significantly elevated in mouse-sutured corneas and inflamed LECs. Silencing cKIF6 impaired LEC viability, proliferation, migration, and tube formation, leading to reduced lymphangiogenesis in both in vitro and in vivo models. Mechanistically, cKIF6 acted as a miR-582 sponge, resulting in elevated MSMO1 expression and increased cholesterol content in LECs. The augmented proliferation, migration, and tube formation abilities of cKIF6-overexpressing LECs were attenuated by the inhibitor of cholesterol biosynthesis.

Conclusions

The cKIF6 regulates lymphangiogenesis by targeting cholesterol metabolism, making it a promising therapeutic target for lymphangiogenesis-related diseases.

CircITGA7 overexpression suppresses HCC progression via miR-330/BCL11B axis regulation

As a kind of prevalent malignancy globally, hepatocellular carcinoma (HCC) is characterized by significant morbidity and mortality due to the difficulties in early diagnosis and limited treatment options. Circular RNAs (circRNAs) are a type of circular single-stranded RNA molecule formed by the back-splicing of the 5' end and the 3' end of linear RNA, possessing multiple biological functions. In recent years, numerous reports have demonstrated that circRNAs are potential biomarkers and therapeutic targets for HCC. In this study, we found that circITGA7 is significantly downregulated in HCC tissue compared to adjacent non-tumor tissue. Functional experiments such as CCK8, EdU, colony formation and wound healing assays proved that overexpression of circITGA7 can effectively inhibit the proliferation, migration and invasion of HCC cells. Further research found that circITGA7 can inhibit miR-330 to release BCL11B expression, thereby promoting P53 expression, blocking the cell cycle and promoting apoptosis in HCC cells. In addition, circITGA7 can impede the proliferation of HCC cells in vivo. Therefore, circITGA7 is a potential biomarker for the diagnosis of HCC development and a potential target for the treatment of HCC.

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

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

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.

A Novel Hidden Protein p-414aa Encoded by circSETD2(14,15) Inhibits Vascular Remodeling

BACKGROUND

Phenotypic switching of vascular smooth muscle cells (VSMCs), leading to neointimal hyperplasia, is a fundamental cause of vascular remodeling diseases such as atherosclerosis and hypertension. Novel hidden proteins encoded by circular RNAs play crucial roles in disease progression, yet their involvement in vascular remodeling diseases has not been comprehensively studied. This study identifies a novel protein derived from a circular RNA in VSMCs and demonstrates its potential role in regulating vascular remodeling.

METHODS

Cell proliferation assays were performed to investigate the effects of circSETD2(14,15) on VSMC proliferation. Techniques such as vector construction, immunoprecipitation-mass spectrometry, and dual-luciferase reporter gene were used to confirm that circSETD2(14,15) encoded a novel protein, p-414aa. The interaction between p-414aa and HuR (human antigen R) was validated with techniques such as coimmunoprecipitation, mass spectrometry, and proximity ligation assay. Through experiments including RNA sequencing and RNA immunoprecipitation, the interaction between HuR and C-FOS (C-Fos proto-oncogene) mRNA was revealed. The role of p-414aa in neointimal hyperplasia was assessed with a carotid artery ligation model in male mice.

RESULTS

Overexpression of circSETD2(14,15) inhibits VSMC phenotypic switching. The novel protein p-414aa, encoded by circSETD2(14,15), interacts with HuR to reduce C-FOS mRNA stability, thereby suppressing VSMC proliferation and ultimately inhibiting neointimal hyperplasia in male mice.

