Circular RNAs are a large class of animal RNAs with regulatory potency

Comprehensive analysis of circRNAs and lncRNAs involvement in the development of skeletal muscle in myostatin-deficient rabbits

Myostatin (MSTN) protein, lncRNAs, and circRNAs regulate skeletal muscle growth and development. This work aims to compare the expression patterns of circRNAs and lncRNAs in the gluteus maximus tissue of wild-type (WT) and MSTN gene knockout (KO) rabbits. Within the gluteus maximus tissue of three WT and four MSTN KO rabbits, we analyzed the expression profiles of circRNAs and lncRNAs. After identifying the differently expressed RNAs, the biological pathways implicated were ascertained by performing enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). We identified differences in the expression of 251 circRNAs (79 upregulated and 172 downregulated), 176 lncRNAs (53 upregulated and 123 downregulated), and 1178 mRNAs (408 upregulated and 770 downregulated) between WT and MSTN KO rabbits. Target genes were significantly enriched in pathways associated with protein synthesis and catabolism, such as oxidative phosphorylation, ubiquitin-mediated proteolysis, the FoxO signaling pathway, and the pentose phosphate pathway, as identified through GO and KEGG enrichment analyses. The constructed network indicates that a class of circRNAs and lncRNAs is engaged in MSTN-mediated regulation of skeletal muscle development. These findings provide valuable insights for innovative therapeutic, diagnostic, and preventive approaches to muscle disorders.

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.

Comprehensive circRNA expression profile and hub genes screening during human liver development

BACKGROUND

Understanding the expression of non-coding RNA in the liver during embryonic development provides important insights into liver diseases. Therefore, we investigated circular RNA (circRNA) roles in human liver development, an unexplored research domain.

METHODS

Using high-throughput sequencing and bioinformatics, we analysed foetal liver samples across developmental stages (7-20 weeks post-conception). Differentially expressed (DE) genes were identified and subjected to enrichment analysis using Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and Disease Ontology (DO). Modular analysis was performed using the Search Tool for Retrieval of Interacting Genes (STRING), followed by construction of a protein-protein interaction (PPI) network using Cytoscape software. The key genes were screened using Molecular Complex Detection (MCODE). The mRNA levels of hub genes were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR).

RESULTS

There were 645 DE circRNAs and 5,145 DE mRNAs between human livers at the three growth stages (HB, EH, and LH). It was found that the activity of circRNAs was boosted remarkably in the hepatoblastic stage. Enrichment analysis found they mainly involved in nervous system regulation of liver function, embryonic organ development and digestive system development. In addition, DE circRNAs were primarily involved in the PI3K-AKT, MAPK and calcium pathways, potentially contributing to adult liver diseases. Notably, only hsa_circ_001471 and novel_circ_017382 were simultaneously identified at all stages and were persistently downregulated. A co-expression regulatory network involving these circRNAs was established. Three hub genes (LGR5, FOXL1 and RSPO3) were identified from the PPI network of 167 genes and may play key roles in human liver development. The RT-qPCR validation results were in agreement with the sequencing data.

CONCLUSIONS

Our findings provide the first insights into the roles and regulatory networks of circRNAs in human liver development, laying the groundwork for further investigations of molecular and signalling networks.

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.

C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 pathway as a therapeutic target and regulatory mechanism for spinal cord injury

Spinal cord injury involves non-reversible damage to the central nervous system that is characterized by limited regenerative capacity and secondary inflammatory damage. The expression of the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis exhibits significant differences before and after injury. Recent studies have revealed that the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis is closely associated with secondary inflammatory responses and the recruitment of immune cells following spinal cord injury, suggesting that this axis is a novel target and regulatory control point for treatment. This review comprehensively examines the therapeutic strategies targeting the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis, along with the regenerative and repair mechanisms linking the axis to spinal cord injury. Additionally, we summarize the upstream and downstream inflammatory signaling pathways associated with spinal cord injury and the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis. This review primarily elaborates on therapeutic strategies that target the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis and the latest progress of research on antagonistic drugs, along with the approaches used to exploit new therapeutic targets within the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis and the development of targeted drugs. Nevertheless, there are presently no clinical studies relating to spinal cord injury that are focusing on the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis. This review aims to provide new ideas and therapeutic strategies for the future treatment of spinal cord injury.

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.

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

CircRNAs refer to a type of closed circular non-coding RNA without a 5' cap or a 3' poly (A) structure. They are largely distributed in the cytoplasm or localized in exosomes and cannot be easily degraded by RNA exonuclease activity. Their stable expression is broadly observed across eukaryotic species. Insulin resistance (IR) refers to the inability of insulin to exert its normal biological function, as manifested by the impairment of glucose utilization in peripheral tissues (e.g., muscle and fat tissues). IR is a key factor in the pathogenesis of Type 2 diabetes (T2D) and is closely associated with obesity. Recent studies have shown that certain circRNAs play critical roles in obesity-induced diabetes by regulating IR and participating in inflammatory processes. CircRNAs, with their multiple microRNA (miRNA) binding sites, act as miRNA sponges to eliminate the inhibitory actions of miRNAs and up-regulate the expression of target genes. CircRNAs play a significant role in regulating obesity-induced diabetes through their interactions with disease-related miRNAs. In the present study, we explored the biological characteristics of circRNAs and extensively discussed the role of circRNAs in the development of inflammation and IR in adipocytes, highlighting their potential as therapeutic targets for obesity-induced diabetes. Specific circRNAs (e.g., circARF3 and circ-ZNF609) have been identified as key players in modulating IR and inflammatory responses in adipose tissue. CircRNAs are emerging as important regulators of IR and inflammation in adipocytes, with significant potential for therapeutic intervention in obesity-induced diabetes. Further research is needed to elucidate the mechanisms underlying their actions and to explore strategies for targeting circRNAs in clinical applications.

