Mini Review: Circular RNAs as Potential Clinical Biomarkers for Disorders in the Central Nervous System

Evaluation of the role of circular RNA (circ-FAF1) as a diagnostic biomarker for breast cancer in a cohort of Egyptian breast cancer patients

BACKGROUND

The identification of circulating potential biomarkers may help earlier diagnosis of breast cancer, which is critical for effective treatment and better disease outcomes. We aimed to study the role of circ-FAF1 as a diagnostic biomarker in female breast cancer using peripheral blood samples of these patients, and to investigate the relation between circ-FAF1 and different clinicopathological features of the included patients.

METHODS AND RESULTS

This case-control study enrolled 60 female breast cancer patients and 60 age-matched healthy control subjects. For all study subjects, serum samples were collected for RNA extraction followed by reverse transcription and quantitative real time polymerase chain reaction for circ-FAF1 relative expression level. Serum circ-FAF1 was significantly downregulated in the studied patients compared to control subjects (p < 0.001). Low expression level of circ-FAF1 was significantly associated with presence of lymph node spread (p < 0.001), positive metastasis (p = 0.002), estrogen receptor negativity (p < 0.001), HER2 positivity (p < 0.001), and it was moderately correlated with higher Ki-67 index (r=-0.429, p = 0.001). However, circulating circ-FAF1 level had no statistically significant correlation with progesterone receptor status (p = 0.053), tumor histopathological type (p = 0.895) and histological grade (p = 0.369). Using ROC curve, serum circ-FAF1 had an AUC of 0.885, 81.67% diagnostic sensitivity and 76.67% diagnostic specificity.

CONCLUSION

Serum level of circ-FAF1 is a promising biomarker that can help in diagnosis of breast cancer. The low expression in breast cancer was correlated with lymph node spread, presence of metastasis, and with histopathological parameters suggestive of a worse outcome in these patients.

Candidate circRNAs related to skeletal muscle development in Dazu black goats

Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.

Unraveling Dysregulated Cell Signaling Pathways, Genetic and Epigenetic Mysteries of Parkinson's Disease

Parkinson's disease (PD) is a prevalent and burdensome neurodegenerative disorder that has been extensively researched to understand its complex etiology, diagnosis, and treatment. The interplay between genetic and environmental factors in PD makes its pathophysiology difficult to comprehend, emphasizing the need for further investigation into genetic and epigenetic markers involved in the disease. Early diagnosis is crucial for optimal management of the disease, and the development of novel diagnostic biomarkers is ongoing. Although many efforts have been made in the field of recognition and interpretation of the mechanisms involved in the pathophysiology of the disease, the current knowledge about PD is just the tip of the iceberg. By scrutinizing genetic and epigenetic patterns underlying PD, new avenues can be opened for dissecting the pathology of the disorder, leading to more precise and efficient diagnostic and therapeutic approaches. This review emphasizes the importance of studying dysregulated cell signaling pathways and molecular processes associated with genes and epigenetic alterations in understanding PD, paving the way for the development of novel therapeutic strategies to combat this devastating disease.

Penumbra-targeted CircOGDH siRNA-loaded nanoparticles alleviate neuronal apoptosis in focal brain ischaemia

BACKGROUND

Nanoparticles (NPs) are a class of substances that can be loaded with therapeutic agents delivered to specific areas. In our earlier research, we identified a neuron-derived circular RNA (circRNA), circular oxoglutarate dehydrogenase (CircOGDH), as a promising therapeutic target for acute ischaemic stroke. This study dedicated to explore a prospective preliminary strategy of CircOGDH-based NP delivered to the ischaemic penumbra region in middle cerebral artery occlusion/reperfusion (MCAO/R) mice.

METHODS

Immunofluorescence in primary cortex neurons and in vivo fluorescence imaging revealed endocytosis of Poly(lactide-co-glycolide) (PLGA) poly amidoamine(PAMAM)@CircOGDH small interfering RNA (siRNA) NPs. Western blotting analysis and CCK8 assay were performed to evaluate the apoptotic level in ischaemic neurons treated with PLGA-PAMAM@CircOGDH siRNA NPs. Quantitative reverse transcription PCR experiments, mice behaviour test, T2 MRI analysis, Nissl and TdT-mediated dUTP nick end labeling (TUNEL) co-staining were performed to evaluate the apoptosis level of ischaemic penumbra neurons in MCAO/R mice. Biosafety evaluation of NPs in MCAO/R mice was detected by blood routine examination, liver and kidney function examination and HE staining.

RESULTS

PLGA-PAMAM@CircOGDH siRNA NPs were successfully assembled. Endocytosis of PLGA-PAMAM@CircOGDH siRNA NPs in ischaemic neurons alleviated neuronal apoptotic level in vitro and in vivo. Furthermore, mice behaviour test showed that the neurological defects of MCAO/R mice were significantly alleviated after the tail injection of PLGA-PAMAM@CircOGDH siRNA NPs, and no toxic effects were observed.

CONCLUSION

In conclusion, our results suggest that PLGA-PAMAM@CircOGDH siRNA NPs can be delivered to the ischaemic penumbra region and alleviate neuron apoptosis in MCAO/R mice and in ischaemic neurons; therefore, our study provides a desirable approach for using circRNA-based NPs for the treatment of ischaemic stroke.

Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer

Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.

Changes in circMyt1l/rno-let-7d-5p/brain-derived neurotrophic factor. A damaged periventricular white matter damage model in neonatal rats

OBJECTIVES

To investigate the function of circMyt1l/rno-let-7d-5p/BDNF in the white matter damage of premature rats.

METHODS

Bioinformatic analysis was used to analyze the differential expression of circMyt1l and its interacting miRNAs and mRNAs in rats with periventricular white matter damage. Rats at postnatal day 3 had their right common carotid artery permanently ligated, and were then exposed for 2 h to 6 % O2, or sham surgery and exposure to normal O2 levels (sham). CircMyt1l and rno-let-7d-5p expression was detected and BDNF protein levels were analyzed at 24, 48, and 72 h post hypoxia-ischemia.

RESULTS

Bioinformatic analysis suggested that circMyt1l, rno-let-7d-5p and BDNF interact. CircMyt1l expression decreased significantly relative to the sham-operated rats (p<0.01) in an exposure time-dependent manner. Contrastingly, rno-let-7d-5p increased significantly relative to the sham-operated rats (p<0.01) in an exposure time dependent manner. BDNF protein levels decreased significantly relative to the sham-operated rats (p<0.05) in an exposure time dependent manner.

CONCLUSIONS

The expression levels of circMyt1l/rno-let-7d-5p/BDNF are interrelated in periventricular white matter damage. Decreased circMyt1l expression of promoted the effect of rno-let-7d-5p and decreased the level of its target, BDNF.

Glycolysis in human cancers: Emphasis circRNA/glycolysis axis and nanoparticles in glycolysis regulation in cancer therapy

The metabolism of cancer has been an interesting hallmark and metabolic reprogramming, especially the change from oxidative phosphorylation in mitochondria to glucose metabolism known as glycolysis occurs in cancer. The molecular profile of glycolysis, related molecular pathways and enzymes involved in this mechanism such as hexokinase have been fully understood. The glycolysis inhibition can significantly decrease tumorigenesis. On the other hand, circRNAs are new emerging non-coding RNA (ncRNA) molecules with potential biological functions and aberrant expression in cancer cells which have received high attention in recent years. CircRNAs have a unique covalently closed loop structure which makes them highly stable and reliable biomarkers in cancer. CircRNAs are regulators of molecular mechanisms including glycolysis. The enzymes involved in the glycolysis mechanism such as hexokinase are regulated by circRNAs to modulate tumor progression. Induction of glycolysis by circRNAs can significantly increase proliferation rate of cancer cells given access to energy and enhance metastasis. CircRNAs regulating glycolysis can influence drug resistance in cancers because of theirimpact on malignancy of tumor cells upon glycolysis induction. TRIM44, CDCA3, SKA2 and ROCK1 are among the downstream targets of circRNAs in regulating glycolysis in cancer. Additionally, microRNAs are key regulators of glycolysis mechanism in cancer cells and can affect related molecular pathways and enzymes. CircRNAs sponge miRNAs to regulate glycolysis as a main upstream mediator. Moreover, nanoparticles have been emerged as new tools in tumorigenesis suppression and in addition to drug and gene delivery, then mediate cancer immunotherapy and can be used for vaccine development. The nanoparticles can delivery circRNAs in cancer therapy and they are promising candidates in regulation of glycolysis, its suppression and inhibition of related pathways such as HIF-1α. The stimuli-responsive nanoparticles and ligand-functionalized ones have been developed for selective targeting of glycolysis and cancer cells, and mediating carcinogenesis inhibition.

Association of Circulating Circular RNAs (hg38_circ_0008980, and CircDLGAP4) in Diagnosis, Diseases Severity, and Prognosis of Ischemic Stroke

Background

Fast diagnosing ischemic stroke (IS) is a critical issue in clinical studies, as it allows more effective therapy and stops the progression of IS. The blood level of circular RNAs (CircRNAs) after stroke may be a rapid diagnostic marker.

