Circular RNAs are abundant, conserved, and associated with ALU repeats

EIciRNAs in focus: current understanding and future perspectives

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

Circ-0069561 as a novel diagnostic biomarker for progression of diabetic kidney disease

BACKGROUND

Circular RNAs (circRNAs) are non-coding RNAs that are key regulators of the initiation and progression of various human diseases. However, the role of circRNAs in diabetic kidney disease (DKD) remains unknown.

METHODS

Whole high-throughput RNA sequencing (RNA-seq) was performed on kidney tissues from clinical DKD patients and controls. Circ-0069561 with significantly up-regulated expression level was selected by real-time PCR (RT-PCR) analysis. RT-PCR and fluorescent in situ hybridization (FISH) further validated the expression and subcellular localization of circ-0069561 in type 2 diabetic mice and DKD patients. The clinical significance of circ-0069561 in DKD was evaluated. The circRNA-miRNA-ferroptosis associated mRNA network was constructed. The biological function of circ-0069561 in mouse podocyte clone 5 (MPC5) was analyzed.

RESULTS

The top 10 up-regulated circular RNAs were selected by RT-PCR validation, and the results demonstrated a significant elevation in the expression level of circ-0069561. The RT-PCR and FISH results demonstrated that the expression of circ-0069561 was elevated in renal tissues of type 2 diabetic mice and DKD patients, with a predominant localization in glomerulus. The ROC curves showed that circ-0069561 had a good diagnostic value in massive proteinuria (area under the curve = 0.889). Kaplan-Meier analysis showed that high expression of circ-0069561 was associated with an increased risk of primary endpoints. The circRNA-miRNA-mRNA network indicated that ferroptosis might be involved in the pathogenesis of DKD. In vitro experiments demonstrated that circ-0069561 aggravated glucose-induced podocyte damage and ferroptosis.

CONCLUSION

Circ-0069561 has the potential to be an ideal biomarker and therapeutic target for DKD progression.

CircMYH9 promotes the mRNA stability of SPAG6 by recruiting EIF4A3 to facilitate the progression of breast cancer

The incidence rate of breast cancer (BC) ranks first among female malignant tumors. Late-stage BC patients are at risk of death from distant metastasis. Circular RNAs (circRNAs) play an important function in cancer development. This study looked at the role of circMYH9 in BC. The nude mouse tumor-bearing experiment was used to verify the role of circMYH9 in regulating BC tumor growth in mice. Gene expression and protein amount were tested by qRT-PCR, western blot, and IHC. The pathological changes in tumor tissues were analyzed by HE staining. Cell viability, proliferation, migration, and invasion were assessed using CCK8, colony formation assay, wound healing assay, and Transwell assay, respectively. The interactions between circMYH9, SPAG6, and EIF4A3 were analyzed by RIP assay. CircMYH9 was significantly upregulated in BC, and its upregulated was related to poor prognosis. CircMYH9 silencing markedly impaired BC cell proliferation, migration, and invasion. Mechanistically, circMYH9 promoted the mRNA stability and expression of SPAG6 by recruiting EIF4A3. As expected, SPAG6 overexpression abrogated inhibition mediated by circMYH9 knockdown on BC cell malignant behaviors. In addition, circMYH9 knockdown inhibited PI3K/Akt signal pathway by increasing PTEN expression in BC cells, while was reversed by SPAG6 upregulation. PTEN inhibition abolished inhibition induced by circMYH9 downregulation on BC malignant progression. Moreover, circMYH9 silencing inhibited tumor growth in mice. CircMYH9 overexpression regulated the PTEN/PI3K/AKT pathway by increasing SPAG6 mRNA stability through recruiting EIF4A3, thereby promoting BC malignant progression.

CircFNDC3B inhibits vascular smooth muscle cells proliferation in abdominal aortic aneurysms by targeting the miR-1270/PDCD10 axis

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

Plasma expression level of Hsa_circ_0099734 is associated with atrial fibrillation and its poor prognosis

BACKGROUND

Atrial fibrillation (AF) is a common arrhythmia characterized by severe complications such as stroke, resulting in high disability and mortality rates. A circular RNA (circRNA) hsa_circ_0099734 was found significantly expressed in the atrial tissue of AF patients and controls in our previous work. In this study, we aim to reveal the association between hsa_circ_0099734 and AF as well as its poor prognosis, offering novel perspectives for clinical treatment.

