The potential of using blood circular RNA as liquid biopsy biomarker for human diseases

Forensic stability evaluation of selected miRNA and circRNA markers in human bloodstained samples exposed to different environmental conditions

Recently, RNA markers have been used to identify tissue origins of different kinds of body fluids. Herein, circRNA and miRNA markers were carried out to examine the presence or absence of peripheral blood (PB) in bloodstained samples exposed to different external environmental conditions, which mimicked PB samples left at the crime scenes. PB samples were placed on sterile swabs and then exposed to different high temperatures (37°C, 55°C and 95°C) and ultraviolet light irradiation for 0 d, 0.5 d, 1 d, 3 d, and 7 d, ultra-low and low temperatures (-80°C, -20°C, and 4°C) for 30 d, 180 d and 365 d and different kinds of disinfectants. Total RNA was extracted from bloodstained samples under the above different conditions, and the expressions of target RNAs (including miR16-5p, miR451a, circ0000095, and two reference genes RNU6b and 18 S rRNA) were detected by the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method. Results showed that these selected RNA markers could be successfully measured at all observation points with their unique degradation rates, which exhibited relative stability in degraded bloodstained samples exposed to different environmental conditions. This study provides insights into the applications of these studied miRNA and circRNA markers in forensic science.

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

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

Examining the evidence for mutual modulation between m6A modification and circular RNAs: current knowledge and future prospects

The resistance of cancer cells to treatment significantly impedes the success of therapy, leading to the recurrence of various types of cancers. Understanding the specific mechanisms of therapy resistance may offer novel approaches for alleviating drug resistance in cancer. Recent research has shown a reciprocal relationship between circular RNAs (circRNAs) and N6-methyladenosine (m6A) modification, and their interaction can affect the resistance and sensitivity of cancer therapy. This review aims to summarize the latest developments in the m6A modification of circRNAs and their importance in regulating therapy resistance in cancer. Furthermore, we explore their mutual interaction and exact mechanisms and provide insights into potential future approaches for reversing cancer resistance.

Circular RNA in cancer

Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.

CircFBXW4 Suppresses Colorectal Cancer Progression by Regulating the MiR-338-5p/SLC5A7 Axis

Dysregulated circular RNAs (circRNAs) contribute to tumourigenesis and cancer progression. However, the expression patterns and biological functions of circRNAs in colorectal cancer (CRC) remain elusive. Here, RNA sequencing and bioinformatics analyses are applied to screen for aberrantly expressed circRNAs. The expression of circFBXW4 in CRC tissues and cell lines is determined by quantitative real-time PCR. A series of in vitro and in vivo biological function assays are implemented to assess the functions of circFBXW4. The regulatory mechanisms linking circFBXW4, miR-338-5p, and SLC5A7 are explored by western blotting, dual luciferase reporter assays, and RNA pull-down assays. CircFBXW4 is dramatically downregulated in CRC tissues and cell lines. circFBXW4 downregulation is clearly correlated with malignant features and patient overall survival in CRC. Functionally, ectopic expression of circFBXW4 strikingly impairs the proliferation, migration, and invasion capacities of CRC cells in vitro and in vivo, whereas circFBXW4 knockdown has the opposite effects. Mechanistically, circFBXW4 competitively binds to miR-338-5p and prevents it from interacting with and repressing its target SLC5A7, thus suppressing the progression of CRC. This study reveals the specific critical role of circFBXW4 in inhibiting CRC progression via the miR-338-5p/SLC5A7 axis and provides an additional target for eradicating CRC.

Knockdown of circ-Gatad1 alleviates LPS induced HK2 cell injury via targeting miR-22-3p/TRPM7 axis in septic acute kidney

BACKGROUND

Sepsis is a life-threatening, systemic inflammatory disease that can lead to a variety of conditions, including septic acute kidney injury (AKI). Recently, multiple circular Rnas (circRNAs) have been implicated in the development of this disease.

METHODS

In this study, we aimed to elucidate the role of circ-Gatad1 in sepsis induced AKI and its potential mechanism of action. High-throughput sequencing was used to investigate abnormal expression of circRNA in AKI and healthy volunteer. Bioinformatics analysis and luciferase reporting analysis were used to clarify the interacted relationship among circRNA, miRNA and mRNA. HK2 cells were treated with lipopolysaccharide (LPS) to establish septic AKI cell model. HK2 cells were employ to analysis the ROS, inflammatory cytokines expression, proliferation and apoptosis under LPS condition.

RESULTS

The result show that the expression of circ-Gatad1 was increased in septic acute kidney patients. Downregulation circ-Gatad1 suppressed LPS-treated induced HK2 cells injury including apoptosis, proliferation ability, ROS and inflammatory cytokines level. Bioinformatics and luciferase report analysis confirmed that both miR-22-3p and TRPM7 were downstream targets of circ-Gatad1. Overexpression of TRPM7 or downregulation of miR-22-3p reversed the protective effect of si-circ-Gatad1 to HK2 after exposure to LPS (5 µg/ml) microenvironment.

CONCLUSION

In conclusion, knockdown of circ-Gatad1 alleviates LPS induced HK2 cell injury via targeting miR-22-3p/TRPM7 axis in septic acute kidney.

Circular RNAs in intracranial aneurysms: Emerging roles in pathogenesis, diagnosis and therapeutic intervention

Intracranial aneurysms (IAs) present a substantial health threat, given the potential for catastrophic ruptures and subarachnoid hemorrhages (SAH). Swift and effective measures for diagnosis and treatment are paramount to enhance patient outcomes and alleviate the associated healthcare burden. In this context, circular RNAs (circRNAs) have emerged as an intriguing area of investigation, offering promise as both diagnostic biomarkers and therapeutic targets for IAs. CircRNAs have demonstrated their influence on critical molecular and cellular processes underpinning IAs pathogenesis, revealing their pivotal role in understanding this complex ailment. Beyond their diagnostic potential, circRNAs hold great potential as prognostic markers, providing crucial insights into IAs rupture risk. The unique circular structure and their regulatory functions make circRNAs an enticing avenue for innovative therapeutic approaches. The ongoing study of circRNAs in the context of IAs is an exciting and rapidly evolving field that has the potential to revolutionize approaches to diagnosis, treatment, and prevention of this life-threatening condition. As research continues to unravel the intricate roles of circRNAs, they are poised to become invaluable tools in clinical practice, enhancing patient care and ultimately reducing the impact of cerebral aneurysms on both individuals and healthcare systems. This comprehensive review delves deeply into the world of circRNAs in the realm of IAs, elucidating their multifaceted roles in the onset and progression of this condition. Moreover, this review ventures into the diagnosis and therapeutic potential of circRNAs, exploring their possible applications in gene therapy and as targets for novel treatment modalities.

Beyond Traditional Medicine: EVs-Loaded Hydrogels as a Game Changer in Disease Therapeutics

Extracellular vesicles (EVs), especially exosomes, have shown great therapeutic potential in the treatment of diseases, as they can target cells or tissues. However, the therapeutic effect of EVs is limited due to the susceptibility of EVs to immune system clearance during transport in vivo. Hydrogels have become an ideal delivery platform for EVs due to their good biocompatibility and porous structure. This article reviews the preparation and application of EVs-loaded hydrogels as a cell-free therapy strategy in the treatment of diseases. The article also discusses the challenges and future outlook of EVs-loaded hydrogels.

