The expanding regulatory mechanisms and cellular functions of circular RNAs

Novel insights into non-coding RNAs and their role in hydrocephalus

A large body of evidence has highlighted the role of non-coding RNAs in neurodevelopment and neuroinflammation. This evidence has led to increasing speculation that non-coding RNAs may be involved in the pathophysiological mechanisms underlying hydrocephalus, one of the most common neurological conditions worldwide. In this review, we first outline the basic concepts and incidence of hydrocephalus along with the limitations of existing treatments for this condition. Then, we outline the definition, classification, and biological role of non-coding RNAs. Subsequently, we analyze the roles of non-coding RNAs in the formation of hydrocephalus in detail. Specifically, we have focused on the potential significance of non-coding RNAs in the pathophysiology of hydrocephalus, including glymphatic pathways, neuroinflammatory processes, and neurological dysplasia, on the basis of the existing evidence. Lastly, we review the potential of non-coding RNAs as biomarkers of hydrocephalus and for the creation of innovative treatments.

The regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies

The crosstalk between the tumour immune microenvironment (TIME) and tumour cells promote immune evasion and resistance to immunotherapy in gastrointestinal (GI) tumours. Post-transcriptional regulation of genes is pivotal to GI tumours progression, and RNA-binding proteins (RBPs) serve as key regulators via their RNA-binding domains. RBPs may exhibit either anti-tumour or pro-tumour functions by influencing the TIME through the modulation of mRNAs and non-coding RNAs expression, as well as post-transcriptional modifications, primarily N6-methyladenosine (m6A). Aberrant regulation of RBPs, such as HuR and YBX1, typically enhances tumour immune escape and impacts prognosis of GI tumour patients. Further, while targeting RBPs offers a promising strategy for improving immunotherapy in GI cancers, the mechanisms by which RBPs regulate the TIME in these tumours remain poorly understood, and the therapeutic application is still in its early stages. This review summarizes current advances in exploring the roles of RBPs in regulating genes expression and their effect on the TIME of GI tumours, then providing theoretical insights for RBP-targeted cancer therapies.

CircATP5C1 promotes triple-negative breast cancer progression by binding IGF2BP2 to modulate CSF-1 secretion

Triple-negative breast cancer (TNBC) is a common malignant disease among females and severely threatens the health of women worldwide. Nowadays, circular RNAs (circRNAs) aroused our interest for their functions in human cancers, including TNBC. However, the mechanism of most circRNAs in the progression of TNBC remains unclear. We found a novel circRNA named circATP5C1, whose function in TNBC remains uncovered. Tissue microarray was used to analyze the association between the expression of circATP5C1 and the prognoses of TNBC patients. Gain-and loss-of-function experiments were performed to validate the biological functions of circATP5C1 in different TNBC cell lines. RNA-seq analyses were conducted to find out the target genes regulated by circATP5C1. RNA pull-down assay and mass spectrometry were used to select the proteins associated with circATP5C1. RNA FISH-immunofluorescence and RNA immunoprecipitation (RIP) were complemented to validate the interaction between circATP5C1 and its binding protein. CircATP5C1 was identified to have predictive function in prognosis of TNBC patients. CircATP5C1 advanced the progression of TNBC cells. Mechanistically, Colony stimulating factor 1 (CSF-1) is a vital downstream gene regulated by circATP5C1. The alteration of CSF-1 expression level was validated due to the interaction between circATP5C1 and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2). Rescue experiments demonstrated that circATP5C1 accelerates the progression of TNBC partly via binding with IGF2BP2 to increase the secretion of CSF-1. This study uncovers a novel mechanism of circATP5C1/IGF2BP2/CSF-1 pathway in regulating progression of TNBC.

Recent advances in RNA-based therapeutics for neurodevelopmental disorders

A significant proportion of neurodevelopmental disorders (NDDs) are caused by gain-of-function (GOF) or loss-of-function (LOF) of specific genes. Strategies to normalize disease gene expression offer therapeutic potential for these disorders. The success and approval of RNA-based therapeutics for various disorders have led to a surge in RNA-based therapeutic research for NDDs with antisense oligonucleotides leading the field. This review discusses recent advances in therapeutic strategies that target pre-mRNA or mRNA for GOF and LOF NDDs that have promising preclinical evidence. These developments highlight important considerations and exciting future avenues for the development of therapies for NDDs.

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

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

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

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

MiR-335-5p Escaped from CircKIAA0586 Adsorption Contributes to Mechanical Overloading-Induced Cartilage Degeneration by Targeting Lymphoid-Specific Helicase

Mechanical overload is a critical contributor to cartilage degeneration in osteoarthritis (OA) pathogenesis. Circular RNA (circRNA) is expected to provide a long-lasting therapy for OA. However, the involvement of the circRNA-associated competitive endogenous RNA network in chondrocyte senescence induced by mechanical overloading remains unestablished. A mechanical overloading-induced chondrocyte senescence model in human primary chondrocytes is constructed, and differences in the expression of circRNAs and miRNAs were analyzed. The biological roles of circKIAA0586/miR-335-5p in chondrocyte senescence and OA progression under mechanical overloading and its downstream targets were determined using gain- and loss-of-function experiments in various biochemical assays in human chondrocytes. The in vivo effects of circKIAA0586 overexpression were also determined in destabilization of the medial meniscus (DMM) OA mice and aged spontaneous OA mice. The mechanical overloading-induced chondrocyte senescence was aggravated by miR-335-5p or circKIAA0586 knockdown. Accumulated DNA damage response was observed following mechanical overloading, which reduced after miR-335-5p inhibition or circKIAA0586 supplementation. MiR-335-5p was regulated by circKIA0586 adsorption. HELLS was prominently down-regulated following mechanical overloading treatment. Moreover, miR-335-5p bound to lymphoid-specific helicase (HELLS) mRNA during mechanical overloading was demonstrated to mediate the nonhomologous end joining (NHEJ) pathway, thereby inducing DNA damage and senescence. In addition, the senescence delaying and cartilage protective functions of circKIAA0586 and HELLS were validated in DMM OA mice and aged spontaneous OA mice. Our findings suggest that miR-335-5p, which escapes circKIAA0586 adsorption, facilitates mechanical overloading-induced chondrocyte senescence and OA progression by impairing the NHEJ pathway through HELLS inhibition. Overall, targeting circKIAA0586/miR-335-5p/HELLS signaling provides a novel therapeutic approach for OA.

