Molecular roles and function of circular RNAs in eukaryotic cells

CircINHA resists granulosa cell apoptosis by upregulating CTGF as a ceRNA of miR-10a-5p in pig ovarian follicles

Mammalian ovarian follicular atresia is a complex and fine-regulated biological process with active involvement of connective tissue growth factor (CTGF). The emergence of studies of endogenous non-coding RNAs has raised a new aspect for exploration of the regulatory mechanisms involved in follicular atresia. Here, we aimed to illustrate a circRNA involved in the CTGF regulatory pathway during the apoptosis and follicular atresia of pig granulosa cells (GCs). We first detected a decreased expression pattern of CTGF during follicular atresia using IHC, FISH and qRT-PCR and confirmed the anti-apoptosis effect of CTGF in GCs in vitro by CTGF siRNA knockdown. Then, we used a dual luciferase activity assay to demonstrate CTGF as a direct functional target of miR-10a-5p, which was upregulated in atresic follicles and promoted the apoptosis of GCs in vitro. The negative effect of miR-10a-5p on GC viability was confirmed by cell cycle assays, cell proliferation/apoptosis assays and the WB detection of marker proteins. More importantly, we identified a novel circRNA, termed circINHA, that was downregulated during atresia in ovarian follicles, and we confirmed a direct interaction between miR-10a-5p and circINHA. Finally, we demonstrated that circINHA promoted GCs proliferation and inhibited GCs apoptosis via CTGF as a competing endogenous RNA (ceRNA) that directly bound to miR-10a-5p. Taken together, this study provides evidence for the circINHA/miR-10a-5p/CTGF regulatory pathway in follicular GC apoptosis and provides novel insights into the role of circRNAs in the modulation of ovarian physiological functions.

Overexpressed circPVT1 in oral squamous cell carcinoma promotes proliferation by serving as a miRNA sponge

Circular RNAs (circRNAs) comprise a novel class of widespread non-coding RNAs that may regulate gene expression in eukaryotes. However, the characterization and function of circRNAs remain elusive in human cancer, including oral squamous cell carcinoma (OSCC). In this study, the expression level of circPVT1 in OSCC was detected and define its functional role in initiation and progression of OSCC. It was identified that circPVT1 was upregulated in OSCC cells and specimens. Knockdown of circPVT1 suppressed cell proliferation as evidenced by Cell Counting kit-8 assay and elevated Ki-67 expression. Mechanistically, it was demonstrated that circPVT1 possessed two targeting sites of microRNA (miRNA/miR)-125b and could effectively sponge miR-125b to release its downstream mRNA targets. Subsequently, the downstream target signal transducer and activator of transcription 3 (STAT3) was verified as a direct target of miR-125b and STAT3 expression was regulated by the circPVT1/miR-125b axis. CircPVT1 functioned as competing endogenous RNA (ceRNA) to increase the STAT3 level and cell proliferation through sponging miR-125b. In conclusion, circPVT1 regulates cell proliferation and may serve as a promising therapeutic target for OSCC patients. Therefore, silencing of circPVT1 could be a future direction to develop a novel treatment strategy.

Down-regulation of hsa_circ_0092125 is related to the occurrence and development of oral squamous cell carcinoma

Circular RNA plays an important role in regulating tumour development and progression and can serve as a biomarker for cancer. This study was performed to investigate the clinical significance of hsa_circ_0092125 expression in oral squamous cell carcinoma (OSCC). The expression of hsa_circ_0092125 in OSCC tissues and cell lines was determined by reverse transcription-quantitative PCR analysis. The association between hsa_circ_0092125 expression and clinicopathological data was determined by χ² test. Overall survival (OS) curves were created using Kaplan-Meier survival analysis, and the differences were examined by log-rank test. Moreover, univariate and multivariate Cox analysis were employed to evaluate the risk factors of the OSCC prognosis. The expression of hsa_circ_0092125 was significantly down-regulated in OSCC tissues and cell lines. A low expression of hsa_circ_0092125 was associated with clinicopathological factors in OSCC patients, including tumour size, TNM stage, and lymph node metastasis. Kaplan-Meier survival analysis indicated that the OS time was shorter in OSCC patients with a lower hsa_circ_0092125 expression level than in those with a higher expression level. In addition, univariate and multivariate Cox analysis identified lower hsa_circ_0092125 expression, tumour size, TNM stage, and lymph node metastasis as independent risk factors for the OSCC prognosis. Thus, down-regulated expression of hsa_circ_0092125 might serve as a biomarker of the OSCC prognosis.

Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition

BACKGROUND

Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line.

RESULTS

In the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line.

CONCLUSION

In the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice.