METHODS

A 1:1 matched case-control study was designed to examine the association between hsa_circ_0099734 and AF. A prospective cohort study was conducted to investigate the association between hsa_circ_0099734 and AF prognosis using Cox proportional hazards regression analysis.

RESULTS

An elevated plasma level of hsa_circ_0099734 was an independent risk factor for AF in a multivariable conditional logistic regression model (OR 3.23, 95 % CI: 1.11-9.44; P = 0.032). Regarding the prognostic role of hsa_circ_0099734, the multivariable Cox regression analysis indicated that a high level of hsa_circ_0099734 in plasma was an independent risk factor for stroke in patients with AF (HR 2.87, 95 % CI: 1.90-4.35; P < 0.001), and also an independent risk factor for all-cause mortality in AF patients (HR 3.16, 95 % CI: 2.25-4.45; P < 0.001). Adding hsa_circ_0099734 to the CHA2DS2-VA score provided better reclassification and net clinical benefit than the ABC risk score.

CONCLUSIONS

The plasma level of hsa_circ_0099734 was associated with AF risk and the occurrence of stroke or all-cause mortality in AF patients. Hsa_circ_0099734 has the potential to be a non-invasive biomarker for predicting AF and its poor prognosis.

CircPICALM promotes neonatal acute kidney injury triggered by hypoxia/reoxygenation via sponging microRNA-204-5p

BACKGROUND

Circular RNAs (circRNAs) have been documented to regulate neonatal acute kidney injury (AKI). Based on previous RNA-sequence findings, circPICALM exhibited significantly disparate expression between AKI newborns and Controls. This study aimed to provide further insights into the regulatory mechanism of circPICALM in neonatal AKI.

METHODS

C57BL/6 mice born 7 days were divided into Control group and hypoxia groups (11%O2 and 8%O2 groups). Human tubule epithelial cells (HK-2) were stimulated with hypoxia/reoxygenation (H/R) to establish an AKI cell model. Through overexpression and knockdown techniques, the regulatory role of circPICALM in H/R-induced kidney injury was explored. Inflammatory cytokines, cell apoptosis, and oxidative stress were also detected to confirm the regulatory function of circPICALM in neonatal AKI.

RESULTS

RT-qPCR confirmed that circPICALM was highly expressed in the serum of AKI newborns, neonatal I/R mice and H/R-treated HK-2 cells. Functionally, circPICALM exacerbated H/R-induced HK-2 cell injury by aggravating apoptosis and mitochondrial oxidative stress, increasing the expression of inflammatory factors, including IL-6, IL-1β, and TNF-α. Conversely, inhibition of circPICALM alleviated H/R injury in the HK-2 cell line. The interaction between circPICALM and miR-204-5p was validated through RNA immunoprecipitation and luciferase assay. Finally, circPICALM functioned as a molecular sponge of miR-204-5p and promoted the upregulation of downstream IL-1β expression.

CONCLUSION

CircPICALM plays a critical role in H/R-induced neonatal AKI by sponging miR-204-5p and then activating the downstream IL-1β signaling axis. The inhibition of circPICALM and subsequent suppression of pro-inflammatory factors could serve as a promising biomarker and therapeutic target for early intervention in neonatal AKI.

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.

Identification of biomarkers of male infertility through the circRNA expression profiling of seminal plasma

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

Non-coding RNAs in plant stress responses: molecular insights and agricultural applications

Non-coding RNAs (ncRNAs) have emerged as crucial regulators in plant responses to environmental stress, orchestrating complex networks that finetune gene expression under both abiotic and biotic challenges. To elucidate this intricate ncRNA crosstalk, this review comprehensively summarizes recent advances in understanding the mechanisms of key regulatory ncRNAs including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), tRNA derived fragments (tRFs) and small interfering RNAs (siRNAs) in mediating plant adaptations to stress conditions. We discuss molecular insights into how these ncRNAs modulate stress signalling pathways, control hormonal responses and interact through elaborate crosstalk mechanisms. We also emphasize emerging biotechnological strategies that leverage both innate and artificial ncRNAs as well as potential approaches for finetuning ncRNA levels to engineer stress-resilient crops. Collectively, continued advances in high-throughput sequencing, functional genomics and computational modelling will deepen our understanding of ncRNA network mediated stress responses, ultimately guiding the design of robust climate-resilient crops.