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.

Construction of a Ligation-Controlled Single-Molecule Biosensor for Simultaneous Measurement of Multiple Cancer-Related circRNAs in Clinical Tissues

Circular RNAs (circRNAs) are noncoding RNAs with covalently closed circular structures that regulate important cellular processes, and their dysregulation is implicated in the pathogenesis and progression of various cancers. Simultaneous and specific detection of multiple circRNAs is of significant importance in the early diagnosis of cancer. Herein, we develop a ligation-controlled single-molecule biosensor for multiplexed measurement of breast cancer-associated circRNAs. This assay integrates the isothermal exponential amplification reaction (EXPAR)-induced generation of multiple DNAzymes with a Au nanoparticle (AuNP)-based spherical nucleic acid nanoprobe. The back-splice junction (BSJ) sequences of circFOXO3 and circMTO1 can serve as the templates to ligate their hairpin probes and helper probes under the catalysis of SplintR ligase, forming complete amplification templates. Afterward, the ligated amplification template can serve as both a primer and a template to initiate the EXPAR, inducing the exponential accumulation of characteristic DNAzyme sequences (i.e., DNAzymes 1 and 2). DNAzymes 1 and 2 can be paired with signal probes 1 and 2 immobilized on the AuNP surface, respectively, inducing cyclic degradation of signal probes to liberate large amounts of Cy5 and Cy3 fluorophores and achieving detection limits of 8.34 aM for circFOXO3 and 9.84 aM for circMTO1. This single-molecule biosensor has been successfully applied for simultaneous analysis of multiple circRNAs in a single cancer cell and differentiation of multiple circRNA levels between breast cancer tissues and healthy para-carcinoma tissues, offering a new paradigm for biomedical research and circRNA-related molecular diagnostics.

Mechanism and Therapeutic Progress of One-Carbon Metabolic Key Enzyme: Serine Hydroxymethyltransferase 2 in Cancer

Serine hydroxymethyltransferase 2 (SHMT2) is a crucial mitochondrial enzyme in 1-carbon (1C) metabolism. It catalyzes the conversion of serine to glycine, generating 1C units essential for purine and pyrimidine synthesis, thereby supporting DNA replication and repair. Abnormally high expression is associated with malignant progression and treatment tolerance in various cancers. This review systematically summarizes the functions of SHMT2 in different types of cancer, underscoring on its roles in metabolism, immune microenvironment, and key signaling pathways (PI3K/AKT/mTOR, JAK-STAT, etc.) and outlines its epigenetic regulation and posttranslational modification mechanisms. Compared with the existing research, we focused on the latest regulatory mechanisms of SHMT2 and its potential in cancer treatment, such as the development and application of small-molecule inhibitors (SHIN2 and AGF347).

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

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

CircMYO9A inhibits influenza A virus replication by dampening hemagglutinin cleavage via increasing SERPINE1/PAI-1 expression

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

Deciphering the role of circular RNAs in cancer progression under hypoxic conditions

Hypoxia, characterized by reduced oxygen levels, plays a pivotal role in cancer progression, profoundly influencing tumor behavior and therapeutic responses. A hallmark of solid tumors, hypoxia drives significant metabolic adaptations in cancer cells, primarily mediated by hypoxia-inducible factor-1α (HIF-1α), a key transcription factor activated in low-oxygen conditions. This hypoxic environment promotes epithelial-mesenchymal transition (EMT), enhancing cancer cell migration, metastasis, and the development of cancer stem cell-like properties, which contribute to therapy resistance. Moreover, hypoxia modulates the expression of circular RNAs (circRNAs), leading to their accumulation in the tumor microenvironment. These hypoxia-responsive circRNAs regulate gene expression and cellular processes critical for cancer progression, making them promising candidates for diagnostic and prognostic biomarkers in various cancers. This review delves into the intricate interplay between hypoxic circRNAs, microRNAs, and RNA-binding proteins, emphasizing their role as molecular sponges that modulate gene expression and signaling pathways involved in cell proliferation, apoptosis, and metastasis. It also explores the relationship between circRNAs and the tumor microenvironment, particularly how hypoxia influences their expression and functional dynamics. Additionally, the review highlights the potential of circRNAs as diagnostic and prognostic tools, as well as their therapeutic applications in innovative cancer treatments. By consolidating current knowledge, this review underscores the critical role of circRNAs in cancer biology and paves the way for future research aimed at harnessing their unique properties for clinical advancements. Specifically, this review examines the biogenesis, expression patterns, and mechanistic actions of hypoxic circRNAs, focusing on their ability to act as molecular sponges for microRNAs and their interactions with RNA-binding proteins. These interactions impact key signaling pathways related to tumor growth, metastasis, and drug resistance, offering new insights into the complex regulatory networks governed by circRNAs under hypoxic stress.

Hsa_circ_0000479 promotes gastric cancer progression by inhibiting BTRC-mediated ubiquitination of G3BP1

An increasing number of studies have shown that circular RNAs (circRNAs) are key regulators of cancer development and progression. RNA-binding proteins (RBPs) play critical roles in the regulation of biological activities, such as RNA synthesis, selective splicing, modification, translocation, and translation; therefore, research on the interactions of circRNAs with RBPs is key to identifying potential targets for cancer treatment. However, the biological roles and mechanisms of circRNAs in gastric cancer (GC) remain largely unknown. We identified differentially expressed circRNAs in GC by analysing Gene Expression Omnibus (GEO) datasets. Concurrently, in vitro functional assays and in vivo animal studies were performed to explore the biological role of circRNAs in GC. We performed western blotting (WB) of labelled proteins, salvage assays, mass spectrometry (MS), and RNA sequencing to investigate the mechanism of circRNAs in GC to explore their effects on GC cell proliferation and metastasis and to validate their potential value as therapeutic targets. Upregulated expression of cyclic RNA EPSTI1 (circEPSTI1; hsa_circ_0000479) was found in GC tissues and was associated with a poor clinical prognosis. hsa_circ_0000479 promotes the proliferation and migration of GC cells in vitro and in vivo. Notably, hsa_circ_0000479 interacts with Ras-GTPase-activated protein-binding protein 1 (G3BP1) in GC cells and inhibits the degradation of G3BP1 via the ubiquitin‒proteasome pathway, whereas hsa_circ_0000479 blocks the binding of G3BP1 to the E3 ligase BTRC. Mechanistic studies suggest that hsa_circ_0000479 promotes GC progression by competitively inhibiting the G3BP1 ubiquitination-mediated degradation facilitated by BTRC. Our results reveal the molecular mechanism by which hsa_circ_0000479 promotes GC progression through BTRC-mediated competitive binding to G3BP1 to inhibit its ubiquitination-mediated degradation, which provides a new theoretical basis for the targeted treatment of GC and elucidates the potential of hsa_circ_0000479-G3BP1-BTRC as a therapeutic target in GC. These findings provide a new direction for the treatment of patients with GC.