Methods

In this study, the blood level of circRNAs was evaluated using a real-time polymerase chain reaction (PCR). We used logistic and linear regression analysis to assess the potential of circRNAs levels with the risk of IS.

Results

circRNA DLG associated protein 4 (CircDLGAP4) was decreased in patients compared with controls, and logistic regression showed its expression negatively associated with IS risk. The expression level of human genome version 38_Circular_0008980 (hg38_circ_0008980) was reduced significantly in patients with small vessel disease (SVD), and the linear regression analysis showed a negative relationship between hg38_circ_0008980 expressions with SVD subtype. hg38_circ_0008980 expression relative to controls showed a significant association with IS risk.

Conclusion

Taken together, we found a significant decrease in the level of hg38_circ_0008980 after IS; it may act as a novel circRNA in IS pathophysiology with a positive correlation with stroke severity.

Circadian gene ARNTL initiates circGUCY1A2 transcription to suppress non-small cell lung cancer progression via miR-200c-3p/PTEN signaling

BACKGROUND

As a subclass of endogenous stable noncoding RNAs, circular RNAs are beginning to be appreciated for their potential as tumor therapeutics. However, the functions and mechanisms by which circRNAs exert protective functions in non-small cell lung cancer (NSCLC) remain largely elusive.

METHODS

The prognostic role of circGUCY1A2 was explored in lung adenocarcinoma specimens. The overexpressed and knockdown plasmids were used to evaluate the effect of circGUCY1A2 on NSCLC cell proliferation and apoptosis efficacy. Luciferase reporter system is used to prove that circGUCY1A2 could bind to miRNA. Chip-PCR was used to prove that circGUCY1A2 could be initiated by transcription factors ARNTL. Subcutaneous tumorigenicity grafts models were established to validate findings in vivo.

RESULTS

The expression of circGUCY1A2 were significantly reduced (P < 0.001) and negatively correlated with tumor size (P < 0.05) in non-small cell lung cancer (NSCLC). CircGUCY1A2 upregulation promoted apoptosis and inhibits cell proliferation and growth of subcutaneous tumorigenicity grafts in nude mice (P < 0.01). In addition, intra-tumor injection of pLCDH-circGUCY1A2 inhibited tumor growth in patient-derived NSCLC xenograft models (PDX). Mechanism studies showed that circGUCY1A2 could act as a sponge to competitively bind miR-200c-3p, promote PTEN expression, and thereby inhibit PI3K/AKT pathway. In addition, we found that the circadian gene ARNTL, which was reduced in NSCLC and prolonged the overall survival of patients, could bind to the promoter of circGUCY1A2, thereby increasing its expression.

CONCLUSIONS

This study is an original demonstration that ARNTL can inhibit the development of lung adenocarcinoma through the circGUCY1A2/miR-200c-3p/PTEN axis, and this finding provides potential targets and therapeutic approaches for the treatment of lung adenocarcinoma.

Prenatal alcohol exposure dysregulates spinal and circulating immune cell circular RNA expression in adult female rats with chronic sciatic neuropathy

Alcohol consumption during pregnancy is associated with Fetal Alcohol Spectrum Disorders (FASD) that results in a continuum of central nervous system (CNS) deficits. Emerging evidence from both preclinical and clinical studies indicate that the biological vulnerability to chronic CNS disease in FASD populations is driven by aberrant neuroimmune actions. Our prior studies suggest that, following minor nerve injury, prenatal alcohol exposure (PAE) is a risk factor for developing adult-onset chronic pathological touch sensitivity or allodynia. Allodynia in PAE rats occurs concurrently with heightened proinflammatory peripheral and spinal glial-immune activation. However, minor nerve-injured control rats remain non-allodynic, and corresponding proinflammatory factors are unaltered. A comprehensive molecular understanding of the mechanism(s) that underlie PAE-induced proinflammatory bias during adulthood remains elusive. Non-coding circular RNAs (circRNAs) are emerging as novel modulators of gene expression. Here, we hypothesized that PAE induces dysregulation of circRNAs that are linked to immune function under basal and nerve-injured conditions during adulthood. Utilizing a microarray platform, we carried out the first systematic profiling of circRNAs in adult PAE rats, prior to and after minor nerve injury. The results demonstrate a unique circRNA profile in adult PAE rats without injury; 18 circRNAs in blood and 32 spinal circRNAs were differentially regulated. Following minor nerve injury, more than 100 differentially regulated spinal circRNAs were observed in allodynic PAE rats. Bioinformatic analysis identified that the parental genes of these circRNAs are linked to the NF-κB complex, a central transcription factor for pain-relevant proinflammatory cytokines. Quantitative real-time PCR was employed to measure levels of selected circRNAs and linear mRNA isoforms. We have validated that circVopp1 was significantly downregulated in blood leukocytes in PAE rats, concurrent with downregulation of Vopp1 mRNA levels. Spinal circVopp1 levels were upregulated in PAE rats, regardless of nerve injury. Additionally, PAE downregulated levels of circItch and circRps6ka3, which are linked to immune regulation. These results demonstrate that PAE exerts long-lasting dysregulation of circRNA expression in blood leukocytes and the spinal cord. Moreover, the spinal circRNA expression profile following peripheral nerve injury is differentially modulated by PAE, potentially contributing to PAE-induced neuroimmune dysregulation.

Systemic lupus erythematosus: From non-coding RNAs to exosomal non-coding RNAs

Systemic lupus erythematosus (SLE), as an immunological illness, frequently impacts young females. Both vulnerabilities to SLE and the course of the illness's clinical symptoms have been demonstrated to be affected by individual differences in non-coding RNA expression. Many non-coding RNAs (ncRNAs) are out of whack in patients with SLE. Because of the dysregulation of several ncRNAs in peripheral blood of patients suffering from SLE, these ncRNAs to be showed valuable as biomarkers for medication response, diagnosis, and activity. NcRNAs have also been demonstrated to influence immune cell activity and apoptosis. Altogether, these facts highlight the need of investigating the roles of both families of ncRNAs in the progress of SLE. Being aware of the significance of these transcripts perhaps elucidates the molecular pathogenesis of SLE and could open up promising avenues to create tailored treatments during this condition. In this review we summarized various non-coding RNAs and Exosomal non-coding RNAs in SLE.

Systematic Analysis of RNA Expression Profiles in Different Ischemic Cortices in MCAO Mice

The prognosis of ischemic stroke patients is highly associated with the collateral circulation. And the competing endogenous RNAs (ceRNAs) generated from different compensatory supply regions may also involve in the regulation of ischemic tissues prognosis. In this study, we found the apoptosis progress of ischemic neurons in posterior circulation-supplied regions (close to PCA, cortex2) was much slower than that in anterior circulation-supplied territory (close to ACA, cortex1) in MCAO-3-h mice. Using the RNA sequencing and functional enrichment analysis, we analyzed the difference between RNA expression profile in cortex1 and cortex2 and the related biological processes. The results indicated that the differential expressed ceRNAs in cortex1 were involved in cell process under acute injury, while the differential expressed ceRNAs in cortex2 was more likely to participate in long-term injury and repair process. Besides, by establishing the miRNA-ceRNA interaction network we further sorted out two specifically distributed miRNAs, namely mmu-miR446i-3p (in cortex1) and mmu-miR3473d (in cortex2). And the specifically increased mmu-miR3473d in cortex2 mainly involved the angiogenesis and cell proliferation after ischemic stroke, which may be the critical reason for the longer therapeutic time window in cortex2. In conclusion, the present study reported the specific changes of ceRNAs in distinct compensatory regions potentially involved in the evolution of cerebral ischemic tissues and the unbalance prognosis after stroke. It provided more evidence for the collateral compensatory effects on patients' prognosis and carried out the new targets for the ischemic stroke therapy.

The molecular mechanism of γ-aminobutyric acid against AD: the role of CEBPα/circAPLP2/miR-671-5p in regulating CNTN1/2 expression

The expression levels of the synaptic-related proteins contactin 1/2 (CNTN1/2) are down-regulated in the brain of Alzheimer's disease (AD), but the mechanism has not been clarified. γ-Aminobutyric acid (GABA) is considered a biologically active ingredient in food. Our previous research revealed that GABA can regulate CEBPα expression in Aβ-treated U251 cells. However, it is uncertain whether GABA can antagonize the pathogenesis of AD. Whether GABA can inhibit the reduction in CNTN1/2 expression by regulating CEBPα/circAPLP2/miR-671-5p in the AD brain remains unclear yet. Here, we demonstrate that GABA could attenuate the deposition of Aβ in the brain and ameliorate cognitive impairments in AD model mice. The expressions of CEBPα, circAPLP2, and CNTN1/2 were decreased and that of miR-671-5p was increased in AD model mouse brains and Aβ-induced SH-SY5Y cells. These alterations were partly reversed by GABA. The CNTN1/2 expression was down-regulated and up-regulated in SH-SY5Y cells treated with miR-671-5p mimics and miR-671-5p inhibitors, respectively. The results from the luciferase reporter assay revealed that miR-671-5p could bind to the 3'-untranslated region of circAPLP2. The silencing of circAPLP2 with the siRNA duplex caused an up-regulation of miR-671-5p and a down-regulation of CNTN1/2 in SH-SY5Y cells. The silencing of CEBPα with the siRNA duplex caused a down-regulation of circAPLP2 or CNTN1/2 and an up-regulation of miR-671-5p. In conclusion, GABA may decrease the deposition of Aβ in the brain, inhibit the down-regulation of CNTN1/2 expression, and ameliorate the cognitive deficits of AD model mice. The CEBPα/circAPLP2/miR-671-5p pathway plays a role in regulating CNTN1/2 expression by GABA in AD.