Noncoding RNA gives agency to the molecular and cellular substrates of learning and memory

In the past decade, there has been a virtual explosion in the appreciation and study of noncoding RNA (ncRNA) in the brain. Rapidly emerging evidence suggests that many classes of ncRNA coordinate processes related to learning and memory, achieved via their precise subcellular localisation and interactions with DNA, mRNA and RNA binding proteins. Here we discuss these mechanisms using examples of recently discovered and well-studied ncRNAs, including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs), which are directly involved in regulating experience-dependent neural plasticity.

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

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

ncRNAs as Key Regulators in Gastric Cancer: From Molecular Subtyping to Therapeutic Targets

Gastric cancer (GC) poses a major global health challenge, underscoring the need for advanced diagnostic and therapeutic approaches. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as pivotal regulators in GC, with their dysregulated expression driving key processes such as tumorigenesis, metastasis, immune evasion, and chemoresistance. The functional diversity of ncRNAs across different GC molecular subtypes highlights their potential as biomarkers for improved subtype classification and patient stratification. Beyond their diagnostic value, ncRNAs demonstrate critical regulatory functions in tumor biology, establishing these RNA molecules as promising targets for therapeutic development. Strategies based on RNA hold considerable promise for addressing critical challenges such as immune escape and drug resistance by modulating key signaling pathways. These approaches can enhance immune responses, reprogram the tumor microenvironment, and reverse resistance mechanisms that compromise treatment efficacy, thereby improving clinical outcomes. Although ncRNAs represent a promising frontier in GC precision medicine, further research is required to fully harness their clinical potential.

Nuclear circGUSBP1 promotes cancer stemness via transcriptional coordination with OCT4

AIMS

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

MATERIALS AND METHODS

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

KEY FINDINGS

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

SIGNIFICANCE

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

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, these sites must be in proximity. Inverted repeat sequences, such as Alu elements, if positioned in the upstream and downstream introns, can base pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing approaches, including the recently developed SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) strategy, to characterize secondary and tertiary interactions in the pre-mRNA that govern backsplicing. Our data confirm that the antisense Alu elements AluSz(-) and AluSq2(+), in the upstream and downstream introns, form a highly paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirms that the presence of these elements favors circularization, but with modest predictive power. Together, our study suggests that secondary structure considerations alone do not fully explain backsplicing and that additional interactions are involved.

Novel Truncated Peptide Derived From circCDYL Exacerbates Cardiac Hypertrophy

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Atrial remodelling and atrial fibrillation self-sustaining: the role of circulating circDGCR8

AIMS

The prediction of atrial fibrillation (AF) progression and post-ablation recurrence is currently based on empirical estimates, leading to suboptimal predictive accuracy. This study investigates whether atrial remodelling, a key factor in the severity of atrial cardiomyopathy, could serve as a shared substrate influencing both AF progression and recurrence. We aimed to identify circular RNAs (circRNAs) associated with atrial remodelling and to evaluate their ability to predict AF progression and recurrence.

METHODS AND RESULTS

We assessed the differential expression of plasma circRNAs between paroxysmal (PAF) and persistent AF (PsAF) patients using microarray analysis. Selected candidate circRNAs were validated through qPCR following rigorous statistical and bioinformatics analysis. circDGCR8 was consistently found to be up-regulated in PsAF compared with PAF patients. Additionally, circDGCR8 was significantly up-regulated in human atrial fibroblasts treated with angiotensin II (AngII). Gain- and loss-of-function studies suggested that circDGCR8 could promote atrial remodelling at cellular level by enhancing collagen production and fibroblast proliferation. Overexpression of circDGCR8 in human cardiac fibroblasts significantly altered the gene expression spectrum, impacting pathways including IL-17 signalling and TNF signalling. Moreover, circDGCR8 levels were positively correlated with atrial fibrosis, as indicated by increased percentages of low voltage zones. The predictive value of circDGCR8 was evaluated in two cohorts: (i) PAF patients monitored for 36 months with progression to PsAF as the endpoint, and (ii) AF patients who underwent radiofrequency ablation followed for 12 months to assess recurrence. In both cohorts, higher level of circDGCR8 was associated with increased risks of AF progression and post-ablation recurrence.

CONCLUSION

Our results suggest that circDGCR8, associated with atrial remodelling, holds potential as a predictive biomarker for both AF progression and post-ablation recurrence.

Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene

The scarecrow (scro) gene encodes a fly homolog of mammalian Nkx2.1, which is vital for early fly development and for optic lobe development. Previously, scro was reported to produce a circular RNA in addition to traditional mRNAs. In this study, we report 12 different scro circular RNAs, which are either mono or multiexonic forms. The most abundant ones are circScro(2) carrying the second exon (E2) only and bi-exonic circScro(3,4) having both the third (E3) and fourth exon (E4). Levels of circScro(2) show an age-dependent increase in adult heads, supporting a general trend of high accumulation of circular RNAs in aged fly brains. In silico analysis of the introns flanking circular RNA exons predicts 2 pairs of intronic complementary sequences; 1 pair residing in introns 1 and 2 and the other in introns 2 and 4. The first pair was demonstrated to be essential for the circScro(2) production in cell-based assays; furthermore, deletion of the region including intronic complementary sequence components in the intron-2 reduces in vivo production of both circScro(2) and circScro(3,4) by 80%, indicating them to be essential for the biogenesis of the 2 circular RNAs. Besides the intronic complementary sequence, the intron regions immediately abutting exons seem to be responsible for a basal level of circular RNA formation. Moreover, ectopic intronic complementary sequence derived from the laccase2 locus is comparably effective in circScro production, buttressing the importance of the hairpin loop structure formed by intronic complementary sequence for the biogenesis of circular RNA. Last, overexpressed scro alters outcomes of both linear and circular RNAs from the endogenous scro locus, suggesting that Scro plays a direct or indirect role in regulating the expression levels of either or both forms.

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

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

MEIS1: From functional versatility to post-transcriptional/translational regulation

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

Circular RNAs modulate cell death in cardiovascular diseases

Cardiovascular diseases (CVDs) remain a global health challenge, with programmed cell death (PCD) mechanisms like apoptosis and necroptosis playing key roles in the progression. Circular RNAs (circRNAs) have recently been recognized as crucial regulators of gene expression, especially in modulating PCD. In current researches, circRNA regulation of apoptosis is the most studied area, followed by autophagy and ferroptosis. Notably, the regulatory role of circRNAs in pyroptosis and necroptosis has also begun to attract attention. From a mechanistic perspective, circRNAs influence cellular processes through several modes of action, including miRNA sponging, protein interactions, and polypeptide translation. Manipulating circRNAs and their downstream targets through inhibition or overexpression offers versatile therapeutic options for CVD treatment. Continued investigation into circRNA-mediated mechanisms may enhance our understanding of CVD pathophysiology and underscore their potential as novel and promising therapeutic targets.

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.

The crosstalk between non-coding RNAs and oxidative stress in cancer progression

As living standards elevate, cancers are appearing in growing numbers among younger individuals globally and these risks escalate with advancing years. One of the reasons is that instability in the cancer genome reduces the effectiveness of conventional drug treatments and chemotherapy, compared with more targeted therapies. Previous research has discovered non-coding RNAs' crucial role in shaping genetic networks involved in cancer cell growth and invasion through their influence on messenger RNA production or protein binding. Additionally, the interaction between non-coding RNAs and oxidative stress, a crucial process in cancer advancement, cannot be overlooked. Essentially, oxidative stress results from the negative effects of radicals within the body and ties directly to cancer gene expression and signaling. Therefore, this review focuses on the mechanism between non-coding RNAs and oxidative stress in cancer progression, which is conducive to finding new cancer treatment strategies.

Non-coding RNAs modulate pyroptosis in diabetic cardiomyopathy: A comprehensive review

Diabetic cardiomyopathy (DCM) is a leading cause of heart failure (HF) among individuals with diabetes, presenting a significant medical challenge due to its complex pathophysiology and the lack of targeted therapies. Pyroptosis, a pro-inflammatory form of programmed cell death (PCD), is the predominant mode of cell death in the primary resident cells involved in DCM. It has been reported to be critical in DCM's onset, progression, and pathogenesis. Non-coding RNAs (ncRNAs), diverse transcripts lacking protein-coding potential, are essential for cellular physiology and the progression of various diseases. Increasing evidence indicates that ncRNAs are pivotal in the pathogenesis of DCM by regulating pyroptosis. This observation suggests that targeting the regulation of pyroptosis by ncRNAs may offer a novel therapeutic approach for DCM. However, a comprehensive review of this topic is currently lacking. Our objective is to elucidate the regulatory role of ncRNAs in pyroptosis associated with DCM and to elucidate the relationships among these factors. Additionally, we explored how ncRNAs influence pyroptosis and contribute to the pathophysiology of DCM. By doing so, we aim to identify new research targets for the clinical diagnosis and treatment of DCM.