RNA modulation in asthma: unraveling the role of splicing and non-coding RNAs in disease pathogenesis

OBJECTIVE

To synthesize the current understanding of RNA-based regulatory mechanisms, focusing on how RNA splicing and non-coding RNAs shape immune responses and airway remodeling in asthma, with the aim of exploring their potential as therapeutic targets for asthma treatment.

DATASOURCE

Recent advances and emerging research in molecular biology and immunology related to RNA splicing, non-coding RNAs (lncRNAs, circRNAs), and N6-methyladenosine (m6A) RNA methylation in asthma pathogenesis.

STUDY SELECTIONS

The review incorporates studies highlighting the roles of alternative RNA splicing, non-coding RNAs (lncRNAs and circRNAs), and RNA methylation (m6A) in regulating immune and inflammatory pathways involved in asthma.

RESULTS

RNA splicing events, non-coding RNAs, and m6A RNA methylation are critical in modulating immune dysregulation, airway remodeling, and inflammation in asthma. These mechanisms influence key inflammatory pathways, mRNA stability, and the overall immune landscape of the disease.

CONCLUSION

RNA splicing and non-coding RNAs represent promising areas of research for understanding asthma's immune pathology and hold potential as novel therapeutic targets for more effective treatment strategies.

Circular RNA ATP9A Stimulates Non-small Cell Lung Cancer Progression via MicroRNA-582-3p/Ribosomal Protein Large P0 Axis and Activating Phosphatidylinositol 3-Kinase/Protein Kinase B Signaling Pathway

Circular RNAs (circRNAs), along with their pathogenic property in non-small cell lung cancer (NSCLC), require comprehensive analyses and explanations. The study is established with the purpose to elucidate the potential molecular mechanism of circATP9A in NSCLC. CircATP9A and microRNA (miR)-582-3p were evaluated by real-time quantitative polymerase chain reaction, and ribosomal protein large P0 (RPLP0), cleaved caspase-3, cleaved Ki-67, epithelial-to-mesenchymal transition (EMT)-associated proteins (N-cadherin and E-cadherin), and core proteins of the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway were by Western blot. The processes of proliferation, apoptosis, migration, and invasion were measured by cell counting kit-8, 5-ethynyl-2'deoxyuridine, flow cytometry, and Transwell. Gene interaction was verified by RNA immunoprecipitation and dual luciferase reporter assay. CircATP9A and RPLP0 were abnormally highly expressed in both NSCLC tissues and cell lines, while miR-582-3p was abnormally low. Knockdown of circATP9A reduced NSCLC proliferation, invasion migration, and EMT and promoted apoptosis. This was further validated in nude mouse xenograft experiments. The inhibitory effect of knockdown of circATP9A on NSCLC was reversed by knockdown of miR-582-3p. In addition, the promoting effect of overexpression of circATP9A on NSCLC was reversed by knockdown of RPLP0. Mechanistically, circATP9A acted as a competitive endogenous RNA, sequestering miR-582-3p away from its target, which in turn modulated the expression of RPLP0. CircATP9A activated the miR-582-3p/RPLP0 axis by regulating the PI3K/Akt pathway in NSCLC cells. CircATP9A stimulates NSCLC progression via miR-582-3p/RPLP0 axis and PI3K/AKT cascade activation.

Emerging roles of exosomal circRNAs in non-small cell lung cancer

Despite the prevalence of non-small cell lung cancer (NSCLC) is high, the limited early detection and management of these tumors are restricted since there is an absence of reliable and precise diagnostic biomarkers and therapeutic targets. Exosomes transport functional molecules for facilitating intercellular communication, especially in the tumor microenvironment, indicating their potential as cancer biomarkers and therapeutic targets. Circular RNA (circRNA), a type of non-coding RNA possessing a covalently closed loop structure, substantial abundance, and tissue-specific expression patterns, is stably enriched in exosomes. In recent years, significant breakthroughs have been made in research on exosomal circRNA in NSCLC. This review briefly introduces the biogenesis, characterizations, and functions of circRNAs and exosomes, and systematically describes the biological functions and mechanisms of exosomal circRNAs in NSCLC. In addition, this study summarizes their role in the progression of NSCLC and discusses their clinical significance as biomarkers and therapeutic targets for NSCLC.

The anti-metastatic effect of elemene in human hepatocellular carcinoma is potentially mediated by inhibiting a novel driver-circBPTF

BACKGROUND

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, with metastasis being one of the primary characteristics. Elemene, a natural product derived from Curcuma wenyujin, has been approved for treating advanced and metastasis HCC patients. However, the molecular mechanism of elemene in HCC is still unclear.

PURPOSE

Dysregulation circular RNA (circRNA) plays a critical role in the progression of HCC. This study aimed to evaluate the anti-HCC mechanism of elemene from circRNA point.

METHODS

Transwell and wound-healing assays were employed to evaluate the function of circBPTF and elemene in vitro. Orthotopic xenograft tumor mouse models were used to explore the metastatic impact of circBPTF in vivo and were evaluated by haematoxylin and eosin (H&E) and immunohistochemistry (IHC). To investigate the effects of elemene on circBPTF, RNA pulldown, western blotting, qPCR, transwell and RNA-seq assays were employed.