CircRalgapa1 facilitates morphine tolerance via miR-873a-5p/A20 axis in mice

Morphine tolerance (MT) caused by long-term use of morphine is a major medical problem. The underlying molecular mechanisms of morphine tolerance remain unclear. Here, we establish the morphine tolerance model in mice and verify whether a novel circRNA, circRalgapa1 is involved in morphine tolerance and its specific molecular mechanism. We show that the expression of circRalgapa1 in the spinal cord is significantly down-expressed in the spinal cord of morphine-tolerant mice. CircRalgapa1 is mainly located in the neuronal cytoplasm and co-localizes with miR-873a-5p. Mechanically, circRalgapa1 acts as competing endogenous RNAs (ceRNAs) to regulate the inhibitory of miR-873a-5p on A20 (also known as tumor necrosis factor α-induced protein 3, TNFAIP3). Functionally, overexpression of circRalgapa1 by intrathecal injection of adeno-associated virus (AAV- circRalgapa1) attenuated the formation of morphine tolerance and partially reversed the development of morphine tolerance. Moreover, overexpression of miR-873a-5p blocked the effect of AAV-circRalgapa1 on alleviating morphine tolerance in mice. In conclusion, chronic morphine administration-mediated down-regulation of circRalgapa1 in the spinal cord contributes to morphine tolerance via miR-873a-5p/A20 axis in mice. Overexpression of circRalgapa1 may be a promising RNA-based therapy for morphine tolerance.

Silencing of the circ-Arhgap5 RNA protects neuronal PC12 cells against injury and depends on the miR-29a-3p/Rock1 axis

Circular RNAs (circRNAs) are abundantly expressed in human central nervous system. Here, we explored the role of circ_Arhgap5 in cerebral ischemia/reperfusion (I/R)-induced nerve injury in PC12 cells and its associated mechanism. Cell proliferation ability was assessed by 5-Ethynyl-2'-deoxyuridine (Edu) assay and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Flow cytometry (FCM) was applied to assess cell apoptotic rate. Cell death was analyzed by lactate dehydrogenase (LDH) assay. Oxygen-glucose deprivation and reoxygenation (OGD/R) up-regulates the expression of circRNA Rho GTPase activating protein 5 (circ_Arhgap5; mmu_circ_0000377) in PC12 cells. OGD/R exposure inhibited the proliferation and induced the apoptosis of PC12 cells, and the silence of circ_Arhgap5 attenuated OGD/R-induced injury in PC12 cells. miR-29a-3p was identified as a target of circ_Arhgap5 in PC12 cells. Circ_Arhgap5 knockdown-mediated protective effects in OGD/R-induced PC12 cells were reversed by the interference of miR-29a-3p. miR-29a-3p interacted with the 3' untranslated region (3'UTR) of Rho-associated coiled-coil-containing protein kinase 1 (Rock1), and circ_Arhgap5 can positively regulate Rock1 expression by sponging miR-29a-3p in PC12 cells. miR-29a-3p overexpression protected PC12 cells against OGD/R-induced damage by down-regulating Rock1. In conclusion, circ_Arhgap5 silencing protected PC12 cells from OGD/R-induced injury through mediating miR-29a-3p/Rock1 axis.

Circular RNAs: New players involved in the regulation of cognition and cognitive diseases

Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.

Landscape of circular RNAs in different types of lung cancer and an emerging role in therapeutic resistance (Review)

Lung cancer is one of the most common malignant tumor types and the leading cause of cancer‑associated death worldwide. Different types of lung cancer exhibit differences in terms of pathophysiology and pathogenesis, and also treatment and prognosis. Accumulating evidence has indicated that circular RNAs (circRNAs) are abnormally expressed among different types of lung cancer and confer important biological functions in progression and prognosis. However, studies comparing different circRNAs in lung cancer subtypes are scarce. Furthermore, circRNAs have an important role in drug resistance and are related to clinicopathological features in lung cancer. Summaries of the association of circRNAs with drug resistance are also scarce in the literature. The present study outlined the biological functions of circRNAs and focused on discriminating differential circRNA patterns and mechanisms in three different types of lung cancer. The emerging roles of circRNAs in the resistance to chemotherapy, targeted therapy, radiotherapy and immunotherapy were also highlighted. Understanding these aspects of circRNAs sheds light on novel physiological and pathophysiological processes of lung cancer and suggests the application of circRNAs as biomarkers for diagnosis and prognosis, as well as therapeutic resistance.

Pathophysiology of Ischemic Stroke: Noncoding RNA Role in Oxidative Stress

Stroke is a neurological disease that causes significant disability and death worldwide. Ischemic stroke accounts for 75% of all strokes. The pathophysiological processes underlying ischemic stroke include oxidative stress, the toxicity of excitatory amino acids, ion disorder, enhanced apoptosis, and inflammation. Noncoding RNAs (ncRNAs) may have a vital role in regulating the pathophysiological processes of ischemic stroke, as confirmed by the altered expression of ncRNAs in blood samples from acute ischemic stroke patients, animal models, and oxygen-glucose-deprived (OGD) cell models. Due to specific changes in expression, ncRNAs can potentially be biomarkers for the diagnosis, treatment, and prognosis of ischemic stroke. As an important brain cell component, glial cells mediate the occurrence and progression of oxidative stress after ischemic stroke, and ncRNAs are an irreplaceable part of this mechanism. This review highlights the impact of ncRNAs in the oxidative stress process of ischemic stroke. It focuses on specific ncRNAs that underlie the pathophysiology of ischemic stroke and have potential as diagnostic biomarkers and therapeutic targets.

Circular RNAs in Alzheimer's Disease: A New Perspective of Diagnostic and Therapeutic Targets

BACKGROUND

Circular RNAs (circRNAs), as covalently closed single-stranded noncoding RNA molecules, have been recently identified to involve in several biological processes, principally through targeting microRNAs. Among various neurodegenerative diseases (NDs), accumulating evidence has proposed key roles for circRNAs in the pathogenesis of Alzheimer's disease (AD); although the exact relationship between these RNA molecules and AD progression is not clear, they have been believed to mostly act as miRNA sponges or gene transcription modulators through correlating with multiple proteins, involved in the accumulation of Amyloid β (Aβ) peptides, as well as tau protein, as AD's pathological hallmark. More interestingly, circRNAs have also been reported to play diagnostic and therapeutic roles during AD progression.

OBJECTIVE

Literature review indicated that circRNAs could essentially contribute to the onset and development of AD. Thus, in the current review, the circRNAs' biogenesis and functions are addressed at first, and then the interplay between particular circRNAs and AD is comprehensively discussed. Eventually, the diagnostic and therapeutic significance of these noncoding RNAs is highlighted in brief.

RESULTS

A large number of circRNAs are expressed in the brain. Thereby, these RNA molecules are noticed as potential regulators of neural functions in healthy circumstances, as well as neurological disorders. Moreover, circRNAs have also been reported to have potential diagnostic and therapeutic capacities in relation to AD, the most prevalent ND.

CONCLUSION

CircRNAs have been shown to act as sponges for miRNAs, thereby regulating the function of related miRNAs, including oxidative stress, reduction of neuroinflammation, and the formation and metabolism of Aβ, all of which developed in AD. CircRNAs have also been proposed as biomarkers that have potential diagnostic capacities in AD. Despite these characteristics, the use of circRNAs as therapeutic targets and promising diagnostic biomarkers will require further investigation and characterization of the function of these RNA molecules in AD.

Differentially expression and function of circular RNAs in ovarian cancer stem cells

Background

Circular RNAs (circRNAs) are noncoding RNAs that regulate miRNA expression; however, their functions in cancer stem cells (CSCs) are not well known.

Methods

To determine the function of differentially expression of circRNAs associated with ovarian CSCs, circRNA profiling was conducted using a circRNA-based microarray on sphere-forming cells derived from A2780 and SKOV3 epithelial ovarian cancer cells termed A2780-SP and SKOV3-SP compared to monolayer cells such as A2780 and SKOV3 cells, respectively. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the biological functions of the circRNAs expressed in CSCs.