Circular RNA discovery with emerging sequencing and deep learning technologies

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

Circ_0008440 Inhibits Proliferation and Promotes Apoptosis of Trophoblast Cells through the miR-194-5p/PFKFB2 Axis

Preeclampsia (PE), an idiopathic hypertensive disorder that arises during pregnancy, poses a serious threat to the health of expectant mothers. Human chorionic trophoblast cells (HTR-8/SVneo) are associated with the development of PE. It has been reported that circ_0008440 expression is abnormally increased in the placental tissues of PE patients. However, the function of circ_0008440 within HTR-8/SVneo cells during PE has yet to be fully elucidated. The study used RT-qPCR and western blot assay to evaluate the expression levels of 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 2 (PFKFB2), circ_0008440, and miR-942-5p in PE patients. Cells viability was measured using cell counting kit-8 (CCK-8) assay. Cell cycle assay and 5-ethynyl-2'-deoxyuridine (EDU) assay were used to measure cell proliferation. Cell apoptosis was assessed using flow cytometry assay. Western blot assay was used to detect protein expression. Dual-luciferase reporter assay and RNA pull-down assay were used to assess the interactions among circ_0008440, miR-942-5p, and PFKFB2 in HTR-8/SVneo cells. The study showed that the expression levels of circ_0008440 and PFKFB2 were significantly increased, while the expression of miR-942-5p was significantly decreased in the placental tissues of PE patients. Silencing of circ_0008440 promoted proliferation and tube formation and inhibited apoptosis of HTR-8/SVneo cells. In terms of molecular mechanism, miR-942-5p inhibitor or overexpression of PFKFB2 could partially reverse the effects of circ_0008440 silencing on the biological characteristics of HTR-8/SVneo cells. Collectively, circ_0008440 could act as a sponge of miR-942-5p to regulate the expression of PFKFB2, which further inhibited viability and proliferation of HTR-8/SVneo cells and promoted cell apoptosis.

Coding circular RNA in human cancer

circular RNA (circRNA) is a covalently closed single-stranded RNA that lacks 5' and 3' ends and has long been considered a noncoding RNA. With the development of high-throughput sequencing and bioinformatics technology, the understanding of circRNA has become increasingly advanced. Recent studies have shown that some cytoplasmic circRNAs can be effectively translated into detectable proteins, further indicating the importance of circRNA in cellular pathology and physiological functions. Internal ribosome entry site (IRES) and N6-methyladenosine (m6A) mediated cap-independent translation initiation are considered potential mechanisms of circRNA translation. Multiple circRNAs have been shown to play crucial roles in human cancer. This paper provides an overview of the nature and functions of circRNA and describes the possible mechanisms underlying the initiation of circRNA translation. We summarized the emerging functions of circRNA-encoded proteins in human cancer. Finally, we discuss the therapeutic potential of circRNAs and the challenges of research in this field. This review on circRNA translation will reveal a hidden human proteome and enhance our understanding of the importance of circRNAs in human malignant tumors.

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.

Circular RNAs increase during vascular cell differentiation and are biomarkers for vascular disease

AIMS

The role of circular RNAs (circRNAs) and their regulation in health and disease are poorly understood. Here, we systematically investigated the temporally resolved transcriptomic expression of circRNAs during differentiation of human induced pluripotent stem cells (iPSCs) into vascular endothelial cells (ECs) and smooth muscle cells (SMCs) and explored their potential as biomarkers for human vascular disease.