Upregulation of YY1 in M2 macrophages promotes secretion of exosomes containing hsa-circ-0000326 via super-enhancers to facilitate prostate cancer progression

The transcription factor YY1 is significantly upregulated in M2 macrophages, which can facilitate the malignant progression of multiple cancers. However, the precise mechanisms underlying the influence of YY1-high M2 macrophages on prostate cancer (PCa) progression remain elusive. Therefore, this study aims to elucidate the specific mechanisms by which YY1-high M2 macrophages influence PCa progression. Cell proliferation was assessed through colony formation and CCK8 assays. To evaluate cell invasion and migration, Transwell and wound healing assays were utilized. We investigated the effects of exosomes derived from M2 macrophages overexpressing YY1 on PCa cells. Subsequently, circRNA microarrays and qRT-PCR identified a high level of hsa-circ-0000326 in exosomes. Nucleoplasmic isolation, luciferase reporter, RNA-pulldown assays elucidated the functions and downstream targets (miR-338-3p and AR) of hsa-circ-0000326. Chromatin immunoprecipitation sequencing, chromatin conformation capture, qRT-PCR, western blotting, and agarose-electrophoresis assays examined YY1's role in transcribing the hsa-circ-0000326 maternal gene MALAT1 as well as its modulation of QKI expression. Our results demonstrated that the secretion of exosomes enriched with hsa-circ-0000326 by YY1-overexpressing M2 macrophages contributes to PCa metastasis. Hsa-circ-0000326 functions as a competitive endogenous RNA against miR-338-3p to promote androgen receptor levels in PCa cells. Mechanistic investigations revealed that YY1 binds to the super-enhancer region of MALAT1 enhancing transcriptional activity for this gene. Simultaneously, YY1 upregulates QKI expression, facilitating splicing events leading to the formation of hsa-circ-0000326. Inhibiting exosomal hsa-circ-0000326 presents a potential therapeutic approach for treating metastatic PCa.

Profiling of lincRNAs and differential regulatory mechanisms in response to nanoplastic toxicity at environmentally relevant concentrations in Caenorhabditis elegans

Polystyrene nanoplastics (PS-NPs) at environmentally relevant concentrations have been shown to be toxic to living organisms, but the role of long noncoding RNAs (lncRNAs) in their toxicity regulation is not yet clear. Using Caenorhabditis elegans (C. elegans) as a model organism, we investigate the mechanisms and roles of lncRNAs in PS-NPs toxicity at environmentally relevant concentrations. In this study, L1 larvae were exposed to 1-100 µg/L of 50 nm PS-NPs for 72 h, and high-throughput transcriptome sequencing was performed. Exposure to PS-NPs at concentrations of 10 µg/L, which is in the range of environmentally relevant concentrations of nanoplastics, or higher can lead to increased reactive oxygen species (ROS) production and decreased locomotion behavior in C. elegans, yet no significant toxic effects were observed for the leachate. The sequencing results revealed significant changes in G protein-coupled receptors and long intergenic noncoding RNAs (lincRNAs), which warranted further investigation. Additionally, a CRISPR-based knockout (KO) mutant library of C. elegans lincRNAs was employed for in-depth mechanistic studies. The findings indicate that multiple lincRNAs are involved in the regulatory response to the toxic effects of PS-NPs. Compared to wild-type nematodes, linc-7, linc-9, linc-13, linc-21, linc-24, linc-49, linc-61, and linc-169 KO nematodes exhibited increased sensitivity to the toxicity of PS-NPs, while linc-11 and linc-50 nematodes showed resistance. Notably, our results indicate that the transcription process of linc-11, rather than its mature transcripts, played a crucial role in the response to PS-NPs. This is evidenced by the differing phenotypes observed in RNA interference (RNAi) knockdown (KD) and CRISPR KO nematodes following exposure to PS-NPs. Our results suggest that transcriptional regulation involving lncRNAs is integral to the organism's response to PS-NPs.

MeRIP-seq data analysis and validation reveal the regulatory role of m6A modified circRNAs in the apoptosis of secondary hair follicle cells in Inner Mongolia cashmere goats

As a widely epigenetic modification, m6A (N6-methyladenosine, m6A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development, stress response, and innate immunity. In this study, bioinformatics analysis, qRT-PCR identification, FISH subcellular localization, and ceRNA network construction were performed on m6A modified circRNAs regulating the apoptosis of secondary hair follicle cells of Inner Mongolia Albas white cashmere goats based on the skin m6A sequencing data of secondary hair follicles in anagen and catagen. The results showed that 8 m6A modified circRNAs regulating the cell apoptosis of secondary hair follicles, namely circRNA_2130, circRNA_0013, circRNA_1203, circRNA_1462, circRNA_1242, circRNA_2308, circRNA_2654 and circRNA_1442 were identified, and they are respectively derived from ANGEL2, APP, GKAP1, HNRNPC, PTBP3, NUCB1, SNRK and ZNF609 genes. Among them, circRNA_0013, circRNA_1442 and circRNA_1462 were located in the cytoplasm of the secondary hair follicle papilla, while circRNA_1203, circRNA_1242, circRNA_2130, circRNA_2308 and circRNA_2654 were located in the nucleus. There are complex and diverse regulatory relationships among 8 circRNAs, with each circRNA targeting one or more miRNAs, revealing that each m6A circRNA can exert regulatory effects through multiple potential miRNA-mRNA axes, to regulate the apoptosis of secondary hair follicle cells of cashmere goats during the growth cycles. This result provides a direction for further elucidating the regulatory mechanism of m6A modified circRNAs in cashmere growth and exploring biomarkers.