Results

The circRNA-based microarray data showed that 159 circRNAs were significantly upregulated (fold change > 1.5) and 55 circRNAs were downregulated in ovarian CSCs compared to monolayer cells. GO and KEGG enrichment analysis of differentially expressed circRNAs in ovarian CSCs showed that they were mainly involved in cell cycle, histone modification, cellular protein metabolic process, cell cycle, apoptotic signaling pathway, and ubiquitin-mediated proteolysis in ovarian cancer. In addition, the hsa-circRNA000963-miRNA-mRNA regulatory network was constructed based on potential target of miRNAs. These analyses involved that the biological function of the hsa-circRNA00096/miRNA/mRNA network was involved in signaling pathways regulating pluripotency of stem cells, PI3K-Akt signaling pathway, cell cycle, p53 signaling pathway, Wnt signaling pathway, calcium modulating pathway, and production of miRNAs involved in gene silencing by miRNA.

Conclusions

Our data demonstrate the expression profiles of circRNAs in ovarian CSCs and suggest that circRNAs may be potential diagnostic and predictive biomarkers of ovarian cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-022-01014-z.

Screening of Human Circular RNAs as Biomarkers for Early Onset Detection of Alzheimer’s Disease

Circular RNAs (circRNAs) are a distinctive type of endogenous non-coding RNAs, and their regulatory roles in neurological disorders have received immense attention. CircRNAs significantly contribute to the regulation of gene expression and progression of neurodegenerative disorders including Alzheimer’s disease (AD). The current study aimed to identify circRNAs as prognostic and potential biomarkers in AD. The differentially expressed circRNAs among subjective cognitive decline, amnestic mild cognitive impairment, and age-matched normal donors were determined through Arraystar Human circRNA Array V2 analysis. The annotations of circRNAs-microRNA interactions were predicted by employing Arraystar’s homemade microRNAs (miRNA) target prediction tool. Bioinformatics analyses comprising gene ontology enrichment, KEGG pathway, and network analysis were conducted. Microarray analysis revealed the 33 upregulated and 11 downregulated differentially expressed circRNAs (FC ≥ 1.5 and p-values ≤ 0.05). The top 10 differentially expressed upregulated and downregulated circRNAs have been chosen for further expression validation through quantitative real-time PCR and subsequently, hsa-circRNA_001481 and hsa_circRNA_000479 were confirmed experimentally. Bioinformatics analyses determined the circRNA-miRNA-mRNA interactions and microRNA response elements to inhibit the expression of miRNAs and mRNA targets. Gene ontology enrichment and KEGG pathways analysis revealed the functional clustering of target mRNAs suggesting the functional verification of these two promising circRNAs. It is concluded that human circRNA_001481 and circRNA_000479 could be utilized as potential biomarkers for the early onset detection of AD and the development of effective therapeutics.

circ-Pank1 promotes dopaminergic neuron neurodegeneration through modulating miR-7a-5p/α-syn pathway in Parkinson's disease

Circular RNA (circRNA) is a type of non-coding RNA that is widely expressed in mammals. It is highly conserved and abundantly expressed in the brain. Here, we report the regulatory role of circRNA derived from the pantothenate kinase 1 (Pank1) gene (circ-Pank1) in Parkinson's disease (PD). Circ-Pank1 is highly expressed in the substantia nigra (SN) of PD model mice treated with rotenone and in the MN9D cell model of dopaminergic neurons. The circ-Pank1 knockdown ameliorated dopaminergic neuron damage and locomotor dysfunction after the treatment with rotenone. We found that circ-Pank1 could adsorb miR-7a-5p and upregulate the expression of α-synuclein (α-syn), which is a molecular hallmark closely related to PD. The inhibition of miR-7a-5p reversed the circ-Pank1 knockdown-induced amelioration of dopaminergic neuron injury. In conclusion, circ-Pank1 is overexpressed in PD and enhances the locomotor dysfunction via the miR-7a-5p/α-syn signaling axis. We revealed the functional role of circRNAs in the progression of PD and provided a potential target for noncoding RNAs in delaying the progression of PD.

Analysis of the circRNA and T-UCR populations identifies convergent pathways in mouse and human models of Rett syndrome

Noncoding RNAs play regulatory roles in physiopathology, but their involvement in neurodevelopmental diseases is poorly understood. Rett syndrome is a severe, progressive neurodevelopmental disorder linked to loss-of-function mutations of the MeCP2 gene for which no cure is yet available. Analysis of the noncoding RNA profile corresponding to the brain-abundant circular RNA (circRNA) and transcribed-ultraconserved region (T-UCR) populations in a mouse model of the disease reveals widespread dysregulation and enrichment in glutamatergic excitatory signaling and microtubule cytoskeleton pathways of the corresponding host genes. Proteomic analysis of hippocampal samples from affected individuals confirms abnormal levels of several cytoskeleton-related proteins together with key alterations in neurotransmission. Importantly, the glutamate receptor GRIA3 gene displays altered biogenesis in affected individuals and in vitro human cells and is influenced by expression of two ultraconserved RNAs. We also describe post-transcriptional regulation of SIRT2 by circRNAs, which modulates acetylation and total protein levels of GluR-1. As a consequence, both regulatory mechanisms converge on the biogenesis of AMPA receptors, with an effect on neuronal differentiation. In both cases, the noncoding RNAs antagonize MeCP2-directed regulation. Our findings indicate that noncoding transcripts may contribute to key alterations in Rett syndrome and are not only useful tools for revealing dysregulated processes but also molecules of biomarker value.

Identification of altered exosomal microRNAs and mRNAs in Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by decreased memory and cognitive functions. Exosomes carry a variety of important information such as proteins, lipids, DNA and RNA of mother cells. It is reported that exosomes play critical roles in nervous system physiology and neurodegenerative diseases. However, the functions of exosomes in AD progression are not fully elucidated. In this study, we detected the expression pattern of mRNAs and miRNAs in exosomes derived from the AD and health mice. A total of 1320 mRNAs and 29 miRNAs were differentially expressed in exosomes between the two groups. Subsequently, the downregulation of Chi3l1 and upregulation of Rhog in AD mice were verified by qRT-PCR. Meanwhile, the downregulation of miR-148a-5p and upregulation of miR-27a-5p in AD group were also tested by qRT-PCR. The functions of differentially expressed mRNAs and potential target genes of miRNAs were determined by GO and KEGG analysis. According to the ceRNA hypothesis, we established an integrated ceRNA network of circRNA-lncRNA-miRNA-mRNA. In conclusion, exosomal lncRNAs, mRNAs, circRNAs and miRNAs were identified to participate in the progression of AD which might be possible biomarkers and therapeutic targets for AD.

circRNAs: Insight Into Their Role in Tumor-Associated Macrophages

Currently, it is well known that the tumor microenvironment not only provides energy support for tumor growth but also regulates tumor signaling pathways and promotes the proliferation, invasion, metastasis, and drug resistance of tumor cells. The tumor microenvironment, especially the function and mechanism of tumor-associated macrophages (TAMs), has attracted great attention. TAMs are the most common immune cells in the tumor microenvironment and play a vital role in the occurrence and development of tumors. circular RNA (circRNA) is a unique, widespread, and stable form of non-coding RNA (ncRNA), but little is known about the role of circRNAs in TAMs or how TAMs affect circRNAs. In this review, we summarize the specific manifestations of circRNAs that affect the tumor-associated macrophages and play a significant role in tumor progression. This review helps improve our understanding of the association between circRNAs and TAMs, thereby promoting the development and progress of potential clinical targeted therapies.

Hsa_circRNA_0045861 promotes renal injury in ureteropelvic junction obstruction via the microRNA-181d-5p/sirtuin 1 signaling axis

Background

Ureteropelvic junction obstruction (UPJO) is one of the most common causes of hydronephrosis in children. This study explored the effects and the regulatory mechanisms of the circular RNA (circRNA) hsa_circRNA_0045861 (circRNA_0045861) in UPJO.

Methods

RNA sequencing was used to identify the differentially expressed circRNAs in UPJO. The effects of circRNA_0045861 on renal cell apoptosis was investigated by flow cytometry and Western blot analysis. Furthermore, we used bioinformatics methods to predict the possible target genes of circRNA_0045861. Fluorescence in-situ hybridization and dual-luciferase reporter assays were performed to validate the target genes of circRNA_0045861. Finally, we evaluated the effects of circRNA_0045861 target gene miR-181d-5p on UPJO-induced renal fibrosis in vivo.

Results

RNA sequencing identified 63 upregulated and 64 downregulated circRNAs in UPJO patients. The expression of circRNA_0045861 was significantly elevated in kidney damage both in vivo and in vitro. Silencing circ_0045861 inhibited transforming growth factor (TGF)-β1-induced apoptosis in vitro in human kidney 2 (HK-2) cells. Furthermore, circ_0045861 was shown to directly interact with the microRNA miR-181d-5p and regulate the expression of sirtuin 1 (SIRT1), thereby promoting the progression of apoptosis and renal injury. In addition, overexpression of miR-181d-5p inhibited cell apoptosis and renal fibrosis in a mouse model through downregulating the SIRT1/p53 pathway.