CONCLUSIONS

We uncover a novel hidden protein derived from circSETD2(14,15), called p-414aa, that inhibits vascular remodeling. CircSETD2(14,15) and p-414aa may serve as potential therapeutic targets for vascular remodeling diseases.

p53 activates circASCC3 to repress R-loops and enhance resistance to chemotherapy

The tumor suppressor p53 can trigger tumor resistance to chemotherapy by facilitating DNA damage repair and maintaining genomic integrity. Here, we report that a p53-induced circular RNA circASCC3 promotes chemotherapeutic resistance by resolving R-loops. Our results reveal that p53 directly activates the transcription of ASCC3, the host gene of circASCC3. In addition, the RNA-binding protein SFPQ is identified to inhibit the formation of circASCC3 by associating with its flanking regions. Importantly, p53 facilitates the formation of circASCC3 by repressing the expression of SFPQ. CircASCC3 has a marginal effect on the survival and growth of cancer cells under normal growing conditions but surprisingly boosts their survival and growth in response to DNA damage stress. Mechanistic analysis reveals that circASCC3 binds to the DEAD-box RNA helicase DDX5 to inhibit its proteasomal degradation. This results in the prevention of R-loop accumulation due to DNA damage, thereby conferring tumor resistance to chemotherapy. Together, our study uncovers that p53 activates circASCC3 to promote R-loop resolution, which maintains genomic stability and potentially contributes to chemoresistance.

Epididymal-Born circRNA Cargo and Its Implications in Male Fertility

The epididymis represents a pivotal organ for sperm maturation and male fertility maintenance. During the epididymal journey, sperm cells undergo morphological and molecular changes that need to acquire the morpho-functional skills necessary for successful oocyte fertilization. Not last, a great enrichment of the spermatozoa RNA payload occurs via an epithelium-derived epididymosome transfer. Currently, circular RNAs (circRNAs), a class of non-coding RNAs (ncRNAs), are acquiring a prominent role in the setting of sperm quality parameters. In this regard, they are considered potential targets in several male infertility conditions. Despite their consolidated role, few notions are known regarding the alleged epididymal backsplicing activity. In the current review, we discuss the main aspects of spermatozoa maturation along the epididymis and the circRNA role in the field of male reproduction. We also report the most recent findings on the circRNA biogenesis that occurs in the epididymal duct, providing new fascinating evidence on epididymal-derived circRNAs. Finally, we show preliminary compelling data on epididymal backsplicing by exploiting the experimental mouse model of aging. Collectively, these data evidence a remarkable role of the epididymis in remodeling the circRNA payload and in shaping its profile in maturating spermatozoa.

Multi-omics approaches for biomarker discovery and precision diagnosis of prediabetes

Recent advancements in multi-omics technologies have provided unprecedented opportunities to identify biomarkers associated with prediabetes, offering novel insights into its diagnosis and management. This review synthesizes the latest findings on prediabetes from multiple omics domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and radiomics. We explore how these technologies elucidate the molecular and cellular mechanisms underlying prediabetes and analyze potential biomarkers with predictive value in disease progression. Integrating multi-omics data helps address the limitations of traditional diagnostic methods, enabling early detection, personalized interventions, and improved patient outcomes. However, challenges such as data integration, standardization, and clinical validation and translation remain to be resolved. Future research leveraging artificial intelligence and machine learning is expected to further enhance the predictive power of multi-omics technologies, contributing to the precision diagnosis and tailored management of prediabetes.

Circular RNAs and host genes act synergistically in regulating cellular processes and functions in skeletal myogenesis