Circular RNA expression profile identifies potential circulating biomarkers for keratoconus

Early diagnosis is important for improving the outcomes of keratoconus (KC). Stable expression and a closed-loop structure of circular RNAs (circRNAs) make them ideal for the diagnosis and treatment of diseases. However, the expression pattern and potential function of circRNAs in KC is not studied yet. Hence, this study explored the circRNA expression profile of KC corneas through transcriptome sequencing and circRNA expression profile analysis. The diagnostic potential of blood circRNAs for KC was explored by analysing the circRNAs' expression levels of fifty paired blood samples from patients with KC and normal controls. The results showed that 107 significantly upregulated and 145 significantly downregulated circRNAs (|fold change| ≥ 2.0, p-value <0.05) were identified in KC tissues. Eight top differently expressed circRNAs were further validated in more cornea samples. Among them, five circRNAs expressed in peripheral blood, and four circRNAs (circ_0006156, circ_0006117, circ_0000284 and circ_0001801) showed significant downregulation in KC patients' peripheral blood too. The blood circ_0000284 expression levels of early, moderate, and advanced KC patients both were significantly lower than the controls. The blood circ_0006117 expression levels present a positive correlation with corrected distance visual acuity values, and a negative correlation with back elevation values of KC eyes. Notably, the expression levels of these circRNAs distinguished KC patients from their healthy counterparts, with the area under the curve (AUC) of circ_0000284, circ_0001801, and circ_0006117 being 0.7306, 0.6871 and 0.6701, respectively. Further, the AUC value for five circRNAs under the logistic regression model was 0.8203, indicating that they can function as effective biomarkers for the KC diagnostics. In conclusion, the expression of circRNAs showed a relationship with KC, with four significantly differentially expressed circRNAs demonstrating potential as biomarkers for the disease.

The pathological mechanisms of circRNAs in mediating intervertebral disc degeneration

Lower back pain (LBP) is a worldwide health problem associated with significant economic and social burden. Intervertebral disc degeneration (IVDD) is a leading cause of LBP. Several studies show that the death of nucleus pulposus cells (NPCs), abnormal metabolism of the extracellular matrix (ECM), and inflammatory response are the key mechanisms behind the pathogenesis of IVDD. Circular RNAs (circRNAs) are key regulators of gene expression and play a significant role in regulating NPCs death, ECM homeostasis, and inflammatory response by acting as microRNAs (miRNAs) sponges in IVDD. However, the regulatory role of circRNAs in mediating IVDD remains unknown. This review comprehensively describes the normal anatomic structure and function of IVD, the pathogenesis of IVDD, the characteristics, synthesis, mechanisms, and function of circRNAs. Moreover, we highlighted the 23 circRNAs that mediate ECM metabolism, 16 circRNAs that mediate NPCs apoptosis, circ_0004354 and circ_0040039 that mediate NPCs pyroptosis, and 5 circRNAs that mediate inflammatory response in IVDD. In addition, this review presents suggestions for future studies, such as the need for further investigation on ferroptosis-related circRNAs in IVDD. This review could provide novel insights into the pathogenesis and treatment of IVDD.

[Circular RNA hsa_circ_0006834 is a potential prognostic biomarker for hepatocellular carcinoma]

OBJECTIVE

To explore the differentially expressed circular RNAs (circRNAs) in hepatocellular carcinoma (HCC) and their association with clinical features and prognosis of HCC patients.

METHODS

RNA sequencing was performed on 56 pairs of HCC and adjacent tissues to identify the differentially expressed circRNAs in HCC, whose expressions were validated by RT-qPCR in another 15 pairs of HCC and adjacent tissues. The correlation of the selected circRNAs with the clinical features and prognosis of the patients was analyzed using Chi-square test, Cox proportional hazards regression model and Kaplan-Meier analysis. The predictive value of the identified circRNA for recurrence-free survival and overall survival of HCC patients was assessed using ROC curves.

RESULTS

We identified 17 significantly up-regulated and 45 down-regulated circRNAs in HCC tissues using RNA sequencing (P < 0.05). Among these circRNAs, hsa_circ_0006834 was found to be significantly down-regulated in HCC tissues, and its expression level was negatively correlated with vascular invasion and Barcelona Clinic Liver Cancer (BCLC) stage and positively with recurrence-free survival and overall survival of the patients (P < 0.05). As an independent prognostic factor for HCC, hsa_circ_0006834 had an AUC of 0.750 and 0.7601 for predicting 2-year recurrence-free survival and overall survival of HCC patients, respectively.

CONCLUSION

hsa_circ_0006834 is a new potential biomarker for evaluating the prognosis of HCC patients.

Exploring the interplay between PARP1 and circRNA biogenesis and function

PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.

The novel β-TrCP protein isoform hidden in circular RNA confers trastuzumab resistance in HER2-positive breast cancer

Trastuzumab notably improves the outcome of human epidermal growth factor receptor 2 (HER2)-positive breast cancer patients, however, resistance to trastuzumab remains a major hurdle to clinical treatment. In the present study, we identify a circular RNA intimately linked to trastuzumab resistance. circ-β-TrCP, derived from the back-splicing of β-TrCP exon 7 and 13, confers trastuzumab resistance by regulating NRF2-mediated antioxidant pathway in a KEAP1-independent manner. Concretely, circ-β-TrCP encodes a novel truncated 343-amino acid peptide located in the nucleus, referred as β-TrCP-343aa, which competitively binds to NRF2, blocks SCFβ-TrCP-mediated NRF2 proteasomal degradation, and this protective effect of β-TrCP-343aa on NRF2 protein requires GSK3 activity. Subsequently, the elevated NRF2 transcriptionally upregulates a cohort of antioxidant genes, giving rise to trastuzumab resistance. Moreover, the translation ability of circ-β-TrCP is inhibited by eIF3j under both basal and oxidative stress conditions, and eIF3j is transcriptionally repressed by NRF2, thus forming a positive feedback circuit between β-TrCP-343aa and NRF2, expediting trastuzumab resistance. Collectively, our data demonstrate that circ-β-TrCP-encoded β-TrCP protein isoform drives HER2-targeted therapy resistance in a NRF2-dependent manner, which provides potential therapeutic targets for overcoming trastuzumab resistance.

circELMOD3 increases and stabilizes TRIM13 by sponging miR-6864-5p and direct binding to inhibit HCC progression

Many circular RNAs (circRNAs) have been identified to be associated with hepatocellular carcinoma (HCC) progression. We aim to explore the diagnostic potential, functions, and mechanism of circELMOD3 in HCC. Differentially expressed circRNAs in HCC and its paired adjacent tissues were identified by RNA sequencing. circELMOD3 was downregulated in HCC tissues and was related to clinicopathological characteristics of HCC patients. Additionally, plasma circELMOD3 was shown to be a highly sensitive and non-invasive biomarker to distinguish HCC from healthy controls. Functional assays showed that circELMOD3 inhibited proliferation and induced apoptosis of HCC cells both in vitro and in vivo. Mechanistically, RNA antisense purification (RAP) and luciferase reporter assays verified that circELMOD3 functioned as a sponge for miR-6864-5p leading to increased expression of its target gene TRIM13. Interestingly, RNA stability test demonstrated that circELMOD3 overexpression led to enhanced stability of its directly bound TRIM13 mRNA, which in turn co-activated the p53 signaling pathway.

Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Glaucoma is the leading cause of irreversible blindness globally. Circular RNAs (circRNAs) play vital roles in various biological processes as microRNA (miRNA) sponges and, thus, have been investigated as potential biomarkers and therapeutic targets in numerous human diseases. However, the underlying mechanisms of circRNAs in the pathogenesis of glaucoma remain unclear. Therefore, transcriptome sequencing was performed to identify relevant circRNAs in peripheral blood samples from patients with primary angle-closure glaucoma. Bioinformatics analysis was performed to investigate the potential roles of differentially expressed circRNAs (DEcircRNAs) in the pathogenesis of glaucoma. In total, 481 differentially expressed genes in addition to 345 DEcircRNAs were identified in patients with glaucoma. Based on a public database, targeted gene analysis identified 11 DEcircRNAs that potentially regulate the expression of five genes as miRNA sponges in glaucoma. In addition, quantitative reverse transcription PCR analysis verified that expression of the circRNA hsa-circ-0000745 was positively correlated with the expression of NEAT1 as a potential target gene. These results suggest that DEcircRNAs are involved in a gene expression regulatory network related to immune cell function and progression of glaucoma. Thus, DEcircRNAs in peripheral blood are potential biomarkers and therapeutic targets for glaucoma.

Identification of biomarkers associated with immune scores in diabetic retinopathy

Background

Diabetic retinopathy (DR) causes irreversible visual impairment in diabetes mellitus (DM) patients. Immunity played a crucial role in DR. Nevertheless, the triggering mechanism of DR was not yet thorough enough. Herein, we aim to identify the immune-associated genes as biomarkers associated with immune scores that can distinguish early DR from DM without DR.

Methods

In this study, total RNA of peripheral blood mononuclear cell (PBMC) samples from 15 non-proliferative DR patients and 15 DM patients without DR were collected and the transcriptome sequencing data were extracted. Firstly, the target genes were obtained by intersecting the differentially expressed genes (DEGs), which were screened by "limma", and the module genes (related to immune scores), which were screened by "WGCNA". In order to screen for the crucial genes, three machine learning algorithms were implemented, and a receiver operating characteristic (ROC) curve was used to obtain the diagnostic genes. Moreover, the gene set enrichment analysis (GSEA) was performed to understand the function of diagnostic genes, and analysis of the proportions of immune cells and their association with diagnostic genes was performed to analyze the pathogenesis of DR. Furthermore, the regulatory network of TF-mRNA-miRNA was built to reveal the possible regulation of diagnostic genes. Finally, the quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the mRNA level of diagnostic genes.

Results

A total of three immune-associated diagnostic genes, namely, FAM209B, POM121L1P, and PTGES, were obtained, and their expression was increased in PBMC samples of DR, and qRT-PCR results confirmed these results. Moreover, the functions of these genes were associated with immune response. The expression of POM121L1P and PTGES was significantly negatively associated with naive B cells, and the expression of FAM209B was significantly negatively associated with immature dendritic cells. Moreover, ESR1 could regulate both FAM209B and PTGES.

Conclusion

This study identified three immune-associated diagnostic genes, FAM209B, POM121L1P, and PTGES, as biomarkers associated with immune scores in DR for the first time. This finding might proffer a novel perspective of the triggering mechanism of DR, and help to understand the role of immune-associated genes in the molecular mechanism of DR more deeply.

Engineered extracellular vesicles in female reproductive disorders

Biologically active and nanoscale extracellular vesicles (EVs) participate in a variety of cellular physiological and pathological processes in a cell-free manner. Unlike cells, EVs not only do not cause acute immune rejection, but are much smaller and have a low risk of tumorigenicity or embolization. Because of their unique advantages, EVs show promise in applications in the diagnosis and treatment of reproductive disorders. As research broadens, engineering strategies for EVs have been developed, and engineering strategies for EVs have substantially improved their application potential while circumventing the defects of natural EVs, driving EVs toward clinical applications. In this paper, we will review the engineering strategies of EVs, as well as their regulatory effects and mechanisms on reproductive disorders (including premature ovarian insufficiency (POI), polycystic ovarian syndrome (PCOS), recurrent spontaneous abortion (RSA), intrauterine adhesion (IUA), and endometriosis (EMS)) and their application prospects. This work provides new ideas for the treatment of female reproductive disorders by engineering EVs.

Nucleus-localized circSLC39A5 suppresses hepatocellular carcinoma development by binding to STAT1 to regulate TDG transcription

Accumulating evidence indicates that circular RNAs (circRNAs) are inextricably linked to cancer development. However, the function and mechanism of nucleus-localized circRNAs in hepatocellular carcinoma (HCC) still require investigation. Here, qRT-PCR and receiver-operating characteristic curve were used to detect the expression and diagnostic potential of circSLC39A5 for HCC. The biological function of circSLC39A5 in HCC was investigated in vitro and in vivo. Nucleoplasmic separation assay, fluorescence in situ hybridization, RNA pulldown, RNA immunoprecipitation, the HDOCK Server, the NucleicNet Webserver, crosslinking-immunoprecipitation, MG132 treatment, and chromatin immunoprecipitation were utilized to explore the potential molecular mechanism of circSLC39A5 in HCC. The results showed that circSLC39A5 was downregulated in both HCC tissues and plasma and was associated with satellite nodules and lymph node metastasis/vascular invasion. CircSLC39A5 was stably expressed in plasma samples under different storage conditions, showing good diagnostic potential for HCC (AUC = 0.915). CircSLC39A5 inhibited proliferation, migration, and invasion, facilitated the apoptosis of HCC cells, and was associated with low expression of Ki67 and CD34. Remarkably, circSLC39A5 is mainly localized in the nucleus and binds to the transcription factor signal transducer and activator of transcription 1 (STAT1), affecting its stabilization and expression. STAT1 binds to the promoter of thymine DNA glycosylase (TDG). Overexpression of circSLC39A5 elevates TDG expression and reverses the increase of proliferating cell nuclear antigen (PCNA) expression and the overactive cell proliferation caused by TDG silencing. Our findings uncovered a novel plasma circRNA, circSLC39A5, which may be a potential circulating diagnostic marker for HCC, and the mechanism by which nucleus-localized circSLC39A5 exerts a transcriptional regulatory role in HCC by affecting STAT1/TDG/PCNA provides new insights into the mechanism of circRNAs.