Conclusions

Circ_0045861 may be a novel candidate circRNA in the pathogenesis of UPJO by acting as a pro-apoptotic factor via the miR-181d-5p/SIRT1 axis.

Influence of dysregulated expression of circular RNA on the diagnosis and prognosis of breast cancer in Asia: a meta-analysis study

OBJECTIVE

Recent studies have reported a correlation between non-coding RNAs such as circular RNAs (circRNAs) and clinical value of various cancers. However, the diagnostic and prognostic role of circRNA in breast cancer remains controversial.

DESIGN

Systematic review and meta-analysis.

METHODS

Diagnostic efficacy was estimated by sensitivity, specificity and area under the curve (AUC). Pooled HRs with 95% CIs estimated overall survival (OS), and ORs with 95% CIs investigated clinical features.

RESULTS

By searching PubMed, Embase, Web of Science, CNKI and Cochrane Library, we obtained a total of 29 studies with 4405 patients. A shorter survival time was associated with high expression levels of tumour-promoter circRNAs (OS: HR=2.43, 95% CI 2.20 to 2.92, p<0.001), and tumour-suppressor circRNAs were related to a favourable prognosis (OS: HR=0.32, 95% CI 0.23 to 0.44, p<0.001). Furthermore, high expression levels of oncogenic circRNAs were associated with poor clinical outcomes; tumour-suppressor circRNAs showed the opposite result. As for the diagnostic role, the outcome indicated an AUC of 0.82 (95% CI 0.78 to 0.85), with 85% sensitivity and 86% specificity to distinguish patients with breast cancer from healthy controls.

CONCLUSION

Dysregulated expression of circRNA was related to diagnosis and prognosis in breast cancer, which indicated it might be a novel biomarker and a target of therapy for breast cancer.

PROSPERO REGISTRATION NUMBER

CRD42020207912.

Circular RNAs: The Novel Actors in Pathophysiology of Spinal Cord Injury

Spinal Cord Injury (SCI) can elicit a progressive loss of nerve cells promoting disability, morbidity, and even mortality. Despite different triggering mechanisms, a cascade of molecular events involving complex gene alterations and activation of the neuroimmune system influence either cell damage or repair. Effective therapies to avoid secondary mechanisms underlying SCI are still lacking. The recent progression in circular RNAs (circRNAs) research has drawn increasing attention and opened a new insight on SCI pathology. circRNAs differ from traditional linear RNAs and have emerged as the active elements to regulate gene expression as well as to facilitate the immune response involved in pathophysiology-related conditions. In this review, we focus on the impact and possible close relationship of circRNAs with pathophysiological mechanisms following SCI, where circRNAs could be the key transcriptional regulatory molecules to define neuronal death or survival. Advances in circRNAs research provide new insight on potential biomarkers and effective therapeutic targets for SCI patients.

Transcriptomic profiling and functional prediction reveal aberrant expression of circular RNAs during osteogenic differentiation in human umbilical cord mesenchymal stromal cells

Circular RNAs (circRNAs) are crucial elements of non-coding RNA, that regulate various biological processes. To date, expression patterns and functional roles of circRNAs during osteogenic differentiation of human umbilical cord mesenchymal stromal cells (hUCMSCs) remain unknown. In this study, we analyzed RNA-sequence data to reveal expression profiles of circRNAs during osteogenesis of hUCMSCs, then elucidated the underlying mechanisms of action. We identified a total of 5457 circRNAs in hUCMSCs, of which 34 and 33 were upregulated and downregulated, respectively. We applied Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses to determine functions and related pathways of differentially expressed circRNAs. Moreover, we applied bioinformatics tools to construct competing endogenous RNA networks, comprising 10 circRNAs, 46 micro RNAs and 413 mRNAs. Furthermore, we predicted protein-coding potential of the upregulated circRNAs then constructed a co-expression network comprising the top 5 upregulated circRNAs and 75 RNA-binding proteins. Next, we validated 6 differentially-expressed circRNAs and found that overexpressing circ-CTTN could promote osteogenesis of hUCMSCs. Overall, our findings indicate that clusters of circRNAs are aberrantly expressed in hUCMSCs during osteogenic differentiation, hence lay a foundation for future research into promoting hUCMSCs osteogenic differentiation and bone regeneration.

Dysregulated expression of circular RNAs serve as diagnostic and prognostic markers in ovarian and cervical cancer: A PRISMA-compliant systematic review and meta-analysis

INTRODUCTION

Recent studies have reported a connection between non-coding RNAs such as circular RNAs (circRNAs) and the prognosis of various cancers. However, the mechanism of circRNA in ovarian cancer and cervical cancer has not been consistent. We evaluated the diagnostic and prognostic roles of circRNAs in ovarian and cervical cancer by meta-analysis.

METHODS

Pooled hazard ratios with 95% confidence intervals were to estimate overall survival. Diagnostic efficacy was estimated by sensitivity, specificity and area under curve.

RESULTS

By searching PubMed, Embase, the Web of Science databases, and other sources, we obtained a total of 22 studies with 2059 patients from Asia population. High expression levels of oncogenic circRNAs were significantly associated with poor prognoses both in ovarian and cervical cancer. However, elevated expression levels of tumor-suppressor circRNAs were linked with favorable survival time in ovarian cancer. As for diagnostic role, the area under the curve value in ovarian cancer and cervical cancer is 0.89 and 0.93, respectively.

CONCLUSIONS

CircRNAs have the prospect of becoming a promising biomarker for diagnosis and prognosis of ovarian and cervical cancer. Accordingly, circRNAs might be novel indicators and targets of therapy for ovarian and cervical cancer.

Serum Circ-FAF1/Circ-ELP3: A novel potential biomarker for breast cancer diagnosis

Background

Recently, measurement of serum circular RNAs (circRNAs) as a non‐invasive tumor marker has been considered more. We designed the present study to investigate the diagnostic efficiency of serum Circ‐ELP3 and Circ‐FAF1, separately and simultaneously, for diagnosis of patients with breast cancer.

Methods

Seventy‐eight female patients diagnosed as primary breast cancer participated in this study. We measured the level of circRNAs in serum specimens of the studied subjects. A receiver operating characteristic (ROC) curve was plotted and the diagnostic efficiency for both circRNAs was determined.

Results

Compared to non‐cancerous controls, Circ‐ELP3 was upregulated in breast cancer patients (p‐value = 0.004). On the other hand, serum Circ‐FAF1 was seen to be decreased in breast cancer patients than controls (p‐value = 0.001). According to ROC curve results, the area under the curve (AUC) for Circ‐ELP3 and Circ‐FAF1 was 0.733 and 0.787, respectively. Furthermore, the calculated sensitivity and specificity for Circ‐ELP3 and Circ‐FAF1 were 65, 64% and 77, 74%, respectively. Merging both circRNAs increased the diagnostic efficiency, with a better AUC, sensitivity and specificity values of 0.891, 96 and 62%, respectively.

Conclusion

Briefly, our results revealed the high diagnostic value for combined circRNAs panel, including Circ‐ELP3 and Circ‐FAF1 as a non‐invasive marker, in detection of breast carcinomas.

Up-regulation of circARF3 reduces blood-brain barrier damage in rat subarachnoid hemorrhage model via miR-31-5p/MyD88/NF-κB axis

Inflammation events have been found to aggravate brain injury and blood-brain barrier (BBB) damage following subarachnoid hemorrhage (SAH). This study probed the role and mechanism of a novel circRNA, circARF3, in regulating the BBB injury in SAH rats and hypoxia-induced vascular endothelial cell (VEC) injury in vitro. Levels of circARF3 and miR-31-5p were monitored by RT-PCR. The expression of inflammatory factors IL-1β and TNF-α was verified by ELISA. In vivo SAH model was constructed in Sprague Dawley (SD) rats. The BBB integrity and cerebral edema, as well as the neurological functions of the rats were evaluated. The apoptotic neurons and microglia in brain lesions were examined by immunohistochemistry (IHC). The MyD88/NF-κB pathway was tested by Western blot. Furthermore, gain-of functional assay were constructed to explore the effects of circARF3 and miR-31-5p in primary cultured brain microvascular endothelial cell (BMEC) injury and microglial inflammation induced by oxygen and glucose deprivation (OGD). circARF3 was significantly down-regulated in plasma and CSF in SAH patients with higher Fisher stages. In the SAH rat model, overexpressing circARF3 improved BBB integrity and neurological score, decreased neuronal apoptosis and microglial activation in ipsilateral basal cortex, with declined miR-31-5p expression and MyD88-NF-κB activation. In vitro, overexpressing circARF3 attenuated OGD-mediated integrity destruction of BMECs and microglial induced neuroinflammation, while overexpressing miR-31-5p had opposite effects. Mechanistically, circARF3 sponged miR-31-5p as an endogenous competitive RNA and dampens its expression, thus inactivating MyD88-NF-κB pathway. CircARF3 attenuates BBB destruction in SAH rats by regulating the miR-31-5p-activated MyD88-NF-κB pathway.