METHODS AND RESULTS

Using high-throughput RNA sequencing and a de novo circRNA detection pipeline, we quantified the daily levels of 31 369 circRNAs in a 2-week differentiation trajectory from human stem cells to proliferating mesoderm progenitors to quiescent, differentiated EC and SMC. We detected a significant global increase in RNA circularization, with 397 and 214 circRNAs up-regulated greater than two-fold (adjusted P < 0.05) in mature EC and SMC, compared with undifferentiated progenitor cells. This global increase in circRNAs was associated with up-regulation of host genes and their promoters and a parallel down-regulation of splicing factors. Underlying this switch, the proliferation-regulating transcription factor MYC decreased as vascular cells matured, and inhibition of MYC led to down-regulation of splicing factors such as SRSF1 and SRSF2 and changes in vascular circRNA levels. Examining the identified circRNAs in arterial tissue samples and in peripheral blood mononuclear cells (PBMCs) from patients, we found that circRNA levels decreased in atherosclerotic disease, in contrast to their increase during iPSC maturation into EC and SMC. Using machine learning, we determined that a set of circRNAs derived from COL4A1, COL4A2, HSPG2, and YPEL2 discriminated atherosclerotic from healthy tissue with an area under the receiver operating characteristic curve (AUC) of 0.79. circRNAs from HSPG2 and YPEL2 in blood PBMC samples detected atherosclerosis with an AUC of 0.73.

CONCLUSION

Time-resolved transcriptional profiling of linear and circRNA species revealed that circRNAs provide granular molecular information for disease profiling. The identified circRNAs may serve as blood biomarkers for atherosclerotic vascular disease.

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 RNAs in inflammatory bowel disease: a review of mechanisms, biomarkers and therapeutic potential

Inflammatory bowel disease (IBD) is an autoimmune disease of unknown etiology characterized by recurrent chronic inflammation of the gastrointestinal tract. The incidence of IBD is increasing and has become a focus of research on digestive diseases. Despite advances in understanding its multifactorial etiology, including genetic predisposition, microbiome dysbiosis, and immune dysregulation. However, the molecular mechanisms driving IBD pathogenesis remain incompletely elucidated. Circular RNA (circRNA) is a stable single-stranded RNA with a closed-loop structure and conserved nature. circRNA possesses multiple functions, such as adsorption of microRNAs and RNA-binding proteins, and is involved in the regulation of gene splicing and transcription, as well as protein translation. However, circRNAs in IBD progression and their clinical potential as biomarkers or therapeutic targets are yet to be systematically explored. In this review, we comprehensively synthesize recent advancements in circRNA research related to IBD, integrating evidence from in vitro, in vivo, and clinical studies. We systematically analyze aberrant circRNA expression profiles in IBD tissues (e.g., intestinal mucosa, peripheral blood, and exosomes) and discuss their mechanism of action contributions to inflammation, intestinal epithelial barrier dysfunction, autophagy, intestinal fibrosis, and colitis-associated cancer (CAC). Furthermore, we evaluate methodologies for circRNA detection and therapeutic modulation, including RNA interference, viral vector delivery, and PLGA MSs delivery system strategies. This review highlights the potential of circRNA-focused strategies in the diagnosis and treatment of IBD, offering a scientific foundation for advancing precision medicine in IBD management.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Circular PVT1 promotes cardiac fibroblast activation interacting with miR-30a-5p and miR-125b-5p

Circular RNAs (circRNAs) are involved in the pathogenesis of several cardiovascular diseases, including heart failure. In this study, we report that circular PVT1 (circPVT1) was upregulated in the left ventricle of 31 ischemic heart failure patients compared to 11 non-ischemic controls. RNA sequencing analysis following circPVT1 knockdown in immortalized human cardiomyocytes identified differentially expressed genes, mainly involved in fibrosis. Notably, in human cardiac fibroblasts, circPVT1 expression significantly increased after TGF-β1 treatment and circPVT1 silencing attenuated the levels of pro-fibrotic markers induced by TGF-β1. RNA pull-down assays validated the interaction between circPVT1 and two fibrosis-related miRNAs, miR-30a-5p and miR-125b-5p. The levels of these miRNAs were not altered upon circPVT1 knockdown. However, the expression of their mRNA targets was deregulated upon circPVT1 silencing, suggesting that circPVT1 modulates miRNA cellular bioavailability. Accordingly, inhibition of either miR-30a-5p or miR-125b-5p restored the expression of TGF-β1-induced pro-fibrotic markers following circPVT1 silencing, indicating that both miR-30a-5p and miR-125b-5p act as downstream effectors of circPVT1 in cardiac fibroblast activation. In conclusion, these findings highlight a pro-fibrotic role for circPVT1, which can regulate cardiac fibroblast activation interacting with the anti-fibrotic miR-30a-5p and miR-125b-5p. The modulation of circPVT1 expression may represent a potential strategy to reduce cardiac fibrosis and remodeling.