Circular RNA hsa_circ_0023404 promotes proliferation, migration and invasion in non-small cell lung cancer by regulating miR-217/ZEB1 axis

BACKGROUND

Circular RNAs (circRNAs) have been considered as key regulators of cancer biology. However, the functional role of hsa_circ_0023404 in non-small cell lung cancer (NSCLC) and its regulatory mechanism are still almost unknown.

METHODS

The expression of hsa_circ_0023404, miR-217 and zinc finger E-box-binding homeobox 1 (ZEB1) was evaluated by quantitative real-time polymerase chain reaction. The role of hsa_circ_0023404 in NSCLC progression was determined using cell count kit-8 assay, transwell migration and invasion assay. Luciferase reporter assay was performed to assess the interaction of hsa_circ_0023404, miR-217 and ZEB1 in NSCLC cells.

RESULTS

The expression of hsa_circ_0023404 was upregulated in NSCLC tissues, as well as in NSCLC cell lines. High hsa_circ_0023404 expression predicted short overall survival in NSCLC. Functionally, knockdown of hsa_circ_0023404 inhibited the proliferation, migration and invasion of NSCLC cells. In the further molecular mechanism study, hsa_circ_0023404 was shown to interact with miR-217/ZEB1 axis to contribute to the growth of NSCLC cells.

CONCLUSION

hsa_circ_0023404 promotes the proliferation, migration and invasion of NSCLC cells by regulating miR-217/ZEB1 axis, providing a fresh perspective on circRNAs in NSCLC development.

Exposure to Ionizing Radiation Triggers Prolonged Changes in Circular RNA Abundance in the Embryonic Mouse Brain and Primary Neurons

The exposure of mouse embryos in utero and primary cortical neurons to ionizing radiation results in the P53-dependent activation of a subset of genes that is highly induced during brain development and neuronal maturation, a feature that these genes reportedly share with circular RNAs (circRNAs). Interestingly, some of these genes are predicted to express circular transcripts. In this study, we validated the abundance of the circular transcript variants of four P53 target genes (Pvt1, Ano3, Sec14l5, and Rnf169). These circular variants were overall more stable than their linear counterparts. They were furthermore highly enriched in the brain and their transcript levels continuously increase during subsequent developmental stages (from embryonic day 12 until adulthood), while no further increase could be observed for linear mRNAs beyond post-natal day 30. Finally, whereas radiation-induced expression of P53 target mRNAs peaks early after exposure, several of the circRNAs showed prolonged induction in irradiated embryonic mouse brain, primary mouse cortical neurons, and mouse blood. Together, our results indicate that the circRNAs from these P53 target genes are induced in response to radiation and they corroborate the findings that circRNAs may represent biomarkers of brain age. We also propose that they may be superior to mRNA as long-term biomarkers for radiation exposure.

MyoD-induced circular RNA CDR1as promotes myogenic differentiation of skeletal muscle satellite cells

Many protein coding and non-coding genes interplay in governing skeletal muscle formation. Nevertheless, comparing with the linear transcripts, functions of covalently closed circular RNAs (circRNAs), the new frontier of regulatory non-coding RNA (ncRNAs) molecules, remain largely unknown. Here, we identify CDR1as (antisense to the cerebellar degeneration-related protein 1 transcript, also termed as ciRS-7), a well-known cancer and neuron circRNA, plays a significant role in virtually controlling muscle differentiation. CDR1as is highly expressed in muscles of the mid-embryonic goat foetus, and activated at the initiation of myogenic differentiation in vitro. MyoD (myogenic differentiation protein 1), a driven transcription factor for myogenesis, promotes CDR1as by binding on its 5' flank region (-646 to -634 bp, neighbouring the predicted transcription start site at -580 bp). Overexpression or knockdown of CDR1as dramatically induces or impedes muscle differentiation program, respectively. By competitively binding to miR-7 (microRNA 7), CDR1as relieves the downregulation of IGF1R (insulin like growth factor 1 receptor) caused by miR-7 and consequently activates muscle differentiation. These results unveil that CDR1as plays critical roles in myogenic differentiation, which extends the versatile functions of CDR1as in mammal development and disease.

Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression

CircRNAs have been reported to exert momentous roles in regulating pathophysiological process and guiding clinical diagnosis and treatment in colorectal cancer (CRC). However, there are still a lot of circRNAs that need to be unearthed. In this study, we evaluated the expression profile of circRNAs in 10 CRC tissues and their corresponding normal-appearing tissues (NATs) by microarray, and identified that hsa_circ_101555 (circ101555) was significantly up-regulated in tumor tissues and closely related to the prognosis of CRC patients. A specific close loop structure of circ101555 was described, which was generated by back-splicing of the host gene CSNK1G1 and showed greater stability than the linear RNA. The results in vitro and in vivo showed that silencing circ101555 expression significantly suppressed cell proliferation, induced apoptosis and impaired the DNA repair capacity of CRC cells, while rescue experiments suggested that down-expression of miR-597-5p could significantly attenuate the biological effects of circ101555 knockdown on CRC cells. Subsequent experiments in vitro, including double fluorescence in situ hybridization (D-FISH) analysis, RIP analysis and biotin-coupled probe pull down assay, confirmed that miR-597-5p was effectively enriched by circ101555, and circ101555 might serve as a sponge of miR-597-5p. Moreover, two putative oncogenes (CDK6 and RPA3) were identified as the miR-597-5p potential targets. Taken together, our results proved that circ101555 might function as a competing endogenous RNA of miR-597-5p to up-regulate CDK6 and RPA3 expression in CRC. Circ101555 could be a useful prognostic indicator in patients with CRC, and silence of circ101555 provided a new attractive therapeutic measure for CRC.

Roles of circular RNAs in immune regulation and autoimmune diseases

Circular RNAs (circRNAs), as a novel class of endogenously expressed non-coding RNAs (ncRNAs), have a high stability and often present tissue-specific expression and evolutionary conservation. Emerging evidence has suggested that circRNAs play an essential role in complex human pathologies. Notably, circRNAs, important gene modulators in the immune system, are strongly associated with the occurrence and development of autoimmune diseases. Here, we focus on the roles of circRNAs in immune cells and immune regulation, highlighting their potential as biomarkers and biological functions in autoimmune diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), primary biliary cholangitis (PBC), and psoriasis, aiming at providing new insights into the diagnosis and therapy of these diseases.

The emerging role of circular RNAs in breast cancer

Breast cancer (BCa) is one of the most frequently diagnosed cancers and leading cause of cancer deaths among females worldwide. Circular RNAs (circRNAs) are a new class of endogenous regulatory RNAs characterized by circular shape resulting from covalently closed continuous loops that are capable of regulating gene expression at transcription or post-transcription levels. With the unique structures, circRNAs are resistant to exonuclease RNase R and maintain stability more easily than linear RNAs. Recently, an increasing number of circRNAs are discovered and reported to show different expression in BCa and these dysregulated circRNAs were correlated with patients’ clinical characteristics and grade in the progression of BCa. CircRNAs participate in the bioprocesses of carcinogenesis of BCa, including cell proliferation, apoptosis, cell cycle, tumorigenesis, vascularization, cell invasion, migration as well as metastasis. Here we concentrated on biogenesis and function of circRNAs, summarized their implications in BCa and discussed their potential as diagnostic and therapeutic targets for BCa.

Circular RNAs in hypertension: challenges and clinical promise

Hypertension (HT), or high blood pressure (BP), is a chronic disease that is common among populations worldwide. The occurrence of HT is one of the leading causes of cardiovascular morbidity and mortality in adults. Although multiple studies have stressed the multifactorial and multigenic nature of HT, uncertainties about its etiology persist, and current diagnostic biomarkers can explain only a small part of the phenotypic variance of BP. Hence, the search for novel biomarkers that enable early disease prevention and guided therapy is warranted. Regulatory circRNAs have emerged as the newest player in HT-related gene networks and hold promise for improving the accuracy of diagnosis. These RNAs are genome products that are formed through back-splicing of specific regions of pre-mRNAs. Evidence suggests that these RNA species are involved in various metabolic diseases. Recent studies have revealed that aberrant expression of circRNAs is relevant to the occurrence and development of HT. Accordingly, circRNAs are proposed as a new generation of predictive biomarkers and potential therapeutic targets for different forms of HT, including pulmonary hypertension and preeclampsia. This paper presents an overview of the findings from current research focusing on the emerging role of circRNAs in the pathogenesis of hypertension. Furthermore, some of the challenges encountered by circRNA studies are highlighted, and perspectives are provided on the future of research in this area.

Circular RNA circ-FoxO3 Inhibits Myoblast Cells Differentiation

CircRNA is a type of closed circular non-coding RNA formed by reverse splicing and plays an important role in regulating the growth and development of plants and animals. To investigate the function of circ-FoxO3 in mouse myoblast cells' (C2C12) differentiation and proliferation, we used RT-qPCR to detect the expression level of circ-FoxO3 in mouse myoblast cells at different densities and different differentiation stages, and the specific interference fragment was used to inhibit the expression level of circ-FoxO3 in myoblast cells to observe its effect on myoblast cells proliferation and differentiation. We found that the expression level of circ-FoxO3 in myoblast cells increased with the prolongation of myoblast cells differentiation time, and its expression level decreased with the proliferation of myoblast cells. At the same time, we found that the differentiation ability of the cells was significantly increased (p < 0.05), but the cell proliferation was unchanged (p > 0.05) after inhibiting the expression of circ-FoxO3 in myoblast cells. Combining the results of bioinformatics analysis and the dual luciferase reporter experiment, we found that circ-FoxO3 is a sponge of miR-138-5p, which regulates muscle differentiation. Our study shows that circ-FoxO3 can inhibit the differentiation of C2C12 myoblast cells and lay a scientific foundation for further study of skeletal muscle development at circRNA levels.