New RNA-Based Breakthroughs in Alzheimer's Disease Diagnosis and Therapeutics

Dementia is described as the fifth leading cause of death worldwide and Alzheimer’s disease (AD) is recognized as the most common, causing a huge impact on health costs and quality of patients’ lives. The main hallmarks that are commonly associated with the pathologic process are amyloid deposition, pathologic Tau phosphorylation and neurodegeneration. It is still unclear how these events are linked to the disease progression, due to the complex pathologic mechanisms. Nevertheless, several hypotheses have been proposed for a better understanding of AD. The AD diagnosis is performed by using a combination of several tools to detect β-amyloid peptide (Aβ) deposits and modifications in cognitive performance, sometimes being expensive and invasive. In the treatment field, there is still an absence of effective treatments to delay or stop the progression of the disease, with most of the approved drugs used to relieve symptoms, and all of them with significant adverse side effects. Considering all limitations, the need to establish new and more effective diagnostic and therapeutic strategies becomes clear. This review aims not only to describe the disease and its impact but also to collect the currently available diagnostic and therapeutic strategies, highlighting new promising RNA-based strategies for AD.

Mobius strip in pancreatic cancer: biogenesis, function and clinical significance of circular RNAs

Pancreatic cancer (PC) is a kind of common digestive system cancer with the worst prognosis for its insidious symptoms and high invasiveness. Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed circular structure, which are more stable and conservative than linear RNAs and process major functions of microRNA (miRNA) sponge, RNA binding protein (RBP) sponge and polypeptide translation template. Incremental researches have proved that circRNAs express aberrantly and play a vital role in various types of cancer. Hence, we reviewed the biogenesis, degradation, characteristics, and biological functions of circRNAs and summarized the roles circRNAs played in the proliferation, invasion, metastasis, chemoresistance and exosome-mediated intercellular communication of PC. We then summed up a workflow regarding circRNA research in cancer and relative specific databases and experimental methods. In the future, more efforts ought to be put into circRNAs research in PC, including basic research of discovering and testifying circRNAs centered ceRNA networks, and clinical research of exploiting exosomal or circulating circRNAs as a diagnostic biomarker, chemotherapy sensitivity predictor and prognostic predictor.

Multiple Sclerosis: circRNA Profile Defined Reveals Links to B-Cell Function

Background and Objectives

To investigate the total circular RNA (circRNA) profile in patients with relapsing-remitting multiple sclerosis (RRMS) and healthy controls (HCs).

Methods

Hybridization microarray was used to define the circRNA profile in peripheral blood mononuclear cells (PBMCs) from 20 untreated patients with RRMS (10 in relapse and 10 in remission) and 10 HCs. We analyzed close to 14,000 individual circRNAs per sample. The discovery set data were validated using quantitative reverse transcription-PCR with an independent cohort of 47 patients with RRMS (19 in relapse and 28 in remission) and 27 HCs.

Results

Microarray analysis revealed 914 transcripts to be differentially expressed between patients with RRMS in relapse and HCs (p < 0.05). We validated 3 circRNAs from 5 showing highest levels of differential expression in the RRMS relapse vs HC group: hsa_circRNA_101348, hsa_circRNA_102611, and hsa_circRNA_104361. Their expression was significantly increased during relapse in RRMS (p = 0.0002, FC = 2.9; p = 0.01, FC = 1.6; and p = 0.001, FC = 1.5, respectively) and in patients showing gadolinium enhancement on brain MRI (hsa_circRNA_101348, p = 0.0039, FC = 2.4; hsa_circRNA_104361, p = 0.029, FC = 1.7). Bioinformatic analysis revealed 15 microRNAs interacting with these circRNAs in a complementary manner and led to the discovery and validation of 3 protein-coding RNAs upregulated in patients with RRMS during relapse. Two of these, AK2 and IKZF3, have previously been implicated in B-cell function.

Discussion

circRNAs display a distinct profile in PBMCs from patients with RRMS, and our results may implicate circRNA in the known disturbed B-cell activity in RRMS and thus represent a novel biomarker for monitoring relapse activity.

The potential roles of circular RNAs as modulators in traumatic spinal cord injury

Spinal cord injury (SCI) may cause long-term physical impairment and bring a substantial burden to both the individual patient and society. Existing therapeutic approaches for SCI have proven inadequate. This is mainly owing to the incomplete understanding of the cellular and molecular events post-injury. Circular RNAs (circRNAs) represent a new class of non-coding RNAs with a covalently closed annular structure that participates in regulating the transcription of certain genes and are linked to various biological processes and diseases. Mounting evidence is indicative that circRNAs are highly expressed in the spinal cord and they play key roles in multiple processes of neurological diseases. Recently, a role for circRNAs as effectors of SCI has emerged, leading to the continuity of relevant research. In this review, we presented current studies with regards to the abnormality of circRNAs mediating SCI by affecting mechanisms of autophagy, apoptosis, inflammation, and neural regeneration. Furthermore, the potential clinical value of circRNAs as therapeutic targets of SCI was also analyzed.

Exosome-Derived MicroRNAs of Human Milk and Their Effects on Infant Health and Development

Multiple biologically active components of human milk support infant growth, health and development. Milk provides a wide spectrum of mammary epithelial cell-derived extracellular vesicles (MEVs) for the infant. Although the whole spectrum of MEVs appears to be of functional importance for the growing infant, the majority of recent studies report on the MEV subfraction of milk exosomes (MEX) and their miRNA cargo, which are in the focus of this review. MEX and the dominant miRNA-148a play a key role in intestinal maturation, barrier function and suppression of nuclear factor-κB (NF-κB) signaling and may thus be helpful for the prevention and treatment of necrotizing enterocolitis. MEX and their miRNAs reach the systemic circulation and may impact epigenetic programming of various organs including the liver, thymus, brain, pancreatic islets, beige, brown and white adipose tissue as well as bones. Translational evidence indicates that MEX and their miRNAs control the expression of global cellular regulators such as DNA methyltransferase 1-which is important for the up-regulation of developmental genes including insulin, insulin-like growth factor-1, α-synuclein and forkhead box P3-and receptor-interacting protein 140, which is important for the regulation of multiple nuclear receptors. MEX-derived miRNA-148a and miRNA-30b may stimulate the expression of uncoupling protein 1, the key inducer of thermogenesis converting white into beige/brown adipose tissue. MEX have to be considered as signalosomes derived from the maternal lactation genome emitted to promote growth, maturation, immunological and metabolic programming of the offspring. Deeper insights into milk's molecular biology allow the conclusion that infants are both "breast-fed" and "breast-programmed". In this regard, MEX miRNA-deficient artificial formula is not an adequate substitute for breastfeeding, the birthright of all mammals.

The influence of circular RNAs on autophagy and disease progression

Circular RNAs (circRNAs) are non-coding RNAs that have attracted considerable attention in recent years. Owing to their distinct circular structure, circRNAs are stable in cells. Autophagy is a catabolic process that helps in the degradation and recycling of harmful or inessential biological macromolecules in cells and enables cells to adapt to stress and changes in the internal and external environments. Evidence has shown that circRNAs influence the course of a disease by regulating autophagy, which indicates that autophagy is involved in the onset and development of various diseases and can affect drug resistance (for example, it affects cisplatin resistance in tumors). In this review, we summarized the role of circRNAs in autophagy and their influence on disease onset and progression as well as drug resistance. The review will expand our understanding of tumors as well as cardiovascular and neurological diseases and also suggest novel therapeutic strategies.Abbreviations: ACR: autophagy-related circRNA; ADSCs: adipogenic mesenchymal stem cells; AMPK: AMP-activated protein kinase; ATG: autophagy related; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; ceRNA: competing endogenous RNA; circRNA: circular RNA; CMA: chaperone-mediated autophagy; EPCs: endothelial progenitor cells; LE/MVBs: late endosomes/multivesicular bodies; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NSCLC: non-small cell lung cancer; PDLSCs: periodontal ligament stem cells; PE: phosphatidylethanolamine; PtdIns: phosphatidylinositol; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate 1,2-dipalmitoyl; PTEN: phosphatase and tensin homolog; RBPs: RNA-binding proteins; SiO₂: silicon dioxide; TFEB: transcription factor EB; ULK: unc-51 like autophagy activating kinase 1.