Vesicular Release and Uptake of Circular LSD1-RNAs from Non-Cancer and Cancer Lung Cells

Lysine-specific demethylase 1 (LSD1) is highly expressed in many cancer types and strongly associated with cancer progression and metastasis. Circular RNAs (circRNAs) are produced by back-splicing and influence the interactive RNA network by microRNA and protein sponging. In the present study, we aimedto identify circRNAs that derive from the LSD1-encoding KDM1A gene, and to investigate their potential to be released and uptaken by lung cancer versus non-cancer epithelial cells. We identified four circLSD1-RNAs by RT-PCR with divergent primers, followed by sequencing. The expression level of circLSD1-RNAs was then studied by quantitative PCR on cellular and extracellular fractions of lung cancer (PC9) and non-cancer primary small airway epithelial (PSAE) cells. Moreover, we established the transgenic overexpression of circLSD1-RNAs. We show that circLSD1-RNAs are primarily located in the cytoplasm, but are packaged and released from lung cancer and non-cancer cells by extracellular vesicles (EVs) and ribonucleoprotein (RNP) complexes, respectively. Proteomics demonstrated a different protein pattern of EV fractions released from PC9 versus PSAE cells. Importantly, released circLSD1-RNAs were differently taken up by PSAE and PC9 cells. In conclusion, our findings provide primary evidence that circLSD1-RNAs participate in the intercellular communication of lung cancer cells with the tumor environment.

Noncoding RNAs in tumorigenesis and tumor therapy

Tumorigenesis is a complicated process in which numerous modulators are involved in different ways. Previous studies have focused primarily on tumor-associated protein-coding genes such as oncogenes and tumor suppressor genes, as well as their associated oncogenic pathways. However, noncoding RNAs (ncRNAs), rising stars in diverse physiological and pathological processes, have recently emerged as additional modulators in tumorigenesis. In this review, we focus on two typical kinds of ncRNAs: long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). We describe the molecular patterns of ncRNAs and focus on the roles of ncRNAs in cancer stem cells (CSCs), tumor cells, and tumor environmental cells. CSCs are a small subset of tumor cells and are generally considered to be cells that initiate tumorigenesis, and dozens of ncRNAs have been defined as critical modulators in CSC maintenance and oncogenesis. Moreover, ncRNAs are widely involved in oncogenetic processes, including sustaining proliferation, resisting cell death, genome instability, metabolic disorders, immune escape and metastasis. We also discuss the potential applications of ncRNAs in tumor diagnosis and therapy. The progress in ncRNA research greatly improves our understanding of ncRNAs in oncogenesis and provides new potential targets for future tumor therapy.

Extracellular vesicles in gastric cancer: role of exosomal lncRNA and microRNA as diagnostic and therapeutic targets

Extracellular vesicles (EVs), including exosomes, play a crucial role in intercellular communication and have emerged as important mediators in the development and progression of gastric cancer. This review discusses the current understanding of the role of EVs, particularly exosomal lncRNA and microRNA, in gastric cancer and their potential as diagnostic and therapeutic targets. Exosomes are small membrane-bound particles secreted by both cancer cells and stromal cells within the tumor microenvironment. They contain various ncRNA and biomolecules, which can be transferred to recipient cells to promote tumor growth and metastasis. In this review, we highlighted the importance of exosomal lncRNA and microRNA in gastric cancer. Exosomal lncRNAs have been shown to regulate gene expression by interacting with transcription factors or chromatin-modifying enzymes, which regulate gene expression by binding to target mRNAs. We also discuss the potential use of exosomal lncRNAs and microRNAs as diagnostic biomarkers for gastric cancer. Exosomes can be isolated from various bodily fluids, including blood, urine, and saliva. They contain specific molecules that reflect the molecular characteristics of the tumor, making them promising candidates for non-invasive diagnostic tests. Finally, the potential of targeting exosomal lncRNAs and microRNAs as a therapeutic strategy for gastric cancer were reviewed as wee. Inhibition of specific molecules within exosomes has been shown to suppress tumor growth and metastasis in preclinical models. In conclusion, this review article provides an overview of the current understanding of the role of exosomal lncRNA and microRNA in gastric cancer. We suggest that further research into these molecules could lead to new diagnostic tools and therapeutic strategies for this deadly disease.

Increased plasma levels of circPTP4A2 and circTLK2 are associated with stroke injury

OBJECTIVE

Accumulating studies have shown that circulating circular RNAs (circRNAs) represent novel biomarkers for many human diseases. We investigated whether plasma circPTP4A2 and circTLK2 levels are associated with stroke severity, infarct volume, stroke etiology, and functional outcome in acute ischemic stroke (AIS) patients.

METHODS

We applied quantitative real-time PCR (qPCR) to measure plasma circPTP4A2 and circTLK2 levels of 236 AIS patients within 72 h of symptoms onset and 136 healthy controls. We further assessed the National Institutes of Health Stroke Scale (NIHSS), infarct size, the Trial of Org 10172 in Acute Stroke Treatment (TOAST) classification and the 90-day modified Rankin scale (mRS) for each patient.

RESULTS

At admission, plasma circPTP4A2 and circTLK2 levels in patients with moderate to severe stroke were significantly higher compared to those with mild stroke. Logistic regression and receiver-operating characteristic (ROC) curve analyses indicated that they might function as predictive biomarkers for moderate to severe stroke. We also observed a medium positive correlation between these two circRNAs and NIHSS. Plasma circPTP4A2 and circTLK2 levels were slight positively correlated with cerebral infarct volume only in anterior circulation infarction (ACI) patients. Levels of both circPTP4A2 and circTLK2 were closely related with large artery atherosclerosis (LAA) stroke. Moreover, changes within 7 days after admission in circPTP4A2 and circTLK2 were able to predict unfavorable clinical outcome 90 days after AIS.

INTERPRETATION

These results demonstrate that plasma circPTP4A2 and circTLK2 strongly correlated with severity, subtypes and prognosis of AIS, and they could serve as promising biomarkers.

Extracellular Vesicles and Cancer Multidrug Resistance: Undesirable Intercellular Messengers?

Cancer multidrug resistance (MDR) is one of the main mechanisms contributing to therapy failure and mortality. Overexpression of drug transporters of the ABC family (ATP-binding cassette) is a major cause of MDR. Extracellular vesicles (EVs) are nanoparticles released by most cells of the organism involved in cell-cell communication. Their cargo mainly comprises, proteins, nucleic acids, and lipids, which are transferred from a donor cell to a target cell and lead to phenotypical changes. In this article, we review the scientific evidence addressing the regulation of ABC transporters by EV-mediated cell-cell communication. MDR transfer from drug-resistant to drug-sensitive cells has been identified in several tumor entities. This was attributed, in some cases, to the direct shuttle of transporter molecules or its coding mRNA between cells. Also, EV-mediated transport of regulatory proteins (e.g., transcription factors) and noncoding RNAs have been indicated to induce MDR. Conversely, the transfer of a drug-sensitive phenotype via EVs has also been reported. Additionally, interactions between non-tumor cells and the tumor cells with an impact on MDR are presented. Finally, we highlight uninvestigated aspects and possible approaches to exploiting this knowledge toward the identification of druggable processes and molecules and, ultimately, the development of novel therapeutic strategies.

RNA-Based Liquid Biopsy in Head and Neck Cancer

Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.