RESULTS

In this study, we demonstrated circBPTF (hsa_circ_0045431) was a previously uncharacterized pro-metastatic regulator in HCC, and elemene could significantly inhibit circBPTF expression and reduced lung metastasis. Mechanistically, circBPTF acted as a molecular sponge for miR-548m, thereby consequently upregulated the expression of RNA polymerase III subunit G (POLR3G) and zinc finger and BTB domain containing 41 (ZBTB41) in HCC cells. Additionally, the biosynthesis of circBPTF was further governed by RNA-binding proteins HNRNPC and HNRNPU. Furthermore, elemene suppressed circBPTF/miR-548m, leading to the downregulation of POLR3G via inhibition of HNRNPC.

CONCLUSION

This study elucidated that circBPTF could promote HCC lung metastasis and indicated that the downregulation of circBPTF was an important mechanism underlying the anti-HCC effects of elemene.

Non-coding RNAs in adipose-derived stem cell exosomes: Mechanisms, therapeutic potential, and challenges in wound healing

The treatment of complex wounds presents a significant clinical challenge due to the limited availability of standardized therapeutic options. Adipose-derived stem cell exosomes (ADSC-Exos) are promising for their capabilities to enhance angiogenesis, mitigate oxidative stress, modulate inflammatory pathways, support skin cell regeneration, and promote epithelialization. These exosomes deliver non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, which facilitate collagen remodeling, reduce scar formation, and expedite wound healing. This study reviews the mechanisms, therapeutic roles, and challenges of non-coding RNA-loaded ADSC-Exos in wound healing and identifies critical directions for future research. It aims to provide insights for researchers into the potential mechanisms and clinical applications of ADSC-Exos non-coding RNAs in wound healing.

Collaborative Duality of CircGLIS3(2) RNA and Protein in human Wound Repair

The discovery of an increasing number of translatable circular RNAs (circRNAs) raises the question of whether their coding and non-coding functions can coexist within the same cell. This study profiles the dynamic expression of circRNAs during human skin wound healing. CircGLIS3(2) is identified, a circRNA whose levels transiently rise in dermal fibroblasts of acute wounds and are abnormally overexpressed in keloids, a fibrotic skin condition. Injury signals such as IL-1α, TGF-β, hypoxia, and ER stress induce both expression and cap-independent translation of CircGLIS3(2). The RNA form of CircGLIS3(2) activates fibroblasts into matrix-secreting cells, while its encoded protein promotes cell proliferation, collectively enhancing wound repair. Mechanistically, CircGLIS3(2) RNA stabilizes the cytoplasmic protein PCOLCE, while its protein binds to BTF3 in the nucleus. Both the RNA and protein are essential for wound closure in human and murine models. CircGLIS3(2)'s bifunctional nature expands its functional spectrum, improving cellular adaptability during environmental changes and offering a promising therapeutic target for wound repair and scar reduction.

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

INTRODUCTION

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSION

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

CircPAFAH1B2 induces chondrocytes mitochondrial dysfunction and promotes cartilage degeneration through binding molecular chaperone ClpB

INTRODUCTION

This study explores the role of circPAFAH1B2 in osteoarthritis (OA) by investigating its influence on nuclear-mitochondrial communication, a largely unexplored area in OA progression. By uncovering how circPAFAH1B2 regulates mitochondrial function, the study aims to identify novel therapeutic targets for OA prevention and treatment.

OBJECTIVES

This study aimed to identify the regulatory role of circPAFAH1B2 in nuclear-mitochondrial communication within chondrocytes and cartilage homeostasis.

METHODS

circPAFAH1B2 expression was determined via quantitative real-time polymerase chain reaction (qRT-PCR) and in situ hybridization. RNA pulldown experiments, proteomic analyses, and RNA immunoprecipitation were conducted to identify the downstream targets of circPAFAH1B2. Gain- and loss-of-function assays were performed to evaluate the regulatory roles of circPAFAH1B2 and the molecular chaperone caseinolytic peptidase B protein homolog (ClpB) in mitochondrial function and chondrocyte homeostasis in cartilage. Cross-linking immunoprecipitation and sequencing were performed to identify binding sites between circPAFAH1B2 and ClpB.

RESULTS

circPAFAH1B2 was upregulated in OA and localized to the cytoplasm of chondrocytes. In vivo and in vitro experiments demonstrated that increased levels of circPAFAH1B2 induced mitochondrial dysfunction and promoted cartilage degeneration. Mechanistic investigations revealed that circPAFAH1B2 bound to and restricted the mitochondrial import of the molecular chaperone ClpB, which disaggregates misfolded mitochondrial proteins, stabilizes mitochondrial homeostasis, and maintains chondrocyte homeostasis. We characterized the binding sites of circPAFAH1B2 and ClpB, and demonstrated that mutation of these sites effectively suppressed circPAFAH1B2-mediated OA phenotypes.

CONCLUSIONS

Our findings indicate that circPAFAH1B2 acts as a molecular decoy blocking ClpB mitochondrial translocation, driving mitochondria-dependent cartilage degradation, which may provide novel therapeutic targets for OA.

Degradation of circular RNA by the ribonuclease DIS3

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

The 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.

Extracellular vesicles: messengers of cross-talk between gastric cancer cells and the tumor microenvironment

Gastric cancer is a common malignancy characterized by an insidious onset and high mortality rate. Exosomes, a special type of extracellular vesicle, contain various bioactive molecules and have been found to play crucial roles in maintaining normal physiological functions and homeostasis in the body. Recent research has shown that the contents of exosome play a significant role in the progression and metastasis of gastric cancer through communication and regulatory functions. These mechanisms involve promoting gastric cancer cell proliferation and drug resistance. Additionally, other cells in the gastric cancer microenvironment can regulate the progression of gastric cancer through exosomes. These include exosomes derived from fibroblasts and immune cells, which modulate gastric cancer cells. Therefore, in this review, we provide a brief overview of recent advances in the contents and occurrence mechanisms of exosome. This review specifically focused on the regulatory mechanisms of exosomes derived from gastric cancer and other cellular subtypes in the tumor microenvironment. Subsequently, we summarize the latest research progress on the use of exosomes in liquid biopsy, discussing the potential of gastric cancer exosomes in clinical applications.