Transcriptome-derived evidence reveals the regulatory network in the skeletal muscle of the fast-growth mstnb-/- male tilapia

Myostatin (Mstn) negatively regulates muscle growth and Mstn deficiency induced "double-skeletal muscle" development in vertebrates, including tilapias. In this study, we performed a transcriptomic analysis of skeletal muscle from both wild-type and mstnb-/- males to investigate the molecular mechanisms underlying skeletal muscle hypertrophy in mstnb-/- mutants. We identified 4697 differentially expressed genes (DEGs), 113 differentially expressed long non-coding RNAs (DE lncRNAs), 211 differentially expressed circular RNAs (DE circRNAs), and 98 differentially expressed microRNAs (DE miRNAs). The DEGs were significantly enriched in proteasome and ubiquitin-mediated proteolysis pathways. Cis- and trans-targeting genes of DE lncRNAs were also notably enriched in the above two pathways. The putative host genes of DE circRNAs linked to myofibrils, contractile fibers, and so on. Additionally, DE miRNAs were associated with ubiquitin-mediated proteolysis and key signaling pathways, including AMPK, FoxO, and mTOR. Furthermore, the core competing endogenous RNA (ceRNA) network was constructed comprising 31 DEGs, 37 DE miRNAs, 14 DE circRNAs, and 45 DE lncRNAs. The key roles of ubiquitin-proteasome system were highlighted in the ceRNA network. Taken together, this study provides a novel perspective on muscle mass increase in Mstn mutants through the repression of protein degradation and facilitates our understanding of the molecular mechanisms of skeletal muscle hypertrophy in fish.

Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis

BACKGROUND

Current experimental data on RNA interactions remain limited, particularly for non-coding RNAs, many of which have only recently been discovered and operate within complex regulatory networks. Researchers often rely on in-silico interaction detection algorithms, such as TargetScan, which are based on biochemical sequence alignment. However, these algorithms have limited performance. RNA-seq expression data can provide valuable insights into regulatory networks, especially for understudied interactions such as circRNA-miRNA-mRNA. By integrating RNA-seq data with prior interaction networks obtained experimentally or through in-silico predictions, researchers can discover novel interactions, validate existing ones, and improve interaction prediction accuracy.

RESULTS

This paper introduces Pi-GMIFS, an extension of the generalized monotone incremental forward stagewise (GMIFS) regression algorithm that incorporates prior knowledge. The algorithm first estimates prior response values through a prior-only regression, interpolates between these prior values and the original data, and then applies the GMIFS method. Our experimental results on circRNA-miRNA-mRNA regulatory interaction networks demonstrate that Pi-GMIFS consistently enhances precision and recall in RNA interaction prediction by leveraging implicit information from bulk RNA-seq expression data, outperforming the initial prior knowledge.

CONCLUSION

Pi-GMIFS is a robust algorithm for inferring acyclic interaction networks when the variable ordering is known. Its effectiveness was confirmed through extensive experimental validation. We proved that RNA-seq data of a representative size help infer previously unknown interactions available in TarBase v9 and improve the quality of circRNA disease annotation.

Circular RNAs inducing the osteogenic differentiation of dental mesenchymal stem cells via microRNA sponging

Circular RNAs (circRNAs) are a distinct type of nonlinear and noncoding RNAs endogenously expressed by pre-mRNA back-splicing and crucial in transcriptional and posttranscriptional regulation. CircRNAs can regulate cellular and molecular pathways through various mechanisms, such as microRNA sponging. Numerous studies have indicated the regulatory roles of circRNAs in the osteogenic differentiation of stem cells (SCs) isolated from different sources. Dental tissue-derived mesenchymal SCs (MSCs) have received considerable attention in artificial bone engineering, in which SCs are used to manufacture functional bone tissues to repair bone defects. Recently, studies have reported the regulatory roles of circRNAs in the osteogenic differentiation of dental-derived MSCs, such as apical papillae, dental pulp, and dental follicle SCs. This review aimed to discuss the findings of studies evaluating the contribution of circRNAs to the osteogenic differentiation of dental-derived MSCs.

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.

Prognostic value of circ_0000043/miR-590-5p in cervical cancer and regulation of tumor progression

OBJECTIVE

To investigate the prognostic value of circ_0000043 in cervical cancer (CC) and its involvement in the modulation of patients' prognostic progression.

METHODS

Clinical data of 136 CC patients were included, postoperative CC and adjacent normal tissues were stored at -80 °C, and patients were followed up for 5 years for prognosis. RT-qPCR detected circ_ 0000043 and miR-590-5p expression, Kaplan-Meier curves recorded for prognostic survival, multivariate cox analysis of patients' prognostic risk factors. Moreover, CCK8 assessed cell proliferation, Transwell detected migration and invasion. Dual luciferase reporter assay and RIP examined the interactions between circ_ 0000043 and miR-590-5p.

RESULTS

circ_ 0000043 was down-regulated in CC patients, and patients with low expression of circ_ 0000043 had worse survival. Low expression of circ_0000043, lymph node metastasis, and FIGO were all unfavorable factors threatening the prognosis of CC. circ_0000043 overexpression markedly inhibited the proliferation, migration, and invasion of cancer cells. miR-590-5p is a direct target miRNA of circ_0000043. miR-590-5p mimic prominently resisted the altered cellular functions induced by circ_0000043.

CONCLUSION

Patients with low circ_0000043 expression have poor prognosis as it fuels CC progression by boosting cancer cell proliferation, migration, and invasion via miR-590-5p. Our study provides new ideas for the prognosis and treatment of CC.

*Mechanisms of circular RNA in drug resistance of lung cancer: therapeutic targets, biomarkers, and future research directions

Lung cancer is one of the most prevalent malignant tumors globally, posing significant challenges to treatment outcomes. Circular RNAs (circRNAs), a novel class of non-coding RNAs, have emerged as crucial regulators in cancer biology, influencing drug resistance, progression, and prognosis. Due to their closed-loop structure, circRNAs demonstrate high stability and resistance to degradation, making them promising diagnostic and therapeutic targets. Here we summarize the mechanisms by which circRNAs mediate drug resistance in lung cancer, focusing on their roles in chemotherapy, targeted therapies, and immunotherapy. We highlight how circRNAs interact with microRNAs (miRNAs) and proteins to regulate signaling pathways and alter drug sensitivity. Additionally, circRNA expression patterns hold potential as biomarkers for predicting treatment response. By synthesizing the latest research, we offer new insights into circRNA functions and suggest future directions for overcoming drug resistance in lung cancer.

Integrated omics reveal the mechanisms underlying softening and aroma changes in pear during postharvest storage and the role of melatonin

BACKGROUND

Pyrus ussuriensis Maxim. are rich in nutrients, with a pleasant aroma and postharvest softening properties. Postharvest softening influences shelf life of fruit and fruit quality. Melatonin is a natural and safe preservative, which can effectively maintain fruit quality after harvesting, and delay softening of fruit. The aim of study was to elucidate mechanism of pear fruit softening and fruit aroma during postharvest storage and effect of melatonin.