Exosomal circRNAs in cancer: Implications for therapy resistance and biomarkers

Despite the advances in cancer treatment in recent years, the development of resistance to cancer therapy remains the biggest hurdle towards curative cancer treatments. Therefore, investigating the molecular mechanisms underlying cancer therapy resistance is of paramount clinical importance. Circular RNAs (circRNAs), novel members of the noncoding RNA family, are endogenous biomolecules in eukaryotes characterized by a covalently closed loop structure with multiple biological functions. Significantly, circRNAs are abundant and stable in exosomes and can be packaged, secreted and transferred to targeted tumour cells, thereby modulating diverse hallmarks of cancer behaviours, such as proliferation, migration, and immune escape. Notably, a great number of exosomal circRNAs are abnormally expressed during cancer treatment and can mediate cancer therapy resistance through complex mechanisms; therefore, targeting exosomal circRNAs is a promising therapeutic method to reverse therapy resistance. This review aimed to elucidate the mechanisms underlying exosomal circRNAs controlling the resistance of cancer to common therapies, such as chemotherapy, targeted therapy, immunotherapy and radiotherapy, and we also discussed the therapeutic potential of exosomal circRNAs as clinical biomarkers and novel targets in cancer clinical management. We also discussed the prospects and challenges of targeting exosomal circRNAs as a novel therapeutic strategy for reversing cancer therapy resistance.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

Motivation

Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

Results

We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research.

Availability and implementation

https://github.com/biomedbigdata/circRNA-sponging.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Comprehensive Analysis of Circular RNAs in Endothelial Cells

Non-coding RNAs constitute a heterogeneous group of molecules that lack the ability to encode proteins but retain the potential ability to influence cellular processes through a regulatory mechanism. Of these proteins, microRNAs, long non-coding RNAs, and more recently, circular RNAs have been the most extensively described. However, it is not entirely clear how these molecules interact with each other. For circular RNAs, the basics of their biogenesis and properties are also lacking. Therefore, in this study we performed a comprehensive analysis of circular RNAs in relation to endothelial cells. We identified the pool of circular RNAs present in the endothelium and showed their spectrum and expression across the genome. Using different computational strategies, we proposed approaches to search for potentially functional molecules. In addition, using data from an in vitro model that mimics conditions in the endothelium of an aortic aneurysm, we demonstrated altered expression levels of circRNAs mediated by microRNAs.

Therapeutic and diagnostic applications of exosomal circRNAs in breast cancer

Circular RNAs (circRNAs) are regulatory elements that are involved in orchestrating gene expression and protein functions and are implicated in various biological processes including cancer. Notably, breast cancer has a significant mortality rate and is one of the most common malignancies in women. CircRNAs have been demonstrated to contribute to the pathogenesis of breast cancer including its initiation, progression, metastasis, and resistance to drugs. By acting as miRNA sponges, circRNAs can indirectly influence gene expression by disrupting miRNA regulation of their target genes, ultimately altering the course of cancer development and progression. Additionally, circRNAs can interact with proteins and modulate their functions including signaling pathways involved in the initiation and development of cancer. Recently, circRNAs can encode peptides that play a role in the pathophysiology of breast cancer and other diseases and their potential as diagnostic biomarkers and therapeutic targets for various cancers including breast cancer. CircRNAs possess biomarkers that differentiate, such as stability, specificity, and sensitivity, and can be detected in several biological specimens such as blood, saliva, and urine. Moreover, circRNAs play an important role in various cellular processes including cell proliferation, differentiation, and apoptosis, all of which are integral factors in the development and progression of cancer. This review synthesizes the functions of circRNAs in breast cancer, scrutinizing their contributions to the onset and evolution of the disease through their interactions with exosomes and cancer-related intracellular pathways. It also delves into the potential use of circRNA as a biomarker and therapeutic target against breast cancer. It discusses various databases and online tools that offer crucial circRNA information and regulatory networks. Lastly, the challenges and prospects of utilizing circRNAs in clinical settings associated with breast cancer are explored.

CircRNA OXCT1 promotes the malignant progression and glutamine metabolism of non-small cell lung cancer by absorbing miR-516b-5p and upregulating SLC1A5

Previous study has demonstrated the high expression of circular RNA 3-oxoacid CoA-transferase 1 (circ-OXCT1) in lung adenocarcinoma tumor tissues. However, the role and possible mechanism of circ-OXCT1 in non-small cell lung cancer (NSCLC) progression was unclear.Quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry (IHC) staining assay were performed to detect the expression of circ-OXCT1, microRNA-516b-5p (miR-516b-5p), solute carrier family 1 member 5 (SLC1A5) and other indicated protein markers. Cell proliferation was measured by Cell counting kit 8 (CCK8), colony formation and 5-Ethynyl-2'-deoxyuridine (EdU) assays. Flow cytometry was employed to detect the rate of apoptotic cells. Cell migration and invasion were measured using transwell assay. The relative glutamine uptake and α-ketoglutarate (α-KG) production was determined using commercial kits. Interaction between miR-516b-5p and circ-OXCT1 or SLC1A5 was predicted by bioinformatics analysis and confirmed via luciferase reporter and RNA immunoprecipitation (RIP) assays. In vivo assay was implemented to demonstrate the effect of circ-OXCT1 in tumor growth.Circ-OXCT1 and SLC1A5 were upregulated and miR-516b-5p was downregulated in NSCLC tissues and cells. Functional experiments revealed that circ-OXCT1 silencing suppressed cell proliferation, migration and invasion, but promoted cell apoptosis in vitro. Circ-OXCT1 knockdown repressed tumor formation in vivo. Besides, miR-516b-5p was a target of circ-OXCT1, and miR-516b-5p inhibitor could relieve circ-OXCT1 absence-mediated effects in NSCLC cells. SLC1A5 was identified as a target of miR-516b-5p. Circ-OXCT1 promoted SLC1A5 expression by target binding with miR-516b-5p.Circ-OXCT1 facilitated NSCLC progression via miR-516b-5p-dependent regulation of SLC1A5, which provided a possible circRNA-targeted therapy for NSCLC.

Circular RNAs: Promising Targets in Osteoporosis

PURPOSE OF REVIEW

Circular RNAs (circRNAs) are RNA transcripts derived from fragments of pre-messenger RNAs through a back-splicing process. An advantage that rises from their circular covalently closed conformation is their high stability, when compared with their linear counterparts. The current review focuses on the emerging roles of circRNAs in osteoporosis, including in osteogenic differentiation and osteoclastogenesis. Their potential as osteoporosis biomarkers will also be discussed.

RECENT FINDINGS

Although firstly described as non-coding, some of these single-stranded RNAs were recently reported to possess protein-coding capacity. On the other hand, the circRNAs exhibit cell and tissue-specific patterns at the transcriptome level in eukaryotes and are regulated throughout the development or disease progression. Even though thousands of these circular transcripts are listed and annotated, only a limited number of studies describe their biological role in bone processes. Recent evidence indicates inhibitory activator roles in both osteoblasts and osteoclasts differentiation and function. Latest screenings in the blood, plasma, or serum of osteoporosis patients support the potential for circRNA signature to be used as biomarkers in osteoporosis, but further validation is required. While intense research into circRNAs has been detailing their biological roles, there remains a need for standardization and further research to fulfil the future potential of this emerging and highly promising class of regulatory molecules.