Exonic CircGUCY1A2 inhibits pulmonary artery smooth muscle cells phenotypic switching via regulating O-glycosylation of COL3A1 in pulmonary hypertension

Pulmonary hypertension (PH) is a fatal disease characterized by pulmonary vascular remodeling, whose regulatory mechanisms remain unclear. Circular RNAs (circRNAs) are a unique class of RNA molecules produced by covalent linkages via back-splicing of linear RNA and play vital roles in regulating physiological and pathological processes. However, the dysregulation of circRNAs and their underlying mechanisms in PH remain unclear. In this study, we identified and investigated the specific functions of circGUCY1A2 in human pulmonary artery smooth muscle cells (PASMCs). We found that circGUYC1A2 expression was markedly downregulated in human PASMCs exposed to hypoxia. Overexpression of circGUCY1A2 impedes the transition of human PASMCs to a synthetic phenotype in vitro and pulmonary vascular remodeling in vivo. Additionally, through mechanistic exploration, we discovered that circGUCY1A2 hindered its glycosylation and attenuated its stability by interacting with the Ser1132 and Ser1145 sites of COL3A1, thereby affecting the expression of osteopontin (OPN) and inhibiting phenotypic switching in human PASMCs. In conclusion, our study revealed that circGUCY1A2 effectively hindered the transition of human PASMCs to a synthetic phenotype by binding to and regulating the O-glycosylation modification of COL3A1. These results identify circGUCY1A2 as a potential therapeutic target and reveal a novel post-transcriptional regulatory mechanism in PH.

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

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

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.

SRSF4-Associated ca-circFOXP1 Regulates Hypoxia-Induced PASMC Proliferation by the Formation of R Loop With Host Gene

BACKGROUND

Pulmonary hypertension (PH) is a rare and fatal disease, the pathological changes of which include pulmonary arterial smooth muscle cell (PASMC) proliferation, which is the pathological basis of pulmonary vascular remodeling. Studies have demonstrated that chromatin-associated circRNA can regulate a variety of biological processes. However, the role of chromatin-associated circRNA in the proliferation of PH remains largely unexplored. In this study, we aimed to identify the function and mechanism of chromatin-associated circRNA in PASMC proliferation in PH.

METHODS

The role of chromatin-associated circFOXP1 (ca-circFOXP1) was investigated in hypoxic mouse PASMCs and SuHX (Sugen5416+hypoxia) model mice through the use of antisense oligonucleotide knockdown and adeno-associated virus-mediated knockdown. Through bioinformatic sequence alignment, chromatin isolation by RNA purification, Cell Counting Kit 8, 5-ethynyl-2-deoxyuridine, Western blot, and other experiments, the function and mechanism of ca-circFOXP1 were verified.

RESULTS

The expression of ca-circFOXP1 was found to be significantly increased in SuHX model mice and hypoxic mouse PASMCs. Moreover, ca-circFOXP1 was found to regulate the level of the host protein FOXP1 (forkhead box protein 1) through the R loop, thereby influencing the phosphorylation activity of SMAD2 (SMAD family member 2) and, consequently, the proliferation of mouse PASMCs. It is noteworthy that the m6A modification was found to promote the formation of the R loop between ca-circFOXP1 and the host gene FOXP1, thereby regulating the expression of the host protein. Furthermore, we have identified that the splicing factor SRSF4 (serine/arginine rich splicing factor 4) can upregulate the expression of ca-circFOXP1 by splicing exons 6 and 9 of FOXP1 pre-mRNA.

CONCLUSIONS

The results demonstrated that the splicing factor SRSF4 upregulated the expression of ca-circFOXP1, and m6A methylation promoted R-loop formation between ca-circFOXP1 and host genes, regulated the level of host protein FOXP1, and then affected the phosphorylation activity of SMAD2, mediating PASMC proliferation, leading to pulmonary vascular remodeling. These results provide a theoretical basis for further study of the pathological mechanisms of hypoxic PH and may provide certain insights.

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.

EIF4A3-Mediated Biogenesis of CircFADS1 Promotes the Progression of Hepatocellular Carcinoma via Wnt/β-Catenin Pathway

Mounting research indicates that circRNAs are pivotal elements in tumorigenesis and progression. Understanding the mechanisms by which circRNAs function in tumors is crucial for identifying undiscovered diagnostic and treatment targets. This research centers on unraveling the mechanisms by which the novel circRNA, circFADS1, influences hepatocellular carcinoma (HCC) progression. CircFADS1 shows elevated expression in HCC and is linked to unfavorable prognosis. Functionally, circFADS1 overexpression accelerates HCC progression through inducing HCC proliferation and inhibited apoptosis. Mechanistically, RNA-seq analysis demonstrates its connection to the Wnt/β-catenin pathway. Moreover, circFADS1 interacts with GSK3β and promotes its ubiquitination and degradation by recruiting the ubiquitin ligase RNF114 while EIF4A3 facilitates the biogenesis of circFADS1. Additionally, circFADS1 is closely linked to lenvatinib resistance. Overall, this study reveals that circFADS1 regulates GSK3β function, influencing the progression of hepatocellular carcinoma. The EIF4A3/circFADS1/GSK3β/β-catenin axis is discovered to hold promise as a novel therapeutic target for hepatocellular carcinoma, while circFADS1 is also a significant factor in lenvatinib resistance.

CircSATB1 Promotes Colorectal Cancer Liver Metastasis through Facilitating FKBP8 Degradation via RNF25-Mediated Ubiquitination

Colorectal cancer (CRC) is one of the most common cancers worldwide and liver metastasis is the leading reason for its mortality. Circular RNAs (circRNAs) are conclusively associated with the progression of various cancers, rendering the exploration of its specific mechanisms in colorectal cancer liver metastasis(CRLM) highly valuable. Combined with GEO (Gene Expression Omnibus) databases and clinical data in our center, we found that high expression of circSATB1 is closely related to the progression of CRLM. Functionally, circSATB1 could significantly promote the metastatic ability of CRC cells in vitro and in vivo. Mechanistically, circSATB1 facilitated the RNF25-mediated ubiquitylation and degradation of FKBP8, releasing its inhibitory effects on mTOR signaling. In this process, circSATB1 acted as a scaffold for RNF25-FKBP8 complexes. Additionally, circSATB1 could be packaged in exosomes and secreted from the CRC primary tumors into plasma. In conclusion, this study uncovered a new circSATB1 that acts as a potent promoter of CRLM and offers novel insights into the precision therapeutic strategies for CRLM.