Noncoding RNAs Act as Tumor-Derived Molecular Components in Inducing Premetastatic Niche Formation

Cancer metastasis has been demonstrated as it is the culmination of a cascade of priming steps. Increasing evidence has shown that tumor-derived molecular components (TDMCs) are known as extra cellular vesicle and nonvesicle factors and serve as versatile intercellular communication vehicles which can mediate signaling in the tumor microenvironment while creating the premetastatic niche. Noncoding RNAs (ncRNAs) as one of the TDMCs have been proved in participating in the formation of the premetastatic niche. Understanding the premetastatic niche formation mechanisms through TDMCs, especially ncRNAs may open a new avenue for cancer metastasis therapeutic strategies. In this review, recent findings regarding ncRNAs function were summarized, and then the interaction with the premetastatic niche formation was studied, which highlight the potential of using ncRNAs for cancer diagnosis and therapeutic effect.

Effects of Qi Teng Xiao Zhuo granules on circRNA expression profiles in rats with chronic glomerulonephritis

Objectives: To screen and study circular RNA (circRNA) expression profiles in QTXZG-mediated treatment of chronic glomerulonephritis (CGN) induced by adriamycin in rats and to research the possible roles and molecular mechanisms of QTXZG. Materials and methods: Next-generation RNA sequencing was used to identify circRNA expression profiles in CGN after QTXZG treatment compared with a CGN model group and a control group. Bioinformatics analysis was performed to predict potential target miRNAs and mRNAs. GO and pathway analyses for potential target mRNAs were used to explore the potential roles of differentially expressed (DE) circRNAs. Results: We identified 31 and 21 significantly DE circRNAs between the model group vs the control group and the model group vs the QTXZG group, respectively. Four circRNAs that resulted from the establishment of the CGN model were reversed following treatment with QTXZG. Further analysis revealed that these four circRNAs may play important roles in the development of CGN. Conclusions: This study elucidated the comprehensive expression profile of circRNAs in CGN rats after QTXZG treatment for the first time. Analysis of the circRNA-miRNA-mRNA-ceRNA network to determine potential function provided a comprehensive understanding of circRNAs that may be involved in the development of CGN. The current study indicated that therapeutic effects of QTXZG on CGN may be due to regulation of circRNA expression.

Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs

To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone.

The circRNA circPTPRA suppresses epithelial-mesenchymal transitioning and metastasis of NSCLC cells by sponging miR-96-5p

BACKGROUND

Non-small cell lung carcinomas (NSCLC) are prevalent, lethal cancers with especially grim prospects due to late-stage detection and chemoresistance. Circular RNAs (circRNAs) are non-coding RNAs that participate in tumor development. However, the role of circRNAs in NSCLC is not well known. This study investigated the role of one circRNA - circPTPRA- in NSCLC and characterized its molecular mechanism of action.

METHODS

circPTPRA expression was analyzed in human NSCLC tumors and matched healthy lung tissue. We performed functional characterization in NSCLC cell lines and a mouse xenograft model of NSCLC to elucidate the molecular role of circPTPRA in epithelial-mesenchymal transitioning (EMT). We also assessed the regulatory action of circPTPRA on the microRNA miR-96-5p and its target the tumor suppressor Ras association domain-containing protein 8 (RASSF8).

FINDINGS

circPTPRA was significantly downregulated in NSCLC tumors relative to matched healthy lung tissue. Lower circPTPRA levels correlated with metastasis and inferior survival outcomes in NSCLC patients. circPTPRA suppressed EMT in NSCLC cell lines and reduced metastasis in the murine xenograft model by sequestering miR-96-5p and upregulating RASSF8. Correlation analyses in patient-derived NSCLC tumor specimens supported the involvement of the circPTPRA/miR-96-5p/RASSF8/E-cadherin axis dysregulation in NSCLC tumor progression.

INTERPRETATION

circPTPRA suppresses EMT and metastasis of NSCLC cell lines by sponging miR-96-5p, which upregulates the downstream tumor suppressor RASSF8. The circPTPRA/miR-96-5p/RASSF8/E-cadherin axis can be leveraged as a potential treatment avenue in NSCLC. FUND: The Key research and development projects of Anhui Province (201904a0720079), the Natural Science Foundation of Anhui Province (1908085MH240), the Graduate Innovation Program of Bengbu Medical College (Byycx1843), the National Natural Science Foundation of Tibet (XZ2017ZR-ZY033) and the Science and Technology Project of Shannan (SNKJYFJF2017-3) and Academic Subsidy Project for Top Talents in Universities of Anhui in 2019 (gxbjZD16).