Circular RNA Expression Profiling by Microarray-A Technical and Practical Perspective

Circular RNAs, as covalently circularized RNA loops, have many unique biochemical properties. Many circRNA biological functions and clinical indications are being continually discovered. Increasingly, circRNAs are being used as a new class of biomarkers, which are potentially superior to linear RNAs due to the unusual cell/tissue/disease specificities and the exonuclease-resistant stabilized circular form in the biofluids. Profiling circRNA expression has been a common step in circRNA research to provide much needed insight into circRNA biology and to facilitate rapid advances in the circRNA field. We will review circRNA microarrays as a practical and effective circRNA profiling technology for regularly equipped biological or clinical research labs, share valuable experiences, and highlight the significant findings from the profiling studies.

Peripheral Blood Mononuclear Cell derived Biomarker detection using eXplainable Artificial Intelligence (XAI) provides better diagnosis of Breast Cancer

The incidence and mortality rate of breast cancer increases yearly by an average of 1.44 % and 0.23 %, respectively. Till 2021, there were 7.8 million women who had been diagnosed with breast cancer within 5 years. Biopsies of tumors are often expensive and invasive and raise the risk of serious complications like infection, excessive bleeding, and puncture damage to nearby tissues and organs. Early detection biomarkers are often variably expressed in different patients and may even be below the detection level at an early stage. Hence PBMC that shows alteration in gene profile as a result of interaction with tumor antigens may serve as a better early detection biomarker. Also, such alterations in immune gene profile in PBMCs are more prone to detection despite variability in different breast cancer mutants.This study aimed to identify potential diagnostic biomarkers for breast cancer using eXplainable Artificial Intelligence (XAI) on XGBoost machine learning (ML) models trained on a binary classification dataset containing the expression data of PBMCs from 252 breast cancer patients and 194 healthy women.After effectively adding SHAP values further into the XGBoost model, ten important genes related to breast cancer development were discovered to be effective potential biomarkers. Our studies showed that SVIP, BEND3, MDGA2, LEF1-AS1, PRM1, TEX14, MZB1, TMIGD2, KIT, and FKBP7 are key genes that impact model prediction. These genes may serve as early, non-invasive diagnostic and prognostic biomarkers for breast cancer patients.

circSPECC1 Promotes Proliferation and Migration of LNCaP Prostate Cancer Cells by Affecting Their Epithelial-Mesenchymal Transition

Objective. To determine the effects of circSPECC1 (hsa_circ_0000745) on the proliferation and migration of LNCaP prostate cancer cells and to explore the potential molecular mechanism. Methods. Stable circSPECC1 shRNA-expressing and circSPECC1-overexpressing LNCaP cell lines were constructed, and relative gene expression levels were determined by RT-PCR. MTT and clonogenic assays were used to assess proliferative ability while a scratch test was used to analyze cell migration. Western blotting was used to determine protein expression levels. The effects of circSPECC1 on the proliferation of LNCaP prostate cancer cells were observed in vivo. Results. circSPECC1 was found to be derived from the SPECC1 (sperm antigen with calponin homology and coiled-coil domains 1) parent gene and to form a loop. Overexpression of circSPECC1 promoted the proliferation and migration of the LNCaP cells, whereas decreased expression of circSPECC1 inhibited these properties. Overexpression of circSPECC1 promoted the expression of MMP-2, MMP-9, VEGF, vimentin, and N-cad but downregulated the expression of E-cad. Decreased expression of circSPECC1 inhibited the expression of MMP-2, MMP-9, VEGF, vimentin, and N-cad but increased the expression of E-cad. Conclusion. circSPECC1 promotes cell proliferation and migration by affecting the epithelial-mesenchymal transition of LNCaP prostate cancer cells.

Circular RNA in autoimmune diseases: special emphasis on regulation mechanism in RA and SLE

BACKGROUND

Autoimmune diseases are diseases caused by tissue damage caused by the body's immune response to autoantibodies. Circular RNAs (CircRNAs) are a kind of special endogenous non-coding RNA that play a biological role by regulating gene transcription.

METHODS

In this work, we searched the PubMed, Web of Science (SCIE), National Science and Technology Library (NSTL), and ScienceDirect Online (SDOL) databases to summarize the impact of circRNAs on autoimmune diseases, especially the results of circRNAs in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).

RESULTS

The study on the function of circRNAs and autoimmune diseases further deepened our understanding of the development and pathogenesis of autoimmune diseases. CircRNAs may act as miRNA sponges to regulate biological processes and affect the occurrence and development of autoimmune diseases. CircRNAs are closely related to the pathogenesis of RA and SLE and may become potential biomarkers for the diagnosis and treatment of RA and SLE.

CONCLUSION

CircRNAs play an important role in the pathogenesis of RA, SLE and other autoimmune diseases, and are expected to provide new biomarkers for the diagnosis and treatment of autoimmune diseases. However, the function and mechanism of circRNAs in autoimmune diseases need more comprehensive research.

Exosomal circular RNAs: A chief culprit in cancer chemotherapy resistance

Chemotherapy is one of the primary treatments for malignant tumors. However, the acquired drug resistance hinders clinical efficacy and leads to treatment failure in most patients. Exosomes are cell-derived vesicles with a diameter of 30-150 nm carrying and delivering substances such as DNAs, RNAs, lipids, and proteins for cellular communication in tumor development. Circular RNAs (circRNAs) present covalently closed-loop RNA structures, which regulate tumor cell proliferation, apoptosis, and metastasis by controlling different genes and signaling pathways. CircRNAs are abundant and stably expressed in exosomes. Recent studies have shown that they play critical roles in chemotherapy resistance in various cancers. In this review, we summarized the origin of exosomes and discussed the regulation mechanism of exosomal circRNAs in cancer drug resistance.

Research on liquid biopsy for cancer: A bibliometric analysis

BACKGROUND

In recent years, liquid biopsy has shown great potential for improving cancer diagnosis and treatment. This study aimed to explore the trends and prospects in liquid biopsy for cancer from a bibliometric perspective.

METHODS

Reviews and articles on liquid biopsy and cancer were collected from the Web of Science Core Collection (WoSCC). Key bibliometric characteristics were analyzed using CiteSpace. Co-occurrence analysis of keywords and co-citation analysis of references was performed.

RESULTS

A total of 6331 publications from 11 years of scientific research were retrieved. Ninety-five countries and 7004 institutions in liquid biopsy and cancer contributed. The United States (US) and China published the most articles. The institution with the most published articles was the University of Texas MD Anderson Cancer Center. The most published journals were Cancer and Frontiers in Oncology. "Bettegowda (2014)" was the most cited reference with the highest burst strength in the last decade. Cluster analysis revealed that the recent hot topics were "circulating tumor cells," "cancer," and "exosomes."

CONCLUSIONS

This bibliometric analysis maps the basic knowledge structure of the field of liquid biopsy for cancer. The field is entering a phase of rapid development. The hot spots identified in this study deserve further investigation.