RESULTS

Ethylene production rate, respiration rate, weight loss of fruit, soluble solid content, titratable acidity were assessed, and transmission electron microscopy, metabolite profiling, and whole-transcriptome RNA-sequencing were performed. Four important pathways that pentose and glucuronate interconversion, galactose metabolism, sphingolipid metabolism and the starch and sucrose metabolism pathway were involved in pear fruit softening. Ethylene production pathway-related genes, such as ACS and ACO were involved in pear fruit softening and expression of that under exogenous melatonin treatment were slightly inhibited. Fruit aroma changed after storage mainly through lipoxygenase pathway under ddH2O treatment and exogenous melatonin treatment changed composition of volatile organic compounds. CeRNA networks associated with pear softening and aroma were established. Mdm-miR159a, mdm-miR396a/b-p3 and mdm-miR408a were found to modulate both fruit softening and aroma formation through ceRNA analysis. Mdm-miR10988-p3 was functionally diverse and as major regulatory components in ceRNA network.

CONCLUSIONS

This study indicated that degradation of cell wall caused pear fruit softening, lipoxygenase pathway mainly affected change of fruit aroma during postharvest storage and exogenous melatonin treatment could improve fruit firmness after storage and alter pear's aroma. The mechanism underlying these effects was elucidated, providing theoretical basis for study of pear fruit softening and preservation technology.

Designer circRNAGFP reduces GFP-abundance in Arabidopsis protoplasts in a sequence-specific manner, independent of RNAi pathways

KEY MESSAGE

We demonstrate non-immunogenic circRNA as a tool for targeted gene regulation in plants, where it acts in an isoform- and sequence-specific manner, enabling future agronomic applications. Circular RNAs (circRNAs) are single-stranded RNA molecules characterized by their covalently closed structure and are emerging as key regulators of cellular processes in mammals, including gene expression, protein function and immune responses. Recent evidence suggests that circRNAs also play significant roles in plants, influencing development, nutrition, biotic stress resistance, and abiotic stress tolerance. However, the potential of circRNAs to modulate target protein abundance in plants remains largely unexplored. In this study, we investigated the potential of designer circRNAs to modulate target protein abundance in plants using Arabidopsis protoplasts as a model system. We show that PEG-mediated transfection with a 50-nt circRNAGFP containing a 30-nt GFP-antisense sequence results in a dose- and sequence-dependent reduction of GFP reporter target protein abundance. Notably, a single-stranded open isoform of circRNAGFP had little effect on protein abundance, indicating the importance of the closed circular structure. Additionally, circRNAGFP also reduced GFP abundance in Arabidopsis mutants defective in RNA interference (RNAi), suggesting that circRNA activity is independent of the RNAi pathway. We also show that circRNA, unlike dsRNA, does not induce pattern-triggered immunity (PTI) in plants. Findings of this proof-of-principle study together are crucial first steps in understanding the potential of circRNAs as versatile tools for modulating gene expression and offer exciting prospects for their application in agronomy, particularly for enhancing crop traits through metabolic pathway manipulation.

hsa_circRNA_092488 Exacerbates the Progression of Deep Vein Thrombosis Through the NLRP3/NF-κB Signaling Pathway

Objective

Deep vein thrombosis (DVT) is a vascular disorder with an incidence rate of about 0.1%. Endothelial progenitor cells (EPCs) are precursor cells of endothelial cells and contribute to vascular repair and regeneration. Circular RNA (circRNA) has become a new focus of research as circRNAs are involved in various biological processes including the progression of DVT. This study explored the upregulation of hsa_circRNA_092488 in DVT patients.

Materials and Methods

The expression of hsa_circRNA_092488 was evaluated in venous blood samples obtained from DVT patients (n=42) and healthy controls (n=42). Gain- and loss-of-function studies of hsa_circRNA_092488 were carried out. The expression levels of related RNAs and proteins were examined by quantitative real-time reverse-transcription polymerase chain reaction, western blotting and immunofluorescence assays. The proliferation, migration, cell cycle progression, and apoptosis of transfected cells were measured by CCK-8 assay, transwell assay, and flow cytometry. The association of hsa_circRNA_092488 and NOD-like receptor protein 3 (NLRP3) in EPCs was revealed using RNA pull-down analysis. Furthermore, the stability of NLRP3 mRNA was examined in transfected EPCs.

Results

Upregulation of hsa_circRNA_092488 was detected in blood samples from DVT patients and it had the ability to suppress the proliferation and migration of EPCs, induce cell cycle arrest from the S to the G0/G1 phase, and trigger cellular apoptosis. Furthermore, NLRP3 was identified as the potential downstream target molecule of hsa_circRNA_092488 and it could exert its regulatory functions by activating the NLRP3/nuclear factor (NF)-κB signaling pathway. Overexpression of hsa_circRNA_092488 in cells notably elevated the protein expression of caspase-1, interleukin-1β, P-NF-κB-p65/NF-κB-p65, and P-IκBα/IκBα, while knockdown of hsa_circRNA_092488 significantly reduced the levels of those proteins in EPCs.

Conclusion

hsa_circRNA_092488/NLRP3/NF-κB signaling could be a novel therapeutic candidate for the treatment of DVT.