Exosomal circRNAs contribute to intestinal development via the VEGF signalling pathway in human term and preterm colostrum

Human breast milk (HBM) provides essential nutrients for newborn growth and development, and contains a variety of biologically active ingredients that can affect gastrointestinal tract and immune system development in breastfed infants. HBM also contains mRNAs, microRNAs and lncRNAs, most of which are encapsulated in milk-derived exosomes and exhibit various important infant development related biological functions. While previous studies have shown that exosomal circRNAs are involved in the intestinal epithelial cells’ proliferation and repair. However, the effect of HBM exosomal circRNAs on intestinal development is not clear. In this study, we identified 6756 circRNAs both in preterm colostrum (PC) and term colostrum (TC), of which 66 were upregulated, and 42 were downregulated (|fold change>2|, p < 0.05) in PC. Pathway analysis showed that the VEGF signalling pathway was involved, and network analysis revealed that the differentially expressed circRNAs bound various miRNAs. Further analyses showed that has_circRNA_405708 and has_circRNA_104707 were involved in the VEGF signalling pathway, and that they all bound various mirRNAs. Exosomes found in preterm colostrum (PC) and term colostrum (TC) promoted VEGF protein expression and induced the proliferation and migration of small intestinal epithelial cells (FHCs). Exosomal circRNAs found in human colostrum (HC) binding to related miRNAs may regulate VEGF signalling, and intestinal development.

Circ0083429 Regulates Osteoarthritis Progression via the Mir-346/SMAD3 Axis

Osteoarthritis (OA) is a degenerative joint disease. Currently, apart from symptomatic treatment or joint replacement, no other effective treatments for OA exist. The mechanisms underlying OA remain elusive and require further research. Circular RNAs (circRNAs) are known to be involved in many diseases; however, their function in OA is not yet fully understood. Here, we identified a novel circRNA, Circ0083429. The role of Circ0083429 in OA was confirmed via western blot (WB), quantitative real-time PCR (qRT-PCR), and immunofluorescence (IF) through knockdown and overexpression experiments. The binding of Circ0083429 to downstream miR-346 and its target gene SMAD3 was predicted via bioinformatics analysis and verified using a luciferase reporter assay and RNA pulldown experiments. Finally, the function of Circ0083429 was evaluated in mouse OA models. In our study, we found that Circ0083429 regulates the homeostasis of the extracellular matrix (ECM) in human chondrocytes. Mechanistically, Circ0083429 affects OA by regulating the mRNA level of SMAD3 through the sponging of microRNA (miRNA)-346. Injecting adeno-associated virus Circ0083429 into the intra-junction of the mouse knee alleviated OA. In conclusion, Circ0083429 regulates the ECM via the regulation of the downstream miRNA-346/SMAD3 in human chondrocytes, which provides a new therapeutic strategy for OA.

Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture

Background

Circular RNAs (circRNAs) are widely expressed in cells and tissues and are involved in biological processes and human diseases. Recent studies have demonstrated that circRNAs can interact with RNA-binding proteins (RBPs), which is considered an important aspect for investigating the function of circRNAs.

Results

In this study, we design a slight variant of the capsule network, called circRB, to identify the sequence specificities of circRNAs binding to RBPs. In this model, the sequence features of circRNAs are extracted by convolution operations, and then, two dynamic routing algorithms in a capsule network are employed to discriminate between different binding sites by analysing the convolution features of binding sites. The experimental results show that the circRB method outperforms the existing computational methods. Afterwards, the trained models are applied to detect the sequence motifs on the seven circRNA-RBP bound sequence datasets and matched to known human RNA motifs. Some motifs on circular RNAs overlap with those on linear RNAs. Finally, we also predict binding sites on the reported full-length sequences of circRNAs interacting with RBPs, attempting to assist current studies. We hope that our model will contribute to better understanding the mechanisms of the interactions between RBPs and circRNAs.

Conclusion

In view of the poor studies about the sequence specificities of circRNA-binding proteins, we designed a classification framework called circRB based on the capsule network. The results show that the circRB method is an effective method, and it achieves higher prediction accuracy than other methods.

A Narrative Review of Circular RNAs in Brain Development and Diseases of Preterm Infants

Circular RNAs (circRNAs) generated by back-splicing are the vital class of non-coding RNAs (ncRNAs). Circular RNAs are highly abundant and stable in eukaryotes, and many of them are evolutionarily conserved. They are blessed with higher expression in mammalian brains and could take part in the regulation of physiological and pathophysiological processes. In addition, premature birth is important in neurodevelopmental diseases. Brain damage in preterm infants may represent the main cause of long-term neurodevelopmental disorders in surviving babies. Until recently, more and more researches have been evidenced that circRNAs are involved in the pathogenesis of encephalopathy of premature. We aim at explaining neuroinflammation promoting the brain damage. In this review, we summarize the current findings of circRNAs properties, expression, and functions, as well as their significances in the neurodevelopmental impairments, white matter damage (WMD) and hypoxic-ischemic encephalopathy (HIE). So we think that circRNAs have a direct impact on neurodevelopment and brain injury, and will be a powerful tool in the repair of the injured immature brain. Even though their exact roles and mechanisms of gene regulation remain elusive, circRNAs have potential applications as diagnostic biomarkers for brain damage and the target for neuroprotective intervention.

The Effect of Melatonin Modulation of Non-coding RNAs on Central Nervous System Disorders: An Updated Review

Melatonin is a hormone produced in and secreted by the pineal gland. Besides its role in regulating circadian rhythms, melatonin has a wide range of protective functions in the central nervous system (CNS) disorders. The mechanisms underlying this protective function are associated with the regulatory effects of melatonin on related genes and proteins. In addition to messenger ribonucleic acid (RNA) that can be translated into protein, an increasing number of non-coding RNAs in the human body are proven to participate in many diseases. This review discusses the current progress of research on the effects of melatonin modulation of non-coding RNAs (ncRNAs), including microRNA, long ncRNA, and circular RNA. The role of melatonin in regulating common pathological mechanisms through these ncRNAs is also summarized. Furthermore, the ncRNAs, currently shown to be involved in melatonin signaling in CNS diseases, are discussed. The information compiled in this review will open new avenues for future research into melatonin mechanisms and provide a further understanding of ncRNAs in the CNS.

Identification of Circular RNA hsa_Circ_0003391 in Peripheral Blood Is Potentially Associated With Alzheimer's Disease

Circular RNAs (circRNAs) have recently been discovered as a novel type of endogenous non-coding RNA that may regulate gene expression in mammals. In the central nervous system (CNS), circRNAs are relevant to many neurological disorders such as Alzheimer's disease (AD). In this study, we attempted to identify an aberrant circRNA, hsa_circ_0003391, which is significantly downregulated in the peripheral blood of patients with AD, and to explore the relationship between hsa_circ_0003391 and the clinical manifestation of AD. The expression of hsa_circ_0003391 had a specific decrease in the peripheral blood of patients with AD compared to those with other types of dementia. To evaluate the potential diagnostic value of the circRNA, we performed a receiver operating characteristic (ROC) curve analysis. The area under the curve (AUC) value was 0.7283 for hsa_circ_0003391, which was statistically significant. The natural form of hsa_circ_0003391 in the peripheral blood was a loop structure with good stability. We found a potential correlation between the expression of hsa_circ_0003391 and the clinical manifestations of AD. Bioinformatic analysis was carried out to predict the latent target microRNAs (miRNA) of hsa_circ_0003391. Furthermore, microRNAs targeted by hsa_circ_0003391 were successfully detected, and miR-574-5p had an expected elevation in the AD groups, suggesting that miR-574-5p might be a potential microRNA target for hsa_circ_0003391. Our results suggest that the downregulation of hsa_circ_0003391 in the peripheral blood has a potential relationship with AD. Our findings not only provide an important latent biomarker but also highlight an important perspective for the following study into AD pathogenesis. This may promote the process of novel therapeutics targeting non-coding RNA.

Circ-ZDHHC5 Accelerates Esophageal Squamous Cell Carcinoma Progression in vitro via miR-217/ZEB1 Axis

Circular RNA (circRNA) exhibits a covalently closed circular conformation and is structurally stable. Nevertheless, the precise effects exerted by circRNA in esophageal squamous cell carcinoma (ESCC) remains uncertain. circRNA was ascertained by a human circRNA array study and was confirmed by the quantification of reverse transcriptase polymerase reactions. A luciferase reporter, fluorescence in situ hybridization experiment was exploited to explore the interaction between circ-ZDHHC5 and miR-217. The function of circ-ZDHHC5 was determined by siRNA-mediated knockout of circ-ZDHHC5 in in vitro proliferation, migration, and invasion. circ-ZDHHC5, rather than linear ZDHHC5 mRNA, rose in the tissues of patients with ESCC, plasma, and ESCC cell lines in comparison with normal controls. Knockdown of circ-ZDHHC5 inhibited tumorigenesis in ESCC cells, and the co-transfection of si-circ-ZDHHC5 and miR-217 mimics further enhanced the above effect. Noticeably, the present study showed that circ-ZDHHC5 was an miR-217 sponge that modulated the expression of zinc finger E-box binding homeobox 1 (ZEB1), further facilitating ESCC tumorigenesis. As revealed by this study, circ-ZDHHC5 can act as a new potential circular biomarker for detecting ESCC. It provides a novel perceptivity for the treatment of ESCC suggesting that circ-ZDHHC5 could impact on ESCC progression by sponging miR-217 with ZEB1.