Hsa_circ_0128846 knockdown attenuates the progression of pancreatic cancer by targeting miR-1270/NR3C1 axis

The considerable role of circular RNAs (circRNAs) make them prospective biomarkers in cancer therapy. Our study aimed to unveil the function of circ_0128846 in pancreatic cancer (PC). The expressions of circ_0128846, miR-1270 and NR3C1 mRNA were measured via RT-qPCR. The expressions of NR3C1 protein and apoptosis-related markers (Bax and Bcl-2) were measured via western blotting. CCK-8, colony-forming, or wound healing assay was respectively utilized to identify cell proliferation, growth and migration. Xenograft model was developed to evaluate tumor growth affected by circ_0128846 in vivo. The putative binding between miR-1270 and circ_0128846 or NR3C1 was testified by dual-luciferase reporter, RIP or pull-down assay. Circ_0128846 showed elevated expression in PC. Circ_0128846 deficiency restrained cancer cell proliferation, colony formation and migratory ability, enhanced cell apoptotic rate, and also impeded tumor development in vivo. Circ_0128846 directly targeted miR-1270 whose expression was declined in PC. The suppressive effects of silencing circ_0128846 on PC cell malignant phenotypes were largely reversed by miR-1270 inhibition. NR3C1 was targeted by miR-1270 and was highly regulated in PC. The repressive effects of NR3C1 knockdown on PC cell malignant phenotypes were partly abolished by miR-1270 inhibition. Circ_0128846 deficiency blocked PC progression via mediating the miR-1270/NR3C1 pathway, which partly illustrated PC pathogenesis.

The Function and Therapeutic Potential of Circular RNA in Cardiovascular Diseases

Circular RNA (circRNA) has a closed-loop structure, and its 3' and 5' ends are directly covalently connected by reverse splicing, which is more stable than linear RNA. CircRNAs usually possess microRNA (miRNA) binding sites, which can bind miRNAs and inhibit miRNA function. Many studies have shown that circRNAs are involved in the processes of cell senescence, proliferation and apoptosis and a series of signalling pathways, playing an important role in the prevention and treatment of diseases. CircRNAs are potential biological diagnostic markers and therapeutic targets for cardiovascular diseases (CVDs). To identify biomarkers and potential effective therapeutic targets without toxicity for heart disease, we summarize the biogenesis, biology, characterization and functions of circRNAs in CVDs, hoping that this information will shed new light on the prevention and treatment of CVDs.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

Motivation

Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

Results

We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via back-splicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues where we identified two distinct types of circRNAs characterized by a distinct ratio of the binding site length. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research.

Availability

https://github.com/biomedbigdata/circRNA-sponging.

Contact

markus.daniel.hoffmann@tum.de ; markus.list@tum.de.

Supplementary Material

Supplementary data are available at Bioinformatics online.

Recent Advances of Circular RNAs as Biomarkers for Osteosarcoma

Osteosarcoma is the most common primary malignant bone tumor in young adult, which is prone to early metastasis and poor prognosis. The current treatment methods need to be improved. Circular RNA is a covalently blocked circular, non-coding RNA that plays an essential role in the occurrence, development, clinical diagnosis, and treatment of various diseases. Recently, an increasing number of circRNAs have been identified in osteosarcoma. Understanding its role in osteosarcoma is conducive to the early detection, diagnosis, and treatment of osteosarcoma. In this paper, we reviewed the mechanism of action of circular RNA in the occurrence and development of osteosarcoma and its clinical application in recent years.

Circ_0075960 targets the miR-202-5p/CTNND1 axis to promote the growth and migration of endometrial carcinoma cells via regulating Wnt/β-catenin signaling activity

BACKGROUND

Endometrial carcinoma (EC) is one of the most common malignant tumors of the female reproductive tract, involving multiple molecular alterations. Circular RNA (circRNA) dysregulation is frequently observed in EC tissues, suggesting the involvement of circRNA in EC development. We aimed to investigate the role of circ_0075960 in EC.

METHODS

Real-time quantitative polymerase chain reaction (RT-qPCR) and western blot assays were applied for expression analysis. CCK-8, EdU, colony formation, flow cytometry and wound healing assays were employed for functional analysis. The predicted binding relationship between miR-202-5p and circ_0075960 or CTNND1 was validated by dual-luciferase reporter experiment. In vivo animal models were constructed in nude mice to verify the role of circ_0075960 in tumor growth.

RESULTS

Circ_0075960 and CTNND1 were upregulated, while miR-202-5p was downregulated in EC. Knockdown of circ_0075960 induced EC cell apoptosis, suppressed cell proliferation and migration, and repressed tumor growth in animal models. MiR-202-5p was targeted by circ_0075960 and it directly bound to CTNND1 3'UTR. The inhibition of circ_0075960 knockdown or miR-202-5p enrichment on EC cell proliferation and migration was reversed by miR-202-5p depletion or CTNND1 overexpression, respectively. Circ_0075960 targeted miR-202-5p to positively regulate CTNND1 expression. Moreover, circ_0075960 knockdown weakened the activity of Wnt/β-catenin signaling via targeting the miR-202-5p/CTNND1 axis.

CONCLUSION

Circ_0075960 targets the miR-202-5p/CTNND1 axis to modulate Wnt/β-catenin signaling activity, thus contributing to the malignant development of EC.

Circular RNAs: pivotal role in the leukemogenesis and novel indicators for the diagnosis and prognosis of acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive hematological malignancy and affected patients have poor overall survival (OS) rates. Circular RNAs (circRNAs) are a novel class of non-coding RNAs (ncRNAs) with a unique loop structure. In recent years, with the development of high-throughput RNA sequencing, many circRNAs have been identified exhibiting either up-regulation or down-regulation in AML patients compared with healthy controls. Recent studies have reported that circRNAs regulate leukemia cell proliferation, stemness, and apoptosis, both positively and negatively. Additionally, circRNAs could be promising biomarkers and therapeutic targets in AML. In this study, we present a comprehensive review of the regulatory roles and potentials of a number of dysregulated circRNAs in AML.

The circHMGCS1-miR-205-5p-ErBB3 axis mediated the Sanggenon C-induced anti-proliferation effects on human prostate cancer

Prostate cancer (PCa) is associated with a high incidence and metastasis rate globally, resulting in an unsatisfactory prognosis and a huge economic burden due to the current deficient of therapeutic strategies. As the most abundant component of Cortex Mori, Sanggenon C (SC) is well known to possess bioactivities in tumors, but its mechanism is poorly understood. Consequently, we attempted to investigate whether SC could modulate circular RNA(s) levels and hence anti-PCa development. We found that SC dramatically promoted cell apoptosis and induced G0/G1 phase arrest in PCa cell lines via the circHMGCS1-miR-205-5p-ErBB3 axis. In brief, circHMGCS1 is highly expressed in PCa and is positively correlated with the degree of malignancy. Over-expression of circHMGCS1 is not only associated with the proliferation of PCa cells but also blocks SC-induced pro-apoptotic effects. As a verified sponge of circHMGCS1, miR-205-5p is down-regulated in PCa tumors, which negatively regulates PCa cell proliferation by modulating ErBB3 expression. After miR-205-5p mimics or inhibitors were used to transfect PCa cells, the effects of circHMGCS1 OE and SC on PCa cells were completely diminished. Similar to miR-205-5p inhibitors, siErBB3 could oppose SC-triggered pro-apoptotic effects on PCa cells. All these results were confirmed in vivo. Together, SC exerts its anti-tumor effects on PCa by inhibiting circHMGCS1 expression and results in the latter losing the ability to sponge miR-205-5p. Subsequently, unfettered miR-205-5p could mostly down-regulate ErBB3 expression by binding to the 5'UTR of ErBB3 mRNA, which eventually resulted in PCa cell cycle arrest and pro-apoptosis.