Circular RNA-OGDH Promotes PANoptosis in Diabetic Cardiomyopathy: A Novel Mechanistic Insight

Diabetic cardiomyopathy (DCM) is a myocardial structural and functional abnormality directly caused by diabetes and is a principal factor in the development of cardiovascular complications in patients with diabetes. The study aims to investigate the role of circOGDH in the development of DCM and elucidate its precise underlying mechanisms. We established two well-characterised diabetic mouse models, C57BL/6J and db/db, and assessed cardiac function by serum lactate dehydrogenase activity assay and echocardiography, as well as quantitative histological analyses of the extent of myocardial fibrosis in combination with HE staining and Masson trichrome staining. The results demonstrated that there was a significant upregulation of circOGDH expression levels in myocardial tissues of mice in a diabetic state, accompanied by increased expression of key effector proteins of PANoptosis. It is noteworthy that the knockdown of circOGDH led to a substantial enhancement in cardiac function indices, a reduction in the area of myocardial fibrosis, and the effective inhibition of the PANoptosis process in myocardial tissues. In the H9c2 cells model, silencing of circOGDH also exhibited significant protective effects, including increased cell survival, reduced levels of oxidative stress, decreased apoptosis, and suppressed expression of PANoptosis-related proteins. Subsequent employing RNA pull-down, RNA immunoprecipitation and co-immunoprecipitation experimental methods have elucidated, for the first time, the molecular mechanism by which circOGDH specifically targets and regulates RIPK3 through the HMGB1 signalling pathway. The present study definitively demonstrated that up-regulation of circOGDH expression in a diabetic state could exacerbate pathological damage in diabetic cardiomyopathy by activating the HMGB1/RIPK3 signalling pathway.

Circ 0020938 inhibits hair follicle stem cells proliferation via the miR-142-5p/DSG4 axis in cashmere goats

BACKGROUND

Shaanbei white cashmere goat is an excellent cashmere goat breed, and its market favored cashmere from the secondary hair follicles. Hair follicles mature around birth and each hair follicle repeatedly undergoes a growth cycle that comprises three distinct stages: anagen, catagen and telogen. Understanding the molecular mechanisms controlling cyclic hair follicle changes is essential for optimizing hair follicle function and improving cashmere production.

METHODS

The circRNA expression profile in the hair follicle cycle was constructed and differentially expressed circRNAs were identified, with particular focus on circ 0020938, which was highly expressed during anagen. The functional assays were performed to assess the effect of circ 0020938 on hair follicle stem cells (HFSCs) proliferation. Competing endogenous RNA (ceRNA) network was constructed to investigate the interaction between circ 0020938, miR-142-5p, and DSG4. Rescue experiment was conducted to validate the impact of circ 0020938 on HFSCs proliferation and DSG4 expression.

RESULTS

We found that circ 0020938 inhibited HFSCs proliferation. Further analysis revealed that circ 0020938 acted as a sponge for miR-142-5p, alleviating the repression of DSG4. Additionally, we confirmed that DSG4 inhibited HFSCs proliferation, suggesting that it play a key role in regulating the balance between proliferation and differentiation during the hair follicle cycle. Rescue experiments showed that the inhibition of HFSCs proliferation by circ 0020938 was partially reversed by miR-142-5p.

CONCLUSION

Our study provides novel insights into the regulatory role of circRNA in HFSCs proliferation during the hair follicle cycle. The results demonstrate that circ 0020938 acts as a miRNA sponge and inhibits HFSCs proliferation through the miR-142-5p/DSG4 axis, thereby contributing to the proper progression of the hair follicle cycle.

Circular RNA and Neuropsychiatric Practice: A Scoping Review of the Literature and Discussion of Unmet Clinical Needs

Circular RNA (circRNA) is a recently characterized species of RNA that is highly enriched in the human brain, differentially expressed in neuropsychiatric disorders, and readily detectable in the peripheral circulation. These characteristics make circRNA an attractive candidate biomarker for neuropsychiatric illness and suggest it as a potential missing link in the understanding of the specific biological underpinnings of neuropsychiatric illness. In this scoping review, the authors summarize the literature on circRNA in neuropsychiatric disorders and add clinical context. The authors searched PubMed, PsycInfo, Embase, the Cochrane Database of Systematic Reviews, and the Cochrane Central Register of Controlled Trials for articles describing research on circRNA and mental disorders published in or after 2012. The authors included peer-reviewed studies with substantive discussions of circRNA and mental disorders that included human participants or cell lines. Only studies written in English or with English translations were considered. Seventy-eight studies met the authors' inclusion criteria. Common and serious neuropsychiatric illnesses were well represented among these studies, including schizophrenia, major depressive disorder, and major neurocognitive disorder. Many studies identified altered circRNA levels in peripheral blood and specific brain regions that were both sensitive to and specific for neuropsychiatric disorders. Few studies discussed the role that circRNA-based diagnostic tests might play in clinical practice, and research on prognostic, therapeutic, or monitoring biomarkers was limited. Although circRNAs have the potential to change the understanding and treatment of neuropsychiatric disorders, the research field would benefit from more clinician involvement in this area to identify and address urgent clinical needs.

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

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

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

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

The Role of Hsa_circ_0087862/miR-149-5p/TRAF6 Regulatory Axis in Colorectal Cancer Progression

Circular RNAs (circRNAs) have been reported to be associated with the progression of various tumors including colorectal cancer (CRC). However, the role and underlying mechanism of hsa_circ_0087862 in CRC remains unclear. Hsa_circ_0087862 expression in CRC tissues was analyzed using two GEO datasets (GSE138589 and GSE126094). Expression of hsa_circ_0087862, miR-149-5p and tumor necrosis factor receptor-associated factor 6 (TRAF6) in CRC cells was detected. The subcellular distribution of hsa_circ_0087862 was analyzed using a Cytoplasmic & Nuclear RNA Purification Kit. The function of hsa_circ_0087862 in CRC cells was detected using CCK-8, Transwell invasion assay, flow cytometry analysis, and Caspase-3 activity assay. The relationships between hsa_circ_0087862, miR-149-5p and TRAF6 were detected using luciferase reporter assay, RIP, or biotinylated RNA pull-down assay. Hsa_circ_0087862 was upregulated in CRC tissues and cells. Hsa_circ_0087862 is resistant to RNase R digestion and predominantly localized in the cytoplasm. Interference with hsa_circ_0087862 inhibited the malignant phenotypes of CRC cells by reducing cell proliferation and invasive abilities and triggering apoptosis. Hsa_circ_0087862 silencing inhibited TRAF6 expression by sponging miR-149-5p in CRC cells. Inhibition of miR-149-5p attenuated the effects of hsa_circ_0087862 on the malignant phenotypes of CRC cells. TRAF6 overexpression abolished the effects of miR-149-5p on cell growth, invasion and apoptosis in CRC cells. In conclusion, hsa_circ_0087862 silencing inhibited the malignant behaviors of CRC cells through inhibiting TRAF6 expression by sponging miR-149-5p.