Circular RNAs (circRNAs) are post-transcriptional regulators generated from backsplicing of pre-mRNAs of host genes. A major circRNA regulatory mechanism involves microRNA (miRNA) sequestering, relieving miRNA-blocked mRNAs for translation and functions. To investigate possible circRNA-host gene relationship, skeletal myogenesis is chosen as a study model for its developmental importance and for readily available muscle tissues from farm animals for studies at different myogenic stages. This review aims to provide an integrated interpretations on methodologies, regulatory mechanisms and possible host gene-circRNA synergistic functional relationships in skeletal myogenesis, focusing on myoblast differentiation and proliferation, core drivers of muscle formation in myogenesis, while other myogenic processes that play supportive roles in the structure, maintenance and function of muscle tissues are also briefly discussed. On literature review,thirty-two circRNAs derived from thirty-one host genes involved in various myogenic stages are identified; twenty-two (68.6 %) of these circRNAs regulate myogenesis by sequestering miRNAs to engage PI3K/AKT and other signaling pathways while four (12.5 %) are translated into proteins for functions. In circRNA-host gene relationship,ten (32.3 %) host genes are shown to regulate myogenesis,nine (29.0 %) are specific to skeletal muscle functions,and twelve (38.8 %) are linked to skeletal muscle disorders.Our analysis of skeletal myogenesis suggests that circRNAs and host genes act synergistically to regulate cellular functions. Such circRNA-host gene functional synergism may also be found in other major cellular processes. CircRNAs may have evolved later than miRNAs to counteract the suppressive effects of miRNAs and to augment host gene functions to further fine-tune gene regulation.

Circ_0090100 induces AHNAK expression to inhibit trophoblast cell proliferation and invasion and accelerate cell apoptosis by segregating miR-139-5p in preeclampsia

The etiology of preeclampsia (PE) is complex and is known to involve the expression of circular RNAs (circRNAs). Among these, the function of circ_0090100 in PE is yet to be fully understood. This study was conducted to examine the expression profile of circ_0090100 in placental tissues from PE patients and to assess its influence on trophoblast cell functions. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the RNA expression levels of circ_0090100, microRNA-139-5p (miR-139-5p), and AHNAK nucleoprotein (AHNAK). Cell viability, proliferation, apoptosis, and invasion were assessed using the CCK-8 assay, EdU incorporation, flow cytometry, and transwell migration assays, respectively. Western blot analysis was performed to detect the protein expression of N-cadherin, Vimentin, and AHNAK. Dualluciferase reporter assay and RNA immunoprecipitation (RIP) assay were conducted to elucidate the relationships between circ_0090100, miR-139-5p, and AHNAK. We found that the expression of circ_0090100 and AHNAK was upregulated, while miR-139-5p. expression was downregulated in PE placental tissues compared to controls. Transfection of a plasmid overexpressing circ_0090100 into JEG-3 and HTR-8/SVneo trophoblast cell lines resulted in reduced cell proliferation and invasion, but increased apoptosis. Mechanistically, circ_0090100 functioned as a miR-139-5p sponge, and miR-139-5p targeted AHNAK. Furthermore, upregulating miR-139-5p reversed the effects of circ_0090100 in JEG-3 and HTR-8/SVneo cells. AHNAK was found to be involved in the regulation of miR-139-5p effects on trophoblast cells. Additionally, circ_0090100 induced the production of AHNAK through miR-139-5p. Therefore, circ_0090100 activated AHNAK to suppress trophoblast cell proliferation and invasion, and promote cell apoptosis, via miR-139-5p.

circPRMT10 regulated by QKI hypermethylation attenuates lung tumorigenesis induced by tobacco carcinogen NNK

Chronic exposure to environmental carcinogens is a major cause of tumorigenesis. A potent tobacco-specific nitrosamine carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), exhibits high carcinogenicity to induce lung cancer. However, the function and mechanism of circular RNA (circRNA) in chemical carcinogenesis, especially the regulation of circRNA formation upon exposure to environmental chemicals, remain unclear. This study identified that circPRMT10 (hsa_circ_0009048) was downregulated in NNK-exposed human bronchial epithelial cells (16HBE and BEAS-2B). Additionally, the RNA-binding protein Quaking (QKI) was responsible for the biogenesis of circPRMT10 through its binding interaction with the flanking introns of circPRMT10. Moreover, NNK exposure resulted in hypermethylation of the QKI promoter, leading to QKI downregulation, which ultimately affected circPRMT10 formation. Using a cell model of chronic exposure to low-dose NNK, we found that overexpression of circPRMT10 significantly inhibited NNK-induced lung carcinogenesis by suppressing cell proliferation, cell cycle progression, and xenograft tumor growth. Finally, moesin (MSN) was identified as a downstream target of circPRMT10 via RNA pull-down and western blot assays and demonstrated a potential role in the regulation of lung cancer development. In conclusion, our findings reveal the underlying mechanisms of circRNA biogenesis following exposure to chemical carcinogens, providing novel insights into the role of circRNAs in chemical carcinogenesis.

DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism

Drug sensitivity is essential for identifying effective treatments. Meanwhile, circular RNA (circRNA) has potential in disease research and therapy. Uncovering the associations between circRNAs and cellular drug sensitivity is crucial for understanding drug response and resistance mechanisms. In this study, we proposed DeepHeteroCDA, a novel circRNA-drug sensitivity association prediction method based on multi-scale heterogeneous network and graph attention mechanism. We first constructed a heterogeneous graph based on drug-drug similarity, circRNA-circRNA similarity, and known circRNA-drug sensitivity associations. Then, we embedded the 2D structure of drugs into the circRNA-drug sensitivity heterogeneous graph and use graph convolutional networks (GCN) to extract fine-grained embeddings of drug. Finally, by simultaneously updating graph attention network for processing heterogeneous networks and GCN for processing drug structures, we constructed a multi-scale heterogeneous network and use a fully connected layer to predict the circRNA-drug sensitivity associations. Extensive experimental results highlight the superior of DeepHeteroCDA. The visualization experiment shows that DeepHeteroCDA can effectively extract the association information. The case studies demonstrated the effectiveness of our model in identifying potential circRNA-drug sensitivity associations. The source code and dataset are available at https://github.com/Hhhzj-7/DeepHeteroCDA.

Transcriptomics reveals the regulatory mechanisms of circRNA in the muscle tissue of cows with ketosis postpartum

The transition period from late pregnancy to early lactation in dairy cows involves significant metabolic changes to cope with the challenges related to energy metabolism. Muscle tissue, as the largest energy-metabolizing tissue in dairy cows, plays a crucial role in energy metabolism. Furthermore, circular RNAs (circRNAs) have been shown to play key roles in various biological events. However, the regulatory mechanisms of energy metabolism and muscle cells mediated by circRNAs in the muscle tissue of ketotic dairy cows remain unclear. Here, we identified a total of 5103 circRNAs in the muscle tissue of ketosis-affected cows. Among these, compared to healthy cows, 57 circRNAs were differentially expressed in the muscle tissue of ketosis-affected cows, with 39 upregulated and 18 downregulated. Functional enrichment analysis based on the source genes of circRNAs indicated that circ-30,628 is closely related to carbon metabolism, and circ-CoQ2 is associated with mitochondrial energy metabolism. Given the sponge effect of circRNAs on miRNAs, we further predicted the network relationships of downstream miRNAs and mRNAs of circ-30,628 and circ-CoQ2, and found that their downstream target genes are involved in signaling pathways such as MAPK, Wnt, FoxO, and autophagy, which is associated with the proliferation, differentiation, energy metabolism, oxidative stress, and mitochondrial function of muscle cells. In summary, these findings provide a theoretical basis for understanding the functions of circRNAs regulating energy metabolism in the muscle tissue of ketosis-affected cows, thereby reducing the accumulation of ketone bodies to prevent the occurrence of ketosis in dairy cows.

CircFak promotes mechanical force-induced osteogenesis via FAK/AKT phosphorylation

OBJECTIVES

Orthodontic treatment is widely applied for addressing orofacial skeletal deformities, with the remodeling of the alveolar bone under mechanical force being the key factor. FAK is essential for cellular response to mechanical force. However, the function of circFak has never been reported. In this study, the microarrays showed that circFak may affect osteogenesis under mechanical force. We aimed to verify the effect of circFak in force-related bone remodeling and investigate the underlying mechanisms.