Selective packaged circular RNAs in milk extracellular vesicles during Staphylococcus aureus infection may have potential against bacterial infection

Extracellular vesicles (EVs) provide a novel intercellular communication mechanism to transfer biologically important molecules to target cells. Although several pieces of evidence have shown that EVs have potential to respond to bacterial infections, our knowledge about the role of circular RNA (circRNA), an important cargo of EV, behind this process remains poor. In particular, the mechanism by which circRNAs are packaged into EVs remains elusive during bacterial infection. In the present study, EVs from bovine milk samples with or without Staphylococcus aureus (S. aureus) infection were isolated. The presence of circRNAs in milk-derived EVs (MEVs) was validated for the first time by PCR amplification with convergent and divergent primers and the RNase R resistance test. Through high-throughput sequencing, the expression profile of circRNAs in EVs was found to be changed during S. aureus infection. Moreover, we demonstrated that circRNAs were selectively packaged into EVs. Finally, bioinformatic analyses predicted the involvement of differentially expressed circRNAs in immune functions. In summary, our findings offer an insight into the packaging mechanism of EV circRNAs and underscore the potential by which host used the EV circRNAs in response to pathogenic bacterial infections.

Expression Profiles of Circular RNA in Human Atrial Fibrillation With Valvular Heart Diseases

Circular RNAs (circRNA) are involved in a variety of human heart diseases, however, circRNA expression profiles and circRNA-miRNA-mRNA regulatory network in human atrial fibrillation (AF) especially with valvular heart diseases (VHD) remain poorly understood. A high-throughput RNA sequencing was used to investigate the differentially expressed circRNAs in left atrial appendage from VHD patients with or without persistent AF. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to predict the potential functions of the host genes of differentially expressed circRNA and their downstream targets. CircRNA-miRNA-mRNA regulatory network was constructed to identify mechanisms underlying circRNAs. qRT-PCR and sanger sequencing were further performed to validate the results. Compared with sinus rhythm (SR) patients, there were 3094 upregulated and 4472 downregulated circRNAs in AF patients respectively. The expression of 10 most differentially expressed circRNAs (circ 255-ITGA7, circ 418-KCNN2, circ 13913-MIB1, circ 44670-BARD1, circ 44782-LAMA2, circ 81906-RYR2, circ 35880-ANO5, circ 22249-TNNI3K, circ 3136-TNNI3K, circ 56186-TNNI3K) between SR and persistent AF patients were verified by qRT-PCR. In addition, specific back-splicing sites of these circRNAs was confirmed by sanger sequencing. GO and KEGG pathway analysis indicated that cAMP signal pathway and Wnt signal pathway might play important role in the development of AF in VHD patients, which might be affected by circRNAs. This study provided a preliminary landscape of circRNAs expression profiles which are involved in persistent AF due to VHD, and established the possibility for future related researches in this field.

Expression and clinical significance of circular RNA hsa_circ_0079787 in the peripheral blood of patients with axial spondyloarthritis

Axial spondyloarthritis (AxSpA) is a chronic rheumatic disease involving the axial skeleton. Recent evidence suggested that certain circular RNAs (circRNAs) have a crucial role in rheumatic diseases. However, the functions of circRNAs in AxSpA have remained largely elusive. The present study identified the utility of the circRNA Homo sapiens (hsa)_circ_0079787 as a potential biomarker for AxSpA. A total of 5 circRNAs (hsa_circ_0002715, hsa_circ_0001947, hsa_circ_0079787, hsa_circ_0000367 and hsa_circ_0035197) were determined in the peripheral blood of 46 patients with AxSpA, 46 patients with systemic lupus erythematosus (SLE) and 25 healthy controls (HC) by reverse transcription‑quantitative PCR analysis. The detailed clinical history of each patient was recorded and the correlations between these circRNAs and clinical characteristics were analyzed. Furthermore, receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic value of hsa_circ_0079787 and other factors for AxSpA. Of the 5 selected circRNAs, the expression of hsa_circ_0079787 was indicated to be significantly reduced in the peripheral blood of patients with AxSpA as compared with the levels in HCs and patients with SLE. The peripheral blood levels of hsa_circ_0079787 in patients with AxSpA were negatively correlated with the Bath Ankylosing Spondylitis Disease Activity Index and positively correlated with the platelet count (PLT) and the lymphocyte‑to‑monocyte ratio. In addition, the expression of peripheral blood hsa_circ_0079787 in male patients with AxSpA was negatively correlated with the mean platelet volume (MPV) and positively correlated with the plateletcrit (PCT). ROC curve analysis suggested that hsa_circ_0079787 and the combination of hsa_circ_0079787‑PLT‑MPV‑PCT had a significant diagnostic value for AxSpA. hsa_circ_0079787 and the combination of hsa_circ_0079787‑PLT‑MPV‑PCT was also able to differentiate between patients with AxSpA and those with SLE. In conclusion, peripheral‑blood hsa_circ_0079787 and the combination of hsa_circ_0079787‑PLT‑MPV‑PCT may provide improved diagnostic accuracy for AxSpA. In addition, the levels of hsa_circ_0079787 in the peripheral blood were correlated with disease activity and severity of AxSpA.

Circular RNAs are a novel type of non-coding RNAs in ROS regulation, cardiovascular metabolic inflammations and cancers

Circular RNAs (circRNAs) are a novel class of endogenous non-coding RNAs characterized by a covalently closed-loop structure generated through a special type of alternative splicing termed back-splicing. Currently, an increasing body of evidence has demonstrated that 1) majority of circRNAs are evolutionarily conserved across species, stable, and resistant to RNase R degradation, and often exhibit cell-specific, and tissue-specific/developmental-stage-specific expression and can be largely independent of the expression levels of the linear host gene-encoded linear RNAs; 2) the biogenesis of circRNAs via back-splicing is different from the canonical splicing of linear RNAs; 3) circRNA biogenesis is regulated by specific cis-acting elements and trans-acting factors; 4) circRNAs regulate biological and pathological processes by sponging miRNAs, binding to RNA-binding protein (RBP), regulators of splicing and transcription, modifiers of parental gene expression, and regulators of protein translation or being translated into peptides in various diseases; 5) circRNAs have been identified for their enrichment and stability in exosomes and detected in body fluids such as human blood, saliva, and cerebrospinal fluids, suggesting that these exo-circRNAs have potential applications as disease biomarkers and novel therapeutic targets; 6) several circRNAs are regulated by oxidative stress and mediate reactive oxygen species (ROS) production as well as promote ROS-induced cellular death, cell apoptosis, and inflammation; 7) circRNAs have also emerged as important regulators in atherosclerotic cardiovascular disease, metabolic disease, and cancers; 8) the potential mechanisms of several circRNAs have been described in diseases, hinting at their potential applications as novel therapeutic targets. In this highlight, we summarized the current understandings of the biogenesis and functions of circRNAs and their roles in ROS regulation and vascular inflammation-associated with cardiovascular and metabolic disease. (Word count: 272).

Circular RNA MGAT1 regulates cell proliferation and apoptosis in hypoxia-induced cardiomyocytes through miR-34a/YAP1 axis

Congenital heart disease (CHD) has severe morbidity and mortality worldwide. Evidence suggests that circularRNAs (circRNAs) are involved in the pathogenesis of human CHD. However, the regulatory mechanism remains uncertain. This study aimed to explore that mechanism. The levels of circular RNA MGAT1 (circMGAT1) and miR-34a were measured by quantitative polymerase chain reaction (qRT-PCR). Expression of yes-associated protein isoform 1 (YAP1) was assessed by western blot. Caspase-3 activity was evaluated by Caspase 3 Activity Assay Kit. CCK-8 assay was carried out to detect cell proliferation of hypoxia-induced AC16 cells. Cell apoptosis was analyzed by flow cytometry. In addition, dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were performed to verify the relationship between miR-34a and circMGAT1 or YAP1 in vitro. The level of circMGAT1 was downregulated, while miR-34a was strikingly increased in CHD tissues and hypoxia-induced AC16 cells. CircMGAT1 was a sponge of miR-34a, and circMGAT1 targeted miR-34a to regulate cell proliferation and apoptosis in hypoxia-induced cardiomyocytes. Dual-luciferase reporter and RIP-assay verified that miR-34a directly targeted YAP1, and the expression of YAP1 was significantly suppressed by miR-34a mimics but was enhanced by miR-34a inhibitor. Interestingly, YAP1 restored the effect of miR-34a on cell proliferation and apoptosis in hypoxia-induced AC16 cells. Besides, circMGAT1 sponged miR-34a to regulate the expression of YAP1. In conclusion, circMGAT1 inhibited cell apoptosis and enhanced cell proliferation by regulating the miR-34a/YAP1 axis, providing a therapy target for the treatment of human CHD.