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

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

Advances in the roles and molecular mechanisms of exosomal circular RNAs in regulating the pre-metastatic niche of tumors

Metastasis remains a major cause of morbidity and mortality in patients with malignant tumors. The pre-metastatic niche is a prerequisite for distant metastasis driven by primary tumors. Circular RNAs (circRNAs), a class of single-stranded closed non-coding RNAs, exhibit high stability, evolutionary conservation, and cell-type specificity. Exosomes, as natural carriers of circRNAs, mediate intercellular communication and contribute to the formation of the pre-metastatic niche; however, the mechanisms by which they do so remain incompletely understood. This review summarizes the biological characteristics and functions of exosomal circRNAs and outlines the molecular pathways through which they shape the tumor pre-metastatic microenvironment, with emphasis on immunosuppression, vascular permeability, extracellular matrix remodeling, and lymphangiogenesis. This is the first review to focus on the functional roles and molecular mechanisms of exosomal circRNAs in pre-metastatic niche regulation, providing a basis for the development of therapeutic strategies targeting metastatic progression.

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

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

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

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

Advances in focal segmental glomerulosclerosis research: genetic causes to non-coding RNAs

Focal Segmental Glomerulosclerosis (FSGS) is a clinicopathological illness characterized by podocyte damage, impairing glomerular filtration, and substantial proteinuria, which often results in end-stage renal disease (ESRD). Divided into primary, secondary, genetic, and idiopathic categories, its diverse origin highlights the intricacy of its diagnosis and treatment. The existing dependence on immunosuppressive medicines highlights their side effects and inconsistent efficacy, underscoring the pressing necessity for innovative, focused treatments. Recent advancements in genomics and molecular biology have shown the significant involvement of genetic alterations, especially in podocyte-associated proteins, in the pathogenesis of FSGS. Identifying possible novel biomarkers for diagnosing FSGS and monitoring disease activity has revitalized interest in this condition. Recent data underscores the significance of non-coding RNAs, including microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs), in the modulation of gene expression and podocyte functionality. Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary. Particular dysregulated miRNAs and circRNAs have demonstrated potential as biomarkers for early diagnosis and disease monitoring. Furthermore, understanding lncRNA-mediated pathways provides novel therapeutic targets. This review consolidates current progress in elucidating the genetic and molecular processes of FSGS, emphasizing biomarker identification and treatment innovation.

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.

Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials

Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.

Identification of a circRNA-miRNA-mRNA interactome associated with Parkinson's disease progression

BackgroundCircular RNAs (circRNAs) constitute a distinctive subclass of RNAs that are known for their regulatory roles in fundamental cellular processes. Due to their increased stability and ubiquitous expression, circular RNAs have been widely studied as potential molecular targets in various diseases, including neurodegenerative diseases. While several studies have found differentially expressed circRNAs associated with Parkinson's disease (PD), none has looked specifically into PD progression.ObjectiveTo elucidate the role of circRNAs in the progression of PD by identifying dysregulated circRNAs associated with PD progression and to pinpoint potential downstream miRNAs and associated differentially expressed gene targets.MethodsIn this study, we have utilized large-scale, longitudinal, and deep RNA-seq data from two independent cohorts, namely the Parkinson's Progression Marker Initiative (PPMI) and the Parkinson's Disease Biomarker Program (PDBP), to characterize circRNA expression in patients of early PD stage.ResultsWe identified six circRNAs significantly differentially expressed in whole blood samples obtained from PD patients over time. Additionally, we were able to map a competing endogenous RNA (ceRNA) network with potential downstream miRNA-mRNA targets and, with the help of co-expression analysis, to identify genes associated with PD progression. Our findings provide compelling evidence for a dysregulated circRNA interactome as an indicator of PD progression, with changes in the expression of these circRNAs and downstream gene targets being significantly associated with changes in UPDRS III scores in PD patients.ConclusionsOur results strongly indicate the association of circular RNAs with PD progression and emphasize its significance as a critical molecular marker.