Multi-omics integration identifies NK cell-mediated cytotoxicity as a therapeutic target in systemic lupus erythematosus

Background

Systemic lupus erythematosus (SLE) is an autoimmune condition that impacts various organs. Given the intricate clinical progression of SLE, it is imperative to explore novel avenues for precise diagnosis and treatment.

Methods

Peripheral blood mononuclear cells (PBMC) were isolated from 6 SLE patients before and after treatment, 7 healthy controls and 7 disease controls. Assay for Transposase Accessible Chromatin with high throughput Sequencing (ATAC-seq) was used to analyze the chromatin accessibility signatures and RNA-seq was used to identify the differentially expressed genes, mRNA, lncRNA, circRNA, miRNA. Then ATAC-seq and RNA-seq were integrated to further analyze hub genes and pathways. Finally, we validated gene expression levels and examined changes in key genes after treatment through in vitro experiments.

Results

Our analysis reveals dynamic changes in chromatin accessibility during the course of disease progression in SLE. Significantly higher numbers of differentially accessible regions, transcripts, genes, mRNA, lncRNA, circRNA, and miRNA were observed in SLE patients compared to other cohorts, with these variances markedly reduced post-treatment. Two gene clusters associated with SLE disease improvement were identified, with a total of 140 genes intersecting with ATAC results. Pathway analysis revealed that NK cell mediated cytotoxicity was the most differentiated and therapeutically altered pathway in SLE patients. Independent sample validation confirmed that the gene expression of this pathway was reduced in SLE patients and associated with disease activity, whereas hydroxychloroquine (HCQ) effectively elevated their expression in vitro.

Conclusion

Our findings suggest that these NK cell signature genes may be associated with the complex pathogenesis of SLE. The restoration of NK cell-mediated cytotoxicity may serve as a useful marker of improvement following SLE treatment.

Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation

Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. Its role in the transdifferentiation of prostate and lung adenocarcinoma into neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC) remains unexplored. Here, we identified circRMST as an exceptionally abundant circRNA predominantly expressed in NEPC and SCLC, with strong conservation between humans and mice. Functional studies using shRNA, siRNA, CRISPR-Cas13, and Cas9 consistently demonstrate that circRMST is essential for tumor growth and the expression of ASCL1, a master regulator of neuroendocrine fate. Genetic knockout of Rmst in NEPC genetic engineered mouse models prevents neuroendocrine transdifferentiation, maintaining tumors in an adenocarcinoma state. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, collectively leading to the loss of ASCL1 transcription.

Tear fluid derived extracellular vesicles for new biomarker discovery

Various cell types release extracellular vesicles (EVs) containing proteins, DNA, and RNA essential for intercellular communication. The bioactive molecules from EVs can reflect disease status and monitor progression, while their communication abilities suggest therapeutic potential. We will review various EV isolation methods, EV-enriched fluids, and studies analyzing differential mi-RNA and protein levels extracted from EVs. Specifically, tear-derived EVs, which protect their molecular content and allow for real-time monitoring of ocular conditions such as Dry Eye Disease (DED), Sjögren's disease (SJD), Ocular graft-versus-host disease (oGVHD), and Diabetic Retinopathy (DR), which all currently remain undiagnosed in patients. EVs also provide potential as carriers for gene transfer, and mesenchymal stem cell (MSCs)-derived EVs are shown to be immunomodulatory, demonstrating promise for autoimmune ocular diseases. Through the multi-omic analysis of tear-fluid content, EVs are promising biomarkers and therapeutic agents in ocular diseases.

Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation

miRNA arm switching is a pivotal regulatory mechanism that allows organisms to fine-tune gene expression by selectively utilizing either the 5p or 3p strand of a miRNA duplex. This process, conserved across species, facilitates adaptive responses to developmental cues, environmental changes, and disease states. By dynamically altering strand selection, arm switching reshapes gene regulatory networks, contributing to phenotypic diversity and evolutionary innovation. Despite its growing recognition, the mechanisms driving arm switching-such as thermodynamic properties and enzyme-mediated processing-remain incompletely understood. This review synthesizes current findings, highlighting arm switching as a highly conserved mechanism with profound implications for the evolution of regulatory networks. We explore how this phenomenon expands miRNA functionality, drives phenotypic plasticity, and co-evolves with miRNA gene duplications to fuel the diversification of biological functions across taxa.

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

In addition to being a major source of animal protein, pigs are an important model for studying development and diseases in humans. Over the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, multi-omics databases specifically designed for pig functional genomics research are still limited. Here, we present PIGOME, a user-friendly database of pig multi-omes. PIGOME currently contains seven types of pig omics datasets, including whole-genome sequencing (WGS), RNA sequencing (RNA-seq), microRNA sequencing (miRNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), bisulfite sequencing (BS-seq), and methylated RNA immunoprecipitation sequencing (MeRIP-seq), from 6901 samples and 392 projects with manually curated metadata, integrated gene annotation, and quantitative trait locus information. Furthermore, various "Explore" and "Browse" functions have been established to provide user-friendly access to omics information. PIGOME implements several tools to visualize genomic variants, gene expression, and epigenetic signals of a given gene in the pig genome, enabling efficient exploration of spatiotemporal gene expression/epigenetic patterns, functions, regulatory mechanisms, and associated economic traits. Collectively, PIGOME provides valuable resources for pig breeding and is helpful for human biomedical research. PIGOME is available at https://pigome.com.

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.