Hypoxia-induced circADAMTS6 in a TDP43-dependent manner accelerates glioblastoma progression via ANXA2/ NF-κB pathway

Circular RNAs (circRNAs) play important roles in the malignant progression of tumours. Herein, we identified an unreported circRNA (hsa-circ-0072688, also named circADAMTS6) that is specifically upregulated in the hypoxic microenvironment of glioblastoma and closely correlated with poor prognosis of gliblastoma patients. We found that circADAMTS6 promotes the malignant progression of glioblastoma by promoting cell proliferation and inhibiting apoptosis. Mechanistically, the hypoxic tumour microenvironment upregulates circADAMTS6 expression through transcription factor activator protein 1 (AP-1) and RNA-binding protein TAR DNA-binding protein 43 (TDP43). Moreover, circADAMTS6 accelerates glioblastoma progression by recruiting and stabilising annexin A2 (ANXA2) in a proteasomes-dependent manner. Furthermore, we found T-5224 (AP-1 inhibitor) treatment induces downregulation of circADAMTS6 and then inhibits tumour growth. In conclusion, our findings highlight the important role of the circADAMTS6/ANXA2 axis based on hypoxic microenvironment in glioblastoma progression, as well as its regulation in NF-κB pathway. Targeting circADAMTS6 is thus expected to become a novel therapeutic strategy for glioblastoma.

Whole Blood-Derived circUSP10 Acts as a Diagnostic Biomarker in Patients With Early-Stage Non-Small-Cell Lung Cancer

Accumulating evidence has indicated that differentially expressed noncoding circular RNAs (circRNAs) play essential roles in the occurrence and development of various types of cancer. Here, we aimed to identify and explore the diagnostic value of hsa_circ_0003026 (named circUSP10) in patients with early non-small-cell lung cancer (NSCLC). The differentially expressed circRNAs were screened from the microarray-based assay of human NSCLC tissues and their corresponding noncancerous tissues, and the candidate circRNAs were further verified in patients with NSCLC using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Circulating circUSP10 was isolated from whole blood of healthy people and patients with NSCLC and was detected by RT-qPCR. In addition, the diagnostic value of circUSP10 in early NSCLC was evaluated by receiver operating characteristic (ROC) curve analysis. We found that circUSP10 was upregulated in tumor tissues from patients with early NSCLC and associated with tumor size and tumor-node-metastasis (TNM) stage. Importantly, circUSP10 was obviously upregulated in the whole blood of patients with NSCLC. Additionally, whole blood-derived circUSP10 showed good diagnostic performance for screening early NSCLC and was relatively stable in blood under adverse conditions. These findings demonstrate that circUSP10 may act as a novel biomarker for the diagnosis of early-stage NSCLC, suggesting the potential of circUSP10 in RNA-based therapy for cancer.

CircNRIP1: An emerging star in multiple cancers

Circular RNAs (circRNAs) are a new class of non-coding RNAs (ncRNAs) with a closed-loop structure that is highly stable and widely present in the eukaryotic cytoplasm. In recent years, circRNA has played a non-negligible role in the occurrence and development of a variety of diseases, which has attracted the research attention of many scholars. Circular RNA nuclear receptor interacting protein 1 (circNRIP1), a newly discovered circRNA, has been confirmed to be closely associated with cervical carcinoma (CC), colorectal cancer (CRC), esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), nasopharyngeal carcinoma (NPC), non-small cell lung cancer (NSCLC), osteosarcoma (OS), ovarian cancer (OC) and papillary thyroid carcinoma (PTC). CircNRIP1 can regulate the activity of ERK1/2, PI3K/AKT, and AKT/mTOR signaling pathways. In this review, the author summarizes the biological functions and target molecular mechanisms in carcinogenesis, to point out the potential clinical values and applications of circNRIP1 in diagnosing and treating cancer.

An evaluation of gastric adenocarcinoma-associated CircRNAs based on microarray meta-analysis and ceRNA networks

Gastric cancer is the fourth leading cause of cancer-related mortality and one of the most commonly diagnosed malignancies worldwide. Gastric adenocarcinoma (GAC) accounts for the majority of gastric cancer cases. Circular RNAs (circRNAs) have been shown to be associated with carcinogenesis and cancer progression. This research aims to investigate GAC-associated circRNAs and the underlying mechanisms of circRNA-miRNA-mRNA networks in the development and progression of GAC. Differentially expressed miRNAs and mRNAs (DEMs and DEGs) were identified in Gene Expression Omnibus (GEO) microarray datasets using the R package Limma. A microarray meta-analysis was performed to identify potential GAC-associated circRNAs with high statistical power, resulting in 13 up-regulated and 19 down-regulated circRNAs. CircRNA-miRNA-mRNA networks were constructed by combining predicted and experimentally validated databases and considering differentially expressed miRNAs and mRNAs. The constructed ceRNA networks revealed the potential regulatory effect of hsa_circ_0002019 and hsa_circ_0074736 on key survival-related genes. The expression levels of these two circRNAs were measured in plasma samples from GAC patients and healthy controls using SYBR Green-based real-time PCR. Axon guidance, cellular senescence, AGE-RAGE signaling pathway in diabetic complications, and AMPK signaling pathway were among the major significant (P-value <0.05) enriched pathways of "main mRNAs" in the constructed ceRNA networks. In conclusion, we identified strongly correlated circRNAs and their likely mechanisms of action in GAC, which may improve the knowledge of regulatory networks underlying GAC formation and contribute to developing better strategies for early diagnosis, prognosis, and treatment.

CircHADHA-augmented autophagy suppresses tumor growth of colon cancer by regulating autophagy-related gene via miR-361

Colon cancer undergoes a traditional pathway from colon polyps to colon cancer. It is of great significance to investigate the key molecules involved in carcinogenesis from polyps to malignancies. Circular RNAs (circRNAs) are stably expressed in human body fluids such as plasma. Here, we demonstrated a differential expression pattern of plasma circRNAs in healthy individuals, colon polyp patients and colon cancer patients using circRNA Arraystar microarray. We explored that circRNA HADHA (circHADHA) was upregulated in plasma from polyp patients, whereas it was downregulated in plasma from colon cancer patients. Overexpression of circHADHA promoted autophagy in colon epithelial cells. Moreover, in colon cancer cells, overexpression of circHADHA promoted autophagy, whereas it inhibited cell proliferation and colony formation. CircHADHA increased the expression of ATG13 via miR-361 in both colon epithelial and cancer cells. ATG13 knockdown reduced autophagy even in the presence of circHADHA in colon cancer cells. Furthermore, the growth of circHADHA-overexpressing colon cancer cell-derived xenograft tumors was significantly decreased compared with control tumors in nude mice. In conclusion, circHADHA was differentially expressed in the plasma of healthy individuals, colon polyp patients and colon cancer patients. CircHADHA promoted autophagy by regulating ATG13 via miR-361 in both colon epithelial and cancer cells. CircHADHA suppressed tumor growth by inducing cell autophagy in colon cancer cells. CircHADHA potentially serves as a biomarker for screening of precursor colon cancer and a therapeutic target for colon cancer treatment.