METHODS

Arraystar microarrays were used to identify differentially expressed circRNAs and microRNAs in response to mechanical stress. The subcellular distribution of circFak was analyzed via RT‒qPCR and FISH. ALP and ARS staining assays were performed to investigate the effects of circFak on osteogenesis. RNA sequencing, bioinformatics analysis, dual-luciferase reporter assays, and RNA immunoprecipitation were accomplished to discover the molecular mechanisms of circFak. AAV-sh-circFak mouse models with tooth movements were established. The role of circFak under mechanical force in vivo was assessed via immunofluorescence and micro-CT analyses.

RESULTS

CircFak expression was significantly upregulated under mechanical force. Osteogenic capacity of osteoblasts was positively correlated with the level of circFak. CircFak promoted mechanical force-induced osteogenesis through miR-425-5p/Ccn3 pathway, and further stimulated the phosphorylation of its parental sourced protein FAK. Our murine models showed that AAV-mediated circFak silencing suppressed osteogenesis.

CONCLUSION

CircFak could obviously promote osteogenesis under mechanical force and may possess ability to become a novel biomarker for prognosis of orthodontic treatments.

5-Methylcytosine-modified circRNA-CCNL2 regulates vascular remdeling in hypoxic pulmonary hypertension through binding to FXR2

Pulmonary hypertension (PH) is a malignant cardiovascular disease with a complex etiology. 5-Methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant RNAs, with a lower frequency of occurrence in circular RNAs (circRNAs). Nevertheless, the function of m5C-modified circRNAs in the pathogenesis of PH remains uncertain. The objective of this study was to investigate the biological role and molecular mechanisms of m5C-modified circRNA-CCNL2 in hypoxic PH pulmonary vascular remodeling. Our findings revealed that hypoxia downregulates circCCNL2 expression, and overexpression of circCCNL2 attenuates PH progression and inhibits the proliferation of pulmonary artery smooth muscle cell (PASMCs). Bioinformatics predictions indicated the presence of m5C modification sites in circCCNL2, which NSUN2 mediated. The downregulation of NSUN2 resulted in a reduction in m5C modification of circCCNL2. It was also observed that the stability of circRNAs was associated with the proliferation of PASMCs. From a mechanistic standpoint, low expression of circCCNL2 resulted in reduced binding of FXR2, while increased association of free FXR2 with CDKL3 led to enhanced proliferation of PASMCs. Notably, circCCNL2 expression was found to be regulated by alternative splicing involving SRSF2, with reduced pre-CCNL2 splicing resulting from low SRSF2 expression, ultimately leading to decreased circCCNL2 expression. This is the first demonstration that m5C-modified circCCNL2 can slow the development of PH and inhibit the proliferation of PASMCs by binding to FXR2. These findings offer new insights into the regulation of circRNAs through m5C modifications and the role of epigenetic reprogramming in PH.

Research progress of circular RNA FOXO3 in diseases (review)

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

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

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

Role of circRNAs in regulating cell death in cancer: a comprehensive review

Despite multiple diagnostic and therapeutic advances, including surgery, radiation therapy, and chemotherapy, cancer preserved its spot as a global health concern. Prompt cancer diagnosis, treatment, and prognosis depend on the discovery of new biomarkers and therapeutic strategies. Circular RNAs (circRNAs) are considered as a stable, conserved, abundant, and varied group of RNA molecules that perform multiple roles such as gene regulation. There is evidence that circRNAs interact with RNA-binding proteins, especially capturing miRNAs. An extensive amount of research has presented the substantial contribution of circRNAs in various types of cancer. To fully understand the linkage between circRNAs and cancer growth as a consequence of various cell death processes, including autophagy, ferroptosis, and apoptosis, more research is necessary. The expression of circRNAs could be controlled to limit the occurrence and growth of cancer, providing a more encouraging method of cancer treatment. Consequently, it is critical to understand how circRNAs affect various forms of cancer cell death and evaluate whether circRNAs could be used as targets to induce tumor death and increase the efficacy of chemotherapy. The current study aims to review and comprehend the effects that circular RNAs exert on cell apoptosis, autophagy, and ferroptosis in cancer to investigate potential cancer treatment targets.