The circular RNA circANK suppresses rice resistance to bacterial blight by inhibiting microRNA398b-mediated defense

Circular RNAs (circRNAs) are prevalent in eukaryotic cells and have been linked to disease progressions. Their unique circular structure and stability make them potential biomarkers and therapeutic targets. Compared with animal models, plant circRNA research is still in its infancy. The lack of effective tools to specifically knock down circRNAs without affecting host gene expression has slowed the progress of plant circRNA research. Here, we have developed a CRISPR-Cas13d tool that can specifically knock down circRNAs in plant systems, successfully achieving the targeted knockdown of circRNAs in rice (Oryza sativa). We further focused on Os-circANK (a circRNA derived from Ankyrin repeat-containing protein), a circRNA differentially expressed in rice upon pathogen infection. Physiological and biochemical experiments revealed that Os-circANK functions as a sponge for miR398b, suppressing the cleavage of Cu/Zn-superoxidase dismutase (CSD)1/CSD2/copper chaperone for superoxide dismutase/superoxidase dismutaseX through competing endogenous RNA, leading to reduced reactive oxygen species levels following Xanthomonas oryzae pv. oryzae (Xoo) infection and a negative regulation of rice resistance to bacterial blight. Our findings indicate Os-circANK inhibits rice resistance to bacterial blight via the microRNA398b(miR398b)/CSD/SOD pathway.

The Role of Ovarian Granulosa Cells Related-ncRNAs in Ovarian Dysfunctions: Mechanism Research and Clinical Exploration

Ovarian dysfunctions, encompassing conditions such as polycystic ovary syndrome (PCOS), premature ovarian failure (POF), premature ovarian insufficiency (POI), and diminished ovarian reserve (DOR), are closely linked to disruptions in follicular development, often tied to granulosa cell (GC) abnormalities. Despite ongoing research, the precise mechanisms underlying these dysfunctions remain elusive. Increasing evidence highlights the pivotal role of non-coding RNAs (ncRNAs) in the pathogenesis of ovarian dysfunctions. As transcripts that do not encode proteins, ncRNAs are capable of regulating gene expression at various levels. They influence GCs by modulating key biological processes including proliferation, apoptosis, autophagy, cell cycle progression, steroidogenesis, mitochondrial function, inflammatory responses, and aging. Disruptions in GC development and function can lead to impaired follicular development, consequently contributing to ovarian dysfunctions. Thus, ncRNAs are likely integral to the regulatory mechanisms underlying these pathologies, exhibiting distinct expression patterns in affected individuals. This review delves into the regulatory roles of ncRNAs in GCs and their implications for ovarian dysfunctions (PCOS, POF, POI, DOR), offering insights into potential biomarkers for ovarian function assessment and novel therapeutic approaches for treating these conditions.

The therapeutic potential of circular RNAs

Over the past decade, research into circular RNA (circRNA) has increased rapidly, and over the past few years, circRNA has emerged as a promising therapeutic platform. The regulatory functions of circRNAs, including their roles in templating protein translation and regulating protein and RNA functions, as well as their unique characteristics, such as increased stability and a favourable immunological profile compared with mRNAs, make them attractive candidates for RNA-based therapies. Here, we describe the properties of circRNAs, their therapeutic potential and technologies for their synthesis. We also discuss the prospects and challenges to be overcome to unlock the full potential of circRNAs as drugs.

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

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

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

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

Expression profiling of circular RNAs in sepsis-induced acute gastrointestinal injury: insights into potential biomarkers and mechanisms

This study aimed to investigate the role of circular RNAs (circRNAs) in sepsis-induced acute gastrointestinal injury (AGI), focusing on their potential as biomarkers and their involvement in disease progression. Peripheral blood samples from 14 patients with sepsis-induced AGI and healthy volunteers were collected. RNA sequencing was performed to profile circRNA and miRNA expression. Differential expression analysis identified key regulatory RNAs. Functional enrichment analysis was conducted to explore biological pathways, and circRNA-miRNA interaction networks were constructed. Significant differences in circRNA and miRNA expression profiles were observed between sepsis-induced AGI patients and healthy controls. Several circRNAs, including hsa_circ_0008381 and hsa_circ_0071375, exhibited stepwise expression increases correlating with AGI severity. Functional enrichment analysis indicated that the host genes of differentially expressed circRNAs are involved in key biological processes like protein ubiquitination, organelle maintenance, and cellular signaling pathways such as mitochondrial biogenesis and lipid metabolism. CircRNA-miRNA interaction networks suggested their role as miRNA sponges, regulating key downstream processes. This study demonstrated the potential of circRNAs as diagnostic biomarkers and therapeutic targets for sepsis-induced AGI. Further research is warranted to validate their clinical utility and unravel their mechanistic roles in AGI progression.

Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications

Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

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

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

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.