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

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

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

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

Hsa_circ_0001944 Regulates FXR/TLR4 Pathway and Ferroptosis to Alleviate Nickel Oxide Nanoparticles-Induced Collagen Formation in LX-2 Cells

Nickel oxide nanoparticles (NiONPs) can induce liver fibrosis, and their mechanism may be related to non-coding RNA, nuclear receptor signal transduction and ferroptosis, but the regulatory relationship between them is not clear. In this study, we aimed to investigate the role of hsa_circ_0001944 in regulating the Farnesol X receptor (FXR)/Toll-like receptor 4 (TLR4) pathway and ferroptosis in NiONPs-induced collagen deposition. We observed decreased FXR expression, increased TLR4 expression and alterations in ferroptosis features in both the rat liver fibrosis and the LX-2 cell collagen deposition model. To investigate the regulatory relationship among FXR, TLR4 and ferroptosis, we treated LX-2 cells with FXR agonist (GW4064), TLR4 inhibitor (TAK-242) and ferroptosis agonist (Erastin) combined with NiONPs. The results showed that TAK-242 alleviated collagen deposition by increasing ferroptosis features. Furthermore, GW4064 reduced the expression of TLR4, increased the ferroptosis features and alleviated collagen deposition. The results indicated that FXR inhibited the expression of TLR4 and enhanced the ferroptosis features, which were involved in the process of collagen deposition in LX-2 cells induced by NiONPs. Subsequently, we predicted that hsa_circ_0001944 might regulate FXR through bioinformatics analysis, and found NiONPs reduced the expression of hsa_circ_0001944 in LX-2 cells. Overexpression of hsa_circ_0001944 increased FXR level, reduced TLR4 level, increased the ferroptosis features and alleviated collagen deposition in LX-2 cells. In summary, we demonstrated that hsa_circ_0001944 regulates the FXR/TLR4 pathway and ferroptosis alleviate collagen formation induced by NiONPs.

Circular RNAs modulate cancer drug resistance: advances and challenges

Acquired drug resistance is a main factor contributing to cancer therapy failure and high cancer mortality, highlighting the necessity to develop novel intervention targets. Circular RNAs (circRNAs), an abundant class of RNA molecules with a closed loop structure, possess characteristics including high stability, which provide unique advantages in clinical application. Growing evidence indicates that aberrantly expressed circRNAs are associated with resistance against various cancer treatments, including targeted therapy, chemotherapy, radiotherapy, and immunotherapy. Therefore, targeting these aberrant circRNAs may offer a strategy to improve the efficiency of cancer therapy. Herein, we present a summary of the most recently studied circRNAs and their regulatory roles on cancer drug resistance. With the advances in artificial intelligence (AI)-based bioinformatics algorithms, circRNAs could emerge as promising biomarkers and intervention targets in cancer therapy.

Circular RNA in liver cancer research: biogenesis, functions, and roles

Liver cancer, characterized by its insidious nature, aggressive invasiveness, and propensity for metastasis, has witnessed a sustained increase in both incidence and mortality rates in recent years, underscoring the urgent need for innovative diagnostic and therapeutic approaches. Emerging research indicates that CircRNAs (circular RNAs) are abundantly and stably present within cells, with their expression levels closely associated with the progression of various malignancies, including hepatocellular carcinoma. In the context of liver cancer progression, circRNAs exhibit promising potential as highly sensitive diagnostic biomarkers, offering novel avenues for early detection, and also function as pivotal regulatory factors within the carcinogenic process. This study endeavors to elucidate the biogenesis, functional roles, and underlying mechanisms of circRNAs in hepatocellular carcinoma, thereby providing a fresh perspective on the pathogenesis of liver cancer and laying a robust foundation for the development of more precise and effective early diagnostic tools and therapeutic strategies.

Advances in RNA therapy for the treatment of autoimmune diseases

Autoimmune diseases (ADs) are a group of complex, chronic conditions characterized by disturbance of immune tolerance, with examples including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and psoriasis. These diseases have unclear pathogenesis, and traditional therapeutic approaches remain limited. However, advances in high-throughput histology technology and scientific discoveries have led to the identification of various pathogenic factors contributing to ADs. Coupled with improvements in RNA nucleic acid-based drug synthesis, design, and delivery, RNA-based therapies have been extensively investigated for their potential in treating ADs. This paper reviews the progress in the use of miRNAs, lncRNAs, circRNAs, siRNAs, antisense oligonucleotides (ASOs), aptamers, mRNAs, and other RNA-based therapies in ADs, focusing on their therapeutic potential and application prospects, providing insights for future research and clinical treatment of autoimmune diseases.

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.

CircRNAs: a novel potential strategy to treat breast cancer

Breast cancer is among the most prevalent malignant tumors worldwide, with triple-negative breast cancer (TNBC) being the most aggressive subtype and lacking effective treatment options. Circular RNAs (circRNAs) are noncoding RNAs that play crucial roles in the development of tumors, including breast cancer. This article examines the progress of research on circRNAs in breast cancer, focusing on four main areas: 1) breast cancer epidemiology, classification, and treatment; 2) the structure, discovery process, characteristics, formation, and functions of circRNAs; 3) the expression, mechanisms, clinical relevance, and recent advances in the study of circRNAs in breast cancer cells and the immune microenvironment, particularly in TNBC; and 4) the challenges and future prospects of the use of circRNAs in BC research.