Identification of the crucial circ-mi-mRNA interaction networks regulating testicular development and spermatogenesis in ganders

Semen quality has an important impact on the reproductive performance of ganders, and the quantity and quality of spermatozoa in semen are the determinants of semen quality. In our practical work, a small number of azoospermic ganders were observed in adult goose breeding populations, but the underlying regulatory mechanisms remain unknown. In the present study, we firstly compared the morphological and histological differences in the testes of ganders from normozoospermic group (NG) and azoospermic group (AG), and then analyzed the testicular expression patterns of circRNAs, miRNAs, and mRNAs between the two groups by using whole-transcriptome sequencing technology. Results from histomorphological analysis demonstrated that the body weight alone was not accountable for the occurrence of gander azoospermia, and the possible cause might be the observed testicular abnormalities. At the morphological level, the left, right, and bilateral testicular weights, the right and bilateral testicular organ indexes, and the long, short, and dorsoventral diameters of the left, right and bilateral testes were significantly lower in AG than in NG (P < 0.05). At the histological level, most testicular histological parameters, such as the testicular parenchymal area, the diameter of seminiferous tubules, and the number of germ cells, were significantly higher (P < 0.05) in NG than in AG. The RNA-seq results showed that a total of 683 differentially expressed circRNAs (DEcircRNAs), 24 differentially expressed miRNAs (DEmiRNAs), and 1,118 differentially expressed Genes (DEGs) were identified in the gander testes between NG and AG. Subsequent functional enrichment analysis revealed that most of the DEGs and the target genes of DEcircRNAs and DEmiRNAs were significantly enriched in either the biological processes related to male gonad development, spermatid development, and regulation of cell differentiation or the KEGG terms including the MAPK, TGF-beta, Wnt, and cell cycle signaling pathways. By constructing the core ceRNA regulatory networks, several key DEcircRNAs, including 1:98100313|98104995, 1:171413706|171419341, 6:3414226|3418193, and 2:115876735|115880760, were identified to regulate the expression of TGFB2 and BCL2 through interactions with specific miRNAs such as novel-miR-265 and novel-miR-266, and such interactions could play crucial roles in regulating the gander testicular cell apoptosis, proliferation, and spermatogenesis. This study provides novel insights into the function and molecular mechanisms of ceRNAs in regulating the gander testicular development and semen quality.

Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition

Thermal adaptability is a crucial characteristic for mammalian pathogenic fungi that originally inhabit natural ecosystems. Thermally dimorphic fungi have evolved a unique ability to respond to host body temperature by shifting from mycelia to yeast. The high similarity of protein-coding genes between these fungi and their relatives suggests the indispensable but often overlooked roles of non-coding elements in fungal thermal adaptation. Here, we systematically delineated the landscape of full-length circRNAs in both mycelial and yeast conditions of Talaromyces marneffei, a typical thermally dimorphic fungus causing fatal Talaromycosis, by optimizing an integrative pipeline for circRNA detection utilizing next- and third-generation sequencing. We found T. marneffei circRNA demonstrated features such as shorter length, lower abundance, and circularization-biased splicing. We then identified and validated that circDS-1, independent of its parental gene, promotes the hyphae-to-yeast transition, maintains yeast morphology, and is involved in virulence regulation. Further analysis and experiments among Talaromyces confirmed that the generation of circDS-1 is driven by a T. marneffei-specific region in the flanking intron of circDS-1. Together, our findings not only provide fresh insights into the role of circRNA in fungal thermal adaptation but also reveal a novel molecular mechanism for the adaptive evolution of functional circRNAs derived from intronic mutations.