CircRASSF2 promotes laryngeal squamous cell carcinoma progression by regulating the miR-302b-3p/IGF-1R axis

Background: Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) broadly expressed in cells of various species. However, the molecular mechanisms that link circRNAs with laryngeal squamous cell carcinoma (LSCC) are not well understood. In the present study, we attempted to provide novel basis for targeted therapy for LSCC from the aspect of circRNA-microRNA (miRNA)-mRNA interaction.Methods: We investigated the expression of circRNAs in three paired LSCC tissues and adjacent non-tumor tissues by microarray analysis. Differentially expressed circRNAs were identified between LSCC tissues and non-cancerous matched tissues, including 527 up-regulated circRNAs and 414 down-regulated circRNAs. We focused on hsa_circ_0059354, which is located on chromosome 20 and derived from RASSF2, and thus we named it circRASSF2.Results: circRASSF2 was found to be significantly up-regulated in LSCC tissues and LSCC cell lines compared with paired adjacent non-tumorous tissues and normal cells. Moreover, knockdown of circRASSF2 significantly inhibited cell proliferation and migration in vitro, which was blocked by miR-302b-3p inhibitor. Bioinformatics analysis predicted that there is a circRASSF2/miR-302b-3p/ insulin-like growth factor 1 receptor (IGF-1R) axis in LSCC progression. Dual-luciferase reporter system validated the direct interaction of circRASSF2, miR-302b-3p, and IGF-1R. Western blot verified that inhibition of circRASSF2 decreased IGF-1R expression. Furthermore, silencing circRASSF2 suppressed LSCC growth in vivo Importantly, we demonstrated that circRASSF2 was up-regulated in serum exosomes from LSCC patients. Altogether, silencing circRASSF2 suppresses progression of LSCC by interacting with miR-302b-3p and decreasing inhibiting IGF-1R expression.Conclusion: In conclusion, these data suggest that circRASSF2 is a central component linking circRNAs to progression of LSCC via an miR-302b-3p/IGF-1R axis.

Establishing essential quality criteria for the validation of circular RNAs as biomarkers

Non-coding RNAs were established in the last decade as a new valuable biomarker class for human diseases. Specifically, circular RNAs (circRNAs) were only recently discovered as a new large group of non-coding RNAs that, due to their circular configuration, are metabolically more stable compared to their linear counterparts and therefore highly suitable for biomarker use. Based on high-throughput sequencing, the catalogs of endogenous circRNAs with disease relevance and correlation continue to grow steadily. As a consequence, circRNAs emerged as novel and attractive biomarkers, indicated by numerous recent publications. Here we would like to stress the need of essential quality criteria for validation and characterization of circular RNAs. In addition to high-throughput sequencing, classical biochemical methods are essential and should be applied for the characterization of this special class of RNAs, in particular to convincingly confirm their circularity.

Biogenesis and Function of Circular RNAs in Health and in Disease

Circular RNAs (circRNAs) are a class of non-coding RNA that were previously thought to be insignificant byproducts of splicing errors. However, recent advances in RNA sequencing confirmed the presence of circRNAs in multiple cell lines and across different species suggesting a functional role of this RNA species. CircRNAs arise from back-splicing events resulting in a circular RNA that is stable, specific and conserved. They can be generated from exons, exon-introns, or introns. CircRNAs have multifaceted functions. They are likely part of the competing endogenous RNA class. They can regulate gene expression by sponging microRNAs, binding proteins or they can be translated into a protein themselves. CircRNAs have been associated with health and disease, some with disease protective effects, some with disease promoting functions. The widespread expression and disease regulatory mechanisms endow circRNAs to be used as functional biomarkers and therapeutic targets for a variety of different disorders. In this concise article we provide an overview of the association of circRNAs with various diseases including cancer, cardiovascular and kidney disease as well as cellular senescence. We conclude with an assessment of the current status and future outlook of this new field of research that carries immense potential with respect to diagnostic and therapeutic approaches of a variety of diseases.