Sperm-Derived CircRNA-1572 Regulates Embryogenesis and Zygotic Genome Activation by Targeting CCNB2 via Bta-miR-2478-L-2

Sperm non-coding RNAs, including micro RNAs, transfer RNA-derived small RNAs, and long non-coding RNAs, are pivotal in cellular cytoskeletal remodeling, early embryonic development, and offspring phenotypes. Despite the identification of circular RNAs (circRNAs) in mammals, the roles of sperm-derived circRNAs in embryogenesis remain largely unexplored. This study identify circRNA-1572, a sperm-derived circRNA deliver into oocytes during fertilization, through whole-transcriptome sequencing of porcine metaphase II (MII) oocytes, purified mature sperm, and in vitro fertilized pronuclear (PN) embryos. Functional assays confirm circRNA-1572 competitively binds to bta-miR-2478-L-2 through a "sponge" mechanism, regulating the expression of the target gene cyclin B2 (CCNB2). Knockdown (KD) of circRNA-1572 or overexpression of bta-miR-2478-L-2 led to reduce levels of CCNB2 mRNA and protein, along with altered fibrous actin (F-actin) distribution and aberrant chromosomal organization, leading to increase developmental arrest and impair zygotic genome activation (ZGA) during early porcine embryogenesis. Importantly, these phenotypes are rescued upon supplementary mRNA of CCNB2. Moreover, SMART-seq analysis reveals KD of CCNB2 resulted in delayed degradation of maternal transcripts in 2-cell embryos and delayed initiation of ZGA in 4-cell. This study provides novel insights into the molecular regulatory functions of sperm-derived circRNAs in early mammalian embryogenesis and underscores the impact of paternal factors on embryonic development.

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

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

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

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

Blocking ITGA5 potentiates the efficacy of anti-PD-1 therapy on glioblastoma by remodeling tumor-associated macrophages

BACKGROUND

Glioblastoma (GBM) is largely refractory to antibodies against programmed cell death 1 (anti-PD-1) therapy. Fully understanding the cellular heterogeneity and immune adaptations in response to anti-PD-1 therapy is necessary to design more effective immunotherapies for GBM. This study aimed to dissect the molecular mechanisms of specific immunosuppressive subpopulations to drive anti-PD-1 resistance in GBM.

METHODS

We systematically analysed single-cell RNA sequencing and spatial transcriptomics data from GBM tissues receiving anti-PD-1 therapy to characterize the microenvironment alterations. The biological functions of a novel circular RNA (circRNA) were validated both in vitro and in vivo. Mechanically, co-immunoprecipitation, RNA immunoprecipitation and pull-down assays were conducted.

RESULTS

Mesenchymal GBM (MES-GBM) cells, which were associated with a poor prognosis, and secreted phosphoprotein 1 (SPP1)+ myeloid-derived macrophages (SPP1+ MDMs), a unique subpopulation of MDMs with complex functions, preferentially accumulated in non-responders to anti-PD-1 therapy, indicating that MES-GBM cells and SPP1+ MDMs were the main anti-PD-1-resistant cell subpopulations. Functionally, we determined that circular RNA succinate dehydrogenase complex assembly factor 2 (circSDHAF2), which was positively associated with the abundance of these two anti-PD-1-resistant cell subpopulations, facilitated the formation of a regional MES-GBM and SPP1+ MDM cell interaction loop, resulting in a spatially specific adaptive immunosuppressive microenvironment. Mechanically, we found that circSDHAF2 promoted MES-GBM cell formation by stabilizing the integrin alpha 5 (ITGA5) protein through N-glycosylation. Meanwhile, the N-glycosylation of the ITGA5 protein facilitated its translocation into exosomes and subsequent delivery to MDMs to induce the formation of SPP1+ MDMs, which in turn maintained the MES-GBM cell status and induced T-cell dysfunction via the SPP1-ITGA5 pathway, ultimately promoting GBM immune escape. Importantly, our findings demonstrated that antibody-mediated ITGA5 blockade enhanced anti-PD-1-mediated antitumor immunity.

CONCLUSIONS

This work elucidated the potential tissue adaptation mechanism of intratumoral dynamic interactions between MES-GBM cells, MDMs and T cells in anti-PD-1 non-responders and identified the therapeutic potential of targeting ITGA5 to reduce anti-PD-1 resistance in GBM.

Roles of circRNAs in viral pathogenesis

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

Oxidative stress-induced circSOD2 inhibits osteogenesis through sponging miR-29b in metabolic-associated fatty liver disease

BACKGROUND

Metabolic-associated fatty liver disease (MAFLD) is characterized by lipid accumulation in hepatocytes and is closely associated with oxidative stress. Increasing clinical evidence indicates that MAFLD is linked to bone metabolic disorders, including osteoporosis. Recent studies indicate that the expression profiles of liver circular RNAs (circRNAs) are altered in MAFLD. However, the effects of these changes on bone metabolism remain poorly understood.

AIM

To investigate the effects and mechanism of differently expressed circRNAs secreted by the liver on osteogenic differentiation in MAFLD.

METHODS

RNA sequencing was performed to identify highly expressed circRNAs in the liver, validated by quantitative real-time reverse transcription polymerase chain reaction, and localized using fluorescence in situ hybridization (FISH). A mouse model induced by a high-fat diet was used to simulate MAFLD.

RESULTS

CircSOD2 was significantly upregulated in liver tissues and primary hepatocytes from subjects with MAFLD. CircSOD2 was induced by oxidative stress and attenuated by antioxidants in the mouse model. In addition, circSOD2 was delivered from hepatocytes to bone marrow mesenchymal stem cells (BMSCs). Furthermore, circSOD2 inhibited the osteogenic differentiation of BMSCs and in vivo bone formation by sponging miR-29b. Moreover, miR-29b inhibition reversed the stimulatory effect of circSOD2 silencing on osteogenic differentiation of BMSCs and in vivo bone formation. Mechanistically, the interaction between circSOD2 and miR-29b confirmed through a luciferase reporter assay and the co-localization in the cytoplasm evidenced by FISH indicated that circSOD2 acted as a sponge for miR-29b.

CONCLUSION

This study provides a novel mechanism underlying the liver-bone crosstalk, demonstrating that circSOD2 upregulation in hepatocytes, induced by oxidative stress, inhibits osteogenic differentiation of BMSCs by sponging miR-29b. These findings offer a better understanding of the relationship between MAFLD and osteoporosis.