Development of Mathematical Models Using circRNA Combinations (circTulp4, circSlc8a1, and circStrn3) in Mouse Brain Tissue for Postmortem Interval Estimation

The postmortem interval (PMI) is defined as the time interval between physiological death and the examination of the corpse, playing a critical role in forensic investigations. Traditional PMI estimation methods are often influenced by subjective and environmental factors. Circular RNAs (circRNAs), known for their stability, abundance, and conservation in brain tissue, show promise as biomarkers for PMI estimation. However, research on circRNAs in this context remains limited. This study aimed to develop PMI estimation models using circRNAs across multiple temperatures. By employing semi-quantitative reverse transcription-PCR, circTulp4, circSlc8a1, and circStrn3 were identified as reliable biomarkers for mouse brain tissue. Mathematical models were constructed using the reference genes 28S rRNA, mt-co1, and circCDR1as. At 4 °C, most equations had p-values below 0.05, with the equation using circSlc8a1 as a marker exhibiting the highest goodness of fit. Validation results indicated that the equation using circTulp4 as the reference gene had the highest accuracy. When applying the combined aforementioned three circRNAs, the equation using circCDR1as as the reference gene showed better accuracy. At 25 °C, all equations had R2 values greater than 0.86, but most cubic equations had p-values above 0.05. Validation results demonstrated that the circTulp4/mt-co1 equation had the highest accuracy. When applying combined circRNAs, the R2 values improved, and long-term PMI estimation was more accurate than short-term PMI estimation. At 35 °C, the linear equations had significantly poorer goodness of fit compared to nonlinear equations, and nonlinear equations exhibited better accuracy than linear equations. When applying the combined aforementioned three circRNAs, the accuracy of the three reference genes was similar, and the accuracy of long-term PMI estimation was consistently higher than that of short-term estimation. For the three-dimensional models, all R2 values exceeded 0.75 with p-values significantly below 0.0001. Validation results demonstrated higher accuracy at 25 °C and 35 °C, with superior performance for long-term PMI estimation. In summary, this study constructed PMI estimation models under multiple temperature conditions based on highly expressed circRNAs in mouse brain tissue, highlighting circTulp4, circSlc8a1, and circStrn3 as novel biomarkers. These findings offer a complementary tool for PMI estimation, particularly for long-term PMI estimation.

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 review and in silico analysis of the role of noncoding RNAs in retinoblastoma: A step-toward ncRNA precision

Noncoding RNAs (ncRNAs) have greatly revolutionized our understanding of gene regulation and its main role in oncogenesis, particularly in retinoblastoma (RB), the most prevalent type of intraocular malignancy in children. Despite recent significant therapeutic advances, the prognosis for RB remains unclear owing to late diagnosis and resistance to conventional treatments. This review comprehensively explores the multiple roles of ncRNAs-microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and PIWI-interacting RNAs (piRNAs)-in RB pathogenesis. miRNA dysregulation serves as the initial cascade for modulating cell proliferation, apoptosis, and metastasis. Similarly, lncRNAs demonstrate dual behavior, functioning either as oncogenic drivers or tumor suppressors by interacting with several molecular targets and interacting with different signaling pathways, such as the PI3K/Akt and Wnt/β-catenin pathways. Additionally, circRNAs, owing to their persistent stability and unique ability to act as miRNA sponge main binding sites, affect various normal physiological processes, influencing tumor progression and chemoresistance. Emerging data also highlight the intricate crosstalk between piRNAs and other ncRNAs in retinal homeostasis and oncogenesis, with promising future implications for their utility as diagnostic biomarkers in liquid biopsy types. This comprehensive review consolidates the latest knowledge on the molecular mechanisms of noncoding RNAs (ncRNAs) in retinoblastoma (RB), along with in silico analysis of ncRNA-gene interactions, providing a guide for precision medical approaches. However, future research should aim to utilize ncRNAs as a vital clinical tool to improve the early diagnosis, prognosis, and targeted treatment of RB.

Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA

MOTIVATION

Cancer is the second leading cause of death worldwide, and although there have been advances in treatments, including immunotherapies, these often require biopsies which can be costly and invasive to obtain. Due to lack of pre-emptive cancer detection methods, many cases of cancer are detected at a late stage when the definitive symptoms appear. Plasma samples are relatively easy to obtain, and they can be used to monitor the molecular signatures of ongoing processes in the body. Profiling cell-free DNA is a popular method for monitoring cancer, but only a few studies have explored the use of cell-free RNA (cfRNA), which shows the recent footprint of systemic transcription.

RESULTS

Here, we developed FastNeo, a computational method for detecting known neoepitopes in human cfRNA. We show that neoepitopes and other biomarkers detected in cfRNA can discern Hepatocellular carcinoma patients from the healthy patients with a sensitivity of 0.84 and a specificity of 0.79. For colorectal cancer we achieve a sensitivity of 0.87 and a specificity of 0.8. An important advantage of our cfRNA based approach is that it also reports putative neoepitopes which are important for therapeutic purposes.

AVAILABILITY AND IMPLEMENTATION

The FastNeo package is available at https://github.com/yashumayank/FastNeo and https://zenodo.org/records/11521368. The benchmark pipelines to detect Immune Epitope database and Tumor-Specific Neoantigen database neoepitopes using HaplotypeCaller, bcftools, and Lofreq, and to run FastNeo with STAR instead of Bowtie2 are also available in the above github repository.

Role of noncoding RNA and protein interaction in pancreatic cancer

ABSTRACT

Noncoding RNAs (ncRNAs) are a class of RNA molecules with little or no protein-coding potential. Emerging evidence indicates that ncRNAs are frequently dysregulated and play pivotal roles in the pathogenesis of pancreatic cancer. Their aberrant expression can arise from chromosomal abnormalities, dysregulated transcriptional control, and epigenetic modifications. ncRNAs function as protein scaffolds or molecular decoys to modulate interactions between proteins and other biomolecules, thereby regulating gene expression and contributing to pancreatic cancer progression. In this review, we summarize the mechanisms underlying ncRNA dysregulation in pancreatic cancer, emphasize the biological significance of ncRNA-protein interactions, and highlight their clinical relevance. A deeper understanding of ncRNA-protein interactions is essential to elucidate molecular mechanisms and advance translational research in pancreatic cancer.

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.