Dysregulation of Circular RNAs in Myotonic Dystrophy Type 1

Circular RNAs (circRNAs) constitute a recently re-discovered class of non-coding RNAs functioning as sponges for miRNAs and proteins, affecting RNA splicing and regulating transcription. CircRNAs are generated by “back-splicing”, which is the linking covalently of 3′- and 5′-ends of exons. Thus, circRNA levels might be deregulated in conditions associated with altered RNA-splicing. Significantly, growing evidence indicates their role in human diseases. Specifically, myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by expanded CTG repeats in the DMPK gene which results in abnormal mRNA-splicing. In this investigation, circRNAs expressed in DM1 skeletal muscles were identified by analyzing RNA-sequencing data-sets followed by qPCR validation. In muscle biopsies, out of nine tested, four transcripts showed an increased circular fraction: CDYL, HIPK3, RTN4_03, and ZNF609. Their circular fraction values correlated with skeletal muscle strength and with splicing biomarkers of disease severity, and displayed higher values in more severely affected patients. Moreover, Receiver-Operating-Characteristics curves of these four circRNAs discriminated DM1 patients from controls. The identified circRNAs were also detectable in peripheral-blood-mononuclear-cells (PBMCs) and the plasma of DM1 patients, but they were not regulated significantly. Finally, increased circular fractions of RTN4_03 and ZNF609 were also observed in differentiated myogenic cell lines derived from DM1 patients. In conclusion, this pilot study identified circRNA dysregulation in DM1 patients.

Circular RNA hsa_circ_0068871 regulates FGFR3 expression and activates STAT3 by targeting miR-181a-5p to promote bladder cancer progression

BACKGROUND

FGFR3 plays an important role in the development of bladder cancer (BCa). Hsa_circ_0068871 is a circRNA generated from several exons of FGFR3. However, the potential functional role of hsa_circ_0068871 in BCa remains largely unknown. Here we aim to evaluate the role of hsa_circ_0068871 in BCa.

METHODS

We selected miR-181a-5p as the potential target miRNA of hsa_circ_0068871. The expression levels of hsa_circ_0068871 and miR-181a-5p were examined in BCa tissues and paired adjacent normal tissues by quantitative real-time PCR. To characterize the function of hsa_circ_0068871, BCa cell lines were stably infected with lentivirus targeting hsa_circ_0068871, followed by examinations of cell proliferation, migration and apoptosis. In addition, xenografts experiment in nude mice were performed to evaluate the effect of hsa_circ_0068871 in BCa. Biotinylated RNA probe pull-down assay, fluorescence in situ hybridization and luciferase reporter assay were conducted to confirm the relationship between hsa_circ_0068871, miR-181a-5p and FGFR3.

RESULTS

Hsa_circ_0068871 is over-expressed in BCa tissues and cell lines, whereas miR-181a-5p expression is repressed. Depletion of has_circ_0068871 or upregulation of miR-181a-5p inhibited the proliferation and migration of BCa cells in vitro and in vivo. Mechanistically, hsa_circ_0068871 upregulated FGFR3 expression and activated STAT3 by targeting miR-181a-5p to promote BCa progression.

CONCLUSIONS

Hsa_circ_0068871 regulates the miR-181a-5p/FGFR3 axis and activates STAT3 to promote BCa progression, and it may serve as a potential biomarker.

The circRNA circP4HB promotes NSCLC aggressiveness and metastasis by sponging miR-133a-5p

BACKGROUND

Non-small cell lung carcinoma (NSCLC) continues to top the list of cancer mortalities worldwide. The role of circular RNAs (circRNAs) in tumorigenesis has been increasingly appreciated, although it is relatively unexplored in NSCLC. Herein, we report on the role of circP4HB in NSCLC.

METHODS

First, we evaluated circP4HB levels in patient-derived NSCLC tissue versus paired healthy samples. Next, we conducted experiments in vitro in NSCLC cell-lines and in vivo in a murine xenograft NSCLC model to assess the impact of circP4HB on epithelial-mesenchymal transition (EMT) in vitro and metastasis in vivo. The downstream impact of circP4HB on the microRNA miR-133a-5p, and its target the EMT marker vimentin, were also evaluated.

RESULTS

NSCLC tumor specimens exhibited higher circP4HB levels in comparison to paired healthy lung samples and was associated with metastatic disease and poorer survival. circP4HB promoted EMT and vimentin expression in vitro and xenograft metastasis in vivo through sequestration of miR-133a-5p.

CONCLUSION

circP4HB enhances EMT and metastatic disease through miR-133a-5p sequestration, leading to upregulation of vimentin. Therefore, these findings advocate targeting the circP4HB/miR-133a-5p/vimentin axis as a potential therapeutic option for NSCLC patients.