Estimate of circRNAs and microRNAs synergies on clinical advance of psoriasis

BACKGROUND

Noncoding RNAs have recently proven their contributing role in the pathogenesis of numerous diseases. The etiology of psoriasis is still not well defined, and genetic and environmental factors are blamed. We meant to explore the association of circRNAs/microRNAs in psoriasis and inspect their correlation with the clinical features of the disease.

DESIGN AND METHODS

This study included 166 subjects: 83 cases with plaque psoriasis and 83 age- and sex-matched healthy persons as the control group. The expression levels of circRNA000102, circRNA0045272, circRNA0084764, and microRNAs -93,181, 16a, and 21 were estimated by quantitative real-time PCR.

RESULTS

CircRNA0045272 was ten-fold up-regulated, whereas circRNA0084764 and circRNA000102 were about two-fold downregulated in patients vs. control. MicroRNAs -93 and 181 were significantly downregulated in patients vs. control, whereas microRNA -16a and 21 were up-regulated in patients vs. control. CircRNA0045272 was positively correlated with microRNA 181, and circRNA0084764 was positively correlated with microRNA 93 and microRNA 181. CircRNA0045272 had the highest sensitivity (98.8%) and specificity (93.98%), and microRNA-16a had sensitivity (98.80%) with specificity (93.98%).

CONCLUSION

We assume that circRNAs can predict psoriasis occurrence and progression by sponging a set of microRNAs and can modulate several genes that disturb immune cell balance and inflammatory elements in psoriasis.

Chimerism: A whole new perspective in gene regulation

The diversity of molecular entities emerging from a single gene are recognized. Several studies have thus established the cellular role(s) of transcript variants and protein isoforms. A step ahead in challenging the central dogma towards expanding molecular diversity is the identification of fusion genes, chimeric transcripts and chimeric proteins that harbor sequences from more than one gene. The mechanisms for generation of chimeras largely follow similar patterns across all levels of gene regulation but also have interdependence and mutual exclusivity. Whole genome and RNA-seq technologies supported by development of computational algorithms and programs for processing datasets have increasingly enabled the identification of fusion genes and chimeric transcripts, while the discovery of chimeric proteins is as yet more subtle. Earlier thought to be associated with cellular transformation, the contribution of chimeric molecules to normal physiology is also realized and found to influence the expression of their parental genes and regulate cellular pathways. This review offers a collective and comprehensive overview of cellular chimeric entities encompassing the mechanisms involved in their generation, insights on their evolution, functions in gene regulation and their current and novel clinical applications.

Current progress and future perspectives in personal identification of monozygotic twins in forensic medicine

The personal identification of monozygotic (MZ) twins is of great importance in forensic medicine. Due to the extreme similarity in genetic between MZ twins, it is challenging to differentiate them using autosomal STR genotyping. Forensic experts are striving to explore available genetic markers that can differentiate between MZ twins. With the advent of next-generation sequence (NGS), an increasing number of genetic markers have been demonstrated to effectively differentiate between MZ twins. Here, we summarized for the relevant studies on MZ twins' differentiation and discussed the limitations of the underlying markers. In details, single-nucleotide variants (SNVs), copy number variation (CNV), mitochondrial DNA (mtDNA), DNA methylation, and non-coding RNA have been demonstrated considerable value. Furthermore, the utilization of proteomics, metabolomics, and microbiomics has shed light on MZ twin differentiation. Additionally, we introduce the methodologies for MZ differentiation based on external morphological variations observed in the human body. Looking to the future, the process of aging may represent a novel avenue for the differentiation of MZ twins.

Circ-SPATA13 regulates the osteogenic differentiation of human periodontal ligament stem cells through the miR-485-5p_R + 1/BMP7 axis

BACKGROUND

Human periodontal ligament stem cells (PDLSCs) are widely available and have strong osteogenic differentiation ability, which makes them promising tools for bone regeneration. Circular RNAs (circRNAs) play a variety of functions in the process of cell differentiation and are potential therapeutic targets. Here, we identified a new circRNA, circ-SPATA13, and found that it was highly positively correlated with the osteogenic differentiation of PDLSCs. Therefore, in this study, we revealed the significance and mechanism of circ-SPATA13 in the osteogenic differentiation of PDLSCs.

METHODS

PDLSCs were isolated from third molars with incomplete apical development and induced to undergo chondrogenic, adipogenic, or osteogenic differentiation. Surface markers were detected via flow cytometry. Proliferation was assessed with EdU and CCK-8 assays. The circ-SPATA13 and miR-485-5p_R + 1-mediated control of mineral deposition was evaluated through alizarin red and alkaline phosphatase staining. Osteogenesis-related factor expression was detected through western blotting, immunofluorescence, and qRT-PCR. Fluorescence in situ hybridization was used to examine circ-SPATA13 localization within PDLSCs. The relationships among circ-SPATA13, miR-485-5p_R + 1, and BMP7 during PDLSCs osteogenesis were assessed through western blotting, qRT-PCR, dual-luciferase assay, rescue experiment, and bioinformatics approaches.

RESULTS

Primary PDLSCs expressing mesenchymal stem cell surface markers were isolated. Circ-SPATA13 was identified and found to have no impact on PDLSC proliferation, whereas it was a positive regulator of their osteogenic differentiation, a process which was antagonized by miR-485-5p_R + 1. Dual-luciferase reporter assays revealed that circ-SPATA13 was able to function as a molecular sponge to sequester miR-485-5p_R + 1 within PDLSCs, while this miRNA was able to bind to the 3'-UTR of the target mRNA BMP7. In rescue experiments, circ-SPATA13 was confirmed to regulate the osteogenic differentiation of PDLSCs via this miR-485-5p_R + 1/BMP7 axis. Moreover, in vivo experiments in rats demonstrated that the overexpression of circ-SPATA13 in PDLSCs was associated with the promotion of bone formation in a skull defect model system.

CONCLUSION

These data supported the osteogenic functions of circ-SPATA13 in PDLSCs. Mechanistically, this circRNA was found to function as a molecular sponge for miR-485-5p_R + 1, in turn targeting BMP7 to promote the osteogenic differentiation of PDLSCs. This circ-SPATA13/miR-485-5p_R + 1/BMP7 axis may be a novel target for treatments promoting PDLSCs osteogenic differentiation.