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.

circAFF2 promotes the development of AML by binding to PML mRNA

AML is a complex disease caused by multiple molecular mechanisms. As an important regulatory molecule, the role of circRNA in AML is not fully understood. By performing high-throughput sequencing on clinical samples, we systematically identified the differences in circRNA expression and distribution between AML and healthy donor samples. One circular RNA, circAFF2, was found to be significantly upregulated in AML patients. Functional studies showed that knockdown of circAFF2 could significantly inhibit the proliferation of AML cells and promote their apoptosis. Overexpression of circAFF2 can have opposite effects. In vivo experiments showed that transplantation of AML cells with circAFF2 knockdown slowed the proliferation and infiltration and prolonged the survival time of mice compared to controls. Further studies showed that circAFF2 can promote the degradation of PML mRNA by binding to the 3'UTR of PML mRNA, thereby affecting the proliferation and apoptosis of AML cells. In conclusion, our work demonstrates that circAFF2 can bind to PML mRNA to regulate AML cell function, providing new insights into the mechanism of AML development and potential targets for clinical diagnosis and treatment.

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.

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

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

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.

Effects of circPICALM-miR-132-PHKB regulated by METTL3 on proliferation of porcine skeletal muscle satellite cells

Circular RNA (circRNA) is ubiquitously expressed in highly differentiated eukaryotes, playing an extremely vital regulatory role in muscle growth and development. In this study, we identified circPICALM, a novel circRNA which consists of exons 5 to 9 of the PICALM gene, exhibiting differential expression in the longissimus dorsi muscle (LD) of adult (QA) and newborn (QN) Queshan Black pigs. CircPICALM is resistant to RNase R, mainly located in the cytoplasm with potential coding capacities. When circPICALM was over-expressed in porcine skeletal muscle satellite cells (PSMSCs), there was a significant decrease in the expression levels of PCNA, CDK4, CDK1 and CCND1, which consequently inhibited the proliferation of PSMSCs. Conversely, miR-132, a target molecule of circPICALM, was found to promote the proliferation of PSMSCs. In addition, circPICALM can up-regulate the expression of the target gene PHKB by competitively adsorbing miR-132. The circPICALM-ssc-miR-132-PHKB regulatory axis is regulated by METTL3, which increases the m6A level of both PSMSCs and circPICALM, thereby promoting the proliferation of PSMSCs. Overall, this study furnishes a fundamental reference for further in-depth exploration of the specific molecular mechanisms underlying m6A modification and circPICALM in muscle development and progression.

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.

LncRNA-DANCR Promotes ESCC Progression and Function as ceRNA to Regulate DDIT3 Expression by Sponging microRNA-3193

Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cancer development and progression. Among them, Differentiation Antagonizing Non-Protein Coding RNA (DANCR) has been implicated in various malignancies, including esophageal squamous cell carcinoma (ESCC). This study explores the clinical characteristics, prognostic implications, functional roles, and molecular mechanisms of DANCR in ESCC. Our results demonstrate that DANCR is highly expressed in ESCC, and acts as an oncogene in ESCC both in vitro and in vivo. Through bioinformatics analysis and experimental validation, we revealed that DANCR promotes ESCC progression by sponging miR-3193 and regulating its target gene DDIT3 expression. These findings highlight the critical role of DANCR in the development of ESCC and suggest its potential as a prognostic predictor and drug therapeutic target.

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.

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

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

A Novel Protein NAB1-356 Encoded by circRNA circNAB1 Mitigates Atrial Fibrillation by Reducing Inflammation and Fibrosis

Atrial fibrillation (AF) is a common arrhythmia with irregular atrial electrical activity. Circular RNAs (circRNAs) are key regulators in tissue homeostasis, yet their role in AF remains unclear. Here, we investigated the expression and function of circNAB1 in AF using high-throughput sequencing and functional assays in circNAB1 transgenic mice. We identified circNAB1 as a significantly downregulated circRNA in AF patient specimens. Silencing circNAB1 promoted collagen deposition and inflammation, whereas overexpression reduces atrial fibrosis and AF susceptibility in mice, consistent with results observed in human atrial tissues. Mechanistically, circNAB1 translates into a novel protein, NAB1-356, which is highly expressed in human cardiac hypertrophy. NAB1-356 interacts with EGR1 as NAB1 does, decreasing fibrosis and inflammation in the atrium. Furthermore, NAB1-356 also regulates transcription factor Runx1 and Gadd45b transcription, exerting regulatory effects on cytokine expression and fibrosis. Targeting EGR1, Gadd45b, and Runx1 by circNAB1 or siRNAs attenuate AF incidence and cardiac remodeling, suggesting potential therapeutic strategies for AF management. Delivery of circNAB1 improves AF conditions in LKB1 knockout mice, further highlighting its anti-arrhythmic potential. Our findings elucidate the mechanistic role of circNAB1 in AF pathogenesis and suggest its therapeutic implications for cardiac remodeling-associated disorders.

Whole transcriptome sequencing-based identification and functional prediction of salt-tolerant-related circular RNAs in ZM-4 (Malus zumi)

CircRNAs, are a class of covalently closed non-coding RNAs; they have been identified in many plants and play an important role in the response to abiotic stresses. However, little is known about the response of the circRNAs of salt-tolerant apple rootstock resources in response to salt stress. In this study, the leaves and roots of the salt-tolerant Malus resource, ZM-4, and the salt-sensitive rootstock M9T337, were used as test materials and were exposed to 75 mmol/L NaCl stress for 0 h and 24 h. A total of 2502 circRNAs were identified, and 218 and 242 circRNAs were uniquely expressed in M9T337 and ZM-4, respectively. Furthermore, it was shown that the up-regulated parental genes of the differentially expressed circRNAs were enriched in the metabolic pathways and the biosynthesis of secondary metabolites pathway in the leaves and roots of ZM-4 under salt stress, respectively. There were potential regulatory networks of ceRNA among 150 circRNAs, 139 miRNAs, and 397 mRNAs. Novel_circ_000845 and novel_circ_000266 could target and inhibit the expression of mdm-miR156 and up-regulate the expression of the salt-responsive gene SPL6. Six circRNAs, including novel_circ_000898 and novel_circ_001519, could target and inhibit the expression of mdm-miR10995 and up-regulate the expression of the salt-responsive gene COBL7. In conclusion, this study laid the foundation for the post-transcriptional molecular regulation mechanism of salt tolerance in apple rootstock resources.