Reconstruction and analysis of circRNA‑miRNA‑mRNA network in the pathology of cervical cancer

The present study was performed with the aim of understanding the mechanisms of pathogenesis and providing novel biomarkers for cervical cancer by constructing a regulatory circular (circ)RNA‑micro (mi)RNA‑mRNA network. Using an adjusted P-value of <0.05 and an absolute log value of fold-change >1, 16 and 156 miRNAs from GSE30656 and The Cancer Genome Atlas (TCGA), 5,321 mRNAs from GSE63514, 4,076 mRNAs from cervical squamous cell carcinoma and endocervical adenocarcinoma (from TCGA) and 75 circRNAs from GSE102686 were obtained. Using RNAhybrid, Venn and UpSetR plot, 12 circRNA‑miRNA pairs and 266 miRNA‑mRNA pairs were obtained. Once these pairs were combined, a circRNA‑miRNA‑mRNA network with 11 circRNA nodes, 4 miRNA nodes, 153 mRNA nodes and 203 edges was constructed. By constructing the protein‑protein interaction network using Molecular Complex Detection scores >5 and >5 nodes, 7 hubgenes (RRM2, CEP55, CHEK1, KIF23, RACGAP1, ATAD2 and KIF11) were identified. By mapping the 7 hubgenes into the preliminary circRNA‑miRNA‑mRNA network, a circRNA‑miRNA‑hubgenes network consisting of 5 circRNAs (hsa_circRNA_000596, hsa_circRNA_104315, hsa_circRNA_400068, hsa_circRNA_101958 and hsa_circRNA_103519), 2 mRNAs (hsa‑miR‑15b and hsa‑miR‑106b) and 7 mRNAs (RRM2, CEP55, CHEK1, KIF23, RACGAP1, ATAD2 and KIF11) was constructed. There were 22 circRNA‑miRNA‑mRNA regulatory axes identified in the subnetwork. By analyzing the overall survival for the 7 hubgenes using the Gene Expression Profiling Interactive Analysis tool, higher expression of RRM2 was demonstrated to be associated with a significantly poorer overall survival. PharmGkb analysis identified single nucleotide polymorphisms (SNPs) of rs5030743 and rs1130609 of RRM2, which can be treated with cladribine and cytarabine. RRM2 was also indicated to be involved in the gemcitabine pathway. The 5 circRNAs (hsa_circRNA_000596, hsa_circRNA_104315, hsa_circRNA_400068, hsa_circRNA_101958 and hsa_circRNA_103519) may function as competing endogenous RNAs and serve critical roles in cervical cancer. In addition, cytarabine may produce similar effects to gemcitabine and may be an optional chemotherapeutic drug for treating cervical cancer by targeting rs5030743 and rs1130609 or other similar SNPs. However, the specific mechanism of action should be confirmed by further study.

Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors

Genetically encodable sensors have been widely used in the detection of intracellular molecules ranging from metal ions and metabolites to nucleic acids and proteins. These biosensors are capable of monitoring in real-time the cellular levels, locations, and cell-to-cell variations of the target compounds in living systems. Traditionally, the majority of these sensors have been developed based on fluorescent proteins. As an exciting alternative, genetically encoded RNA-based molecular sensors (GERMS) have emerged over the past few years for the intracellular imaging and detection of various biological targets. In view of their ability for the general detection of a wide range of target analytes, and the modular and simple design principle, GERMS are becoming a popular choice for intracellular analysis. In this review, we summarize different design principles of GERMS based on various RNA recognition modules, transducer modules, and reporting systems. Some recent advances in the application of GERMS for intracellular imaging are also discussed. With further improvement in biostability, sensitivity, and robustness, GERMS can potentially be widely used in cell biology and biotechnology.

The interaction of circRNAs and RNA binding proteins: An important part of circRNA maintenance and function

The widespread expression of circular RNAs (circRNAs) is regarded as a feature of gene expression in highly diverged eukaryotes. Recent studies have shown that circRNAs can act as a miRNA sponge to repress miRNA function, participate in splicing of target genes, translate genes into protein and interact with RNA binding proteins (RBPs). RBPs are a broad class of proteins involved in gene transcription and translation, and interaction with RBPs is considered an important part of circRNA function, which can serve as an essential element underlying the functions of circRNAs, including genesis, translation, transcriptional regulation of target genes, and extracellular transport. In this mini-review, we attempt to explore in detail the relationship between circRNAs and RBPs, and the interactions between the two factors. The goal of this review is to investigate the emerging studies of RBPs and circRNAs to better understand how their interaction alters cellular function.