EIF4E-mediated biogenesis of circPHF14 promotes the growth and metastasis of pancreatic ductal adenocarcinoma via Wnt/β-catenin pathway

BACKGROUND

CircRNAs are critically involved in the development and progression of various cancers. However, their functions and mechanisms in pancreatic ductal adenocarcinoma (PDAC) remain largely unknown.

METHODS

CircPHF14 (hsa_circ_0079440) was identified through the analysis of RNA sequencing data from PDAC and normal adjacent tissues. The biological functions of circPHF14 were then evaluated using CCK8, EdU, transwell, colony formation, wound healing assays, as well as pancreatic orthotopic xenograft and liver metastasis models. The interaction mechanisms between circPHF14 and PABPC1, which enhance the stability of WNT7A mRNA, were investigated through RNA pull-down, mass spectrometry, RNA Immunoprecipitation (RIP), and actinomycin D assays. The role of EIF4E in promoting circPHF14 biogenesis was examined using RIP, and western blotting.

RESULTS

In this study, we observed a significant upregulation of circPHF14 in both clinical PDAC samples and cell lines. Functionally, circPHF14 enhanced PDAC proliferation and metastasis both in vitro and in vivo. Mechanistically, circPHF14 interacted with PABPC1 to stabilize WNT7A mRNA, thereby activating the Wnt/β-catenin pathway, which subsequently upregulated SNAI2 and initiated Epithelial-Mesenchymal Transition (EMT) in PDAC. Additionally, EIF4E was found to bind PHF14 pre-mRNA, facilitating circPHF14 biogenesis. Finally, we developed a lipid nanoparticle (LNP) formulation encapsulating sh-circPHF14 plasmids and confirmed its anti-tumor efficacy in a patient-derived xenograft (PDX) model.

CONCLUSION

EIF4E-mediated biogenesis of circPHF14 stabilizes WNT7A mRNA via interaction with PABPC1, which subsequently activates the Wnt/β-catenin pathway, promoting the growth and metastasis of PDAC. These findings indicate that circPHF14 holds promise as a biomarker and therapeutic target for PDAC.

Relationship Between Chronic Pain and Breast Cancer: Insight From Genetic Correlation Analyses and 2-Sample Mendelian Randomization

OBJECTIVE

To evaluate potential genetic causal relationships between chronic pain subtypes like migraine and multi-site chronic pain (MCP) and their impact on breast cancer occurrence and survival rates.

BACKGROUND

The association between chronic pain and breast cancer was reported before, yet the causal nature between them remained uncertain.

METHODS

Data on chronic pain and breast cancer were sourced from publicly available European genome-wide association study (GWAS) datasets. Genetic association between chronic pain and breast cancer phenotypes was assessed using linkage disequilibrium genetic correlation (LDSC). Colocalization analysis further identified potential shared causal variation. Based on Inverse variance weighted method, 2-sample Mendelian Randomization (MR) was conducted to investigate causal associations between migraine, MCP, and breast cancer or breast cancer survival. Sensitive analysis was conducted to ensure the absence of heterogeneity and horizontal pleiotropy.

RESULTS

LDSC demonstrated significant genetic correlations between migraine and both estrogen receptor-negative (ER-) and overall breast cancer, while also revealing a notable genetic association between MCP and ER- and ER+ breast cancer, as well as overall breast cancer. Through colocalization analysis, potential involvement of rs2183271, located in MLLT10 gene, in regulating MCP and ER+ breast cancer was identified. MR analysis revealed the association between migraine and elevated risk of ER- breast cancer (IVW, P = 4.95 × 10-3). Cochran's Q test ensured the absence of heterogeneity and MR-PRESSO global test, MR-Egger intercept test ensured the absence of horizontal pleiotropy.

CONCLUSION

Our results provided new insights into the role of migraine and MCP in breast cancer, paving the way for targeted preventive strategies and future investigations.