Long Noncoding RNA ANRIL: Lnc-ing Genetic Variation at the Chromosome 9p21 Locus to Molecular Mechanisms of Atherosclerosis

Ever since the first genome-wide association studies (GWAS) on coronary artery disease (CAD), the Chr9p21 risk locus has emerged as a top signal in GWAS of atherosclerotic cardiovascular disease, including stroke and peripheral artery disease. The CAD risk SNPs on Chr9p21 lie within a stretch of 58 kilobases of non-protein-coding DNA, containing the gene body of the long noncoding RNA (lncRNA) antisense non coding RNA in the INK4 locus (ANRIL). How risk is affected by the Chr9p21 locus in molecular detail is a matter of ongoing research. Here we will review recent advances in the understanding that ANRIL serves as a key risk effector molecule of atherogenesis at the locus. One focus of this review is the shift in understanding that genetic variation at Chr9p21 not only affects the abundance of ANRIL, and in some cases expression of the adjacent CDKN2A/B tumor suppressors, but also impacts ANRIL splicing, such that 3′-5′-linked circular noncoding ANRIL RNA species are produced. We describe how the balance of linear and circular ANRIL RNA, determined by the Chr9p21 genotype, regulates molecular pathways and cellular functions involved in atherogenesis. We end with an outlook on how manipulating circular ANRIL abundance may be exploited for therapeutic purposes.

Circular RNAs as Therapeutic Agents and Targets

It has recently been reported that thousands of covalently linked circular RNAs (circRNAs) are expressed from human genomes. circRNAs emerge during RNA splicing. circRNAs are circularized in a reaction termed "backsplicing," whereby the spliceosome fuses a splice donor site in a downstream exon to a splice acceptor site in an upstream exon. Although a young field of research, first studies indicate that backsplicing is not an erroneous reaction of the spliceosome. Instead, circRNAs are produced in cells with high cell-type specificity and can exert biologically meaningful and specific functions. These observations and the finding that circRNAs are stable against exonucleolytic decay are raising the question whether circRNAs may be relevant as therapeutic agents and targets. In this review, we start out with a short introduction into classification, biogenesis and general molecular mechanisms of circRNAs. We then describe reports, where manipulating circRNA abundance has been shown to have therapeutic value in animal disease models in vivo, with a focus on cardiovascular disease (CVD). Starting from existing approaches, we outline particular challenges and opportunities for future circRNA-based therapeutic approaches that exploit stability and molecular effector functions of native circRNAs. We end with considerations which designer functions could be engineered into artificial therapeutic circular RNAs.

Circular RNAs: Crucial regulators in the human body (Review)

Circular RNAs (circRNAs) belong to a new type of endogenous non‑coding RNAs (ncRNAs) that are derived from exons and/or introns, and are widely distributed in mammals. The majority of circRNAs have a specific expression profile in cells or tissues, as well as during different stages of development. CircRNAs were originally thought to be the products of mis‑splicing. However, with the assistance of bioinformatics tools and the rapid development of high‑throughput sequencing, an increasing body of evidence has suggested that circRNAs bind micro(mi)RNAs, and have a role as miRNA sponges, thereby regulating target mRNA splicing and transcription. Human diseases are closely associated with circRNAs, especially in cancer as their expression is typically altered during the progression of cancer; this may provide a novel type of biomarker for cancer diagnosis and prognosis. CircRNAs are becoming a key area of interest within the field of cancer research. In the present review, we summarize the known molecular mechanisms and biological origin of circRNAs, as well as their functions, especially those related to human tumors.

Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases

Circular RNAs are generated by back‐splicing of precursor‐mRNAs. Although they have been known for many years, only recently we have started to appreciate their widespread expression and their regulatory functions in a variety of biological processes. Not surprisingly, circular RNA dysregulation and participation in the pathogenic mechanisms have started to emerge in many instances, including cardiovascular diseases. Detection, differential expression analysis and validation are the three critical points for the characterization of any RNA, and circular RNAs are no exception. Their characteristics, however, generate several problems that are yet to be completely addressed, and literature still lacks comprehensive definitions of well‐defined best practices. We present a map of the current knowledge regarding circular RNAs and the critical issues limiting our understanding of their regulation and function. The goal was to provide the readers with the tools to critically decide which of the many approaches available is most suitable to their experimental plan. Although particularly focused on cardiovascular diseases, most critical issues concerning circular RNAs are common to many other fields of investigation.

A Zfp609 circular RNA regulates myoblast differentiation by sponging miR-194-5p

Skeletal muscle development and growth regulatory mechanism is the focus of both animal genetics and medicine. The recent studies indicate that covalently closed circular RNAs (circRNAs) also play important role on muscle development through sequestering specific miRNAs. The present study was conducted to determine the functional roles of circZfp609, a recently identified circRNA, in the regulation of myogenesis in mouse myoblast cell line (C2C12). circZfp609 is predicted to has binding sites of miR-194-5p. circZfp609 knockdown increased the expression of Myf5 and MyoG, which indicated that circZfp609 suppressed myogenic differentiation. Via a luciferase screening assay, circZfp609 is observed to sponge to miR-194-5p with four potential binding sites. Specifically, we show that circZfp609 can sponge miR-194-5p to sequester its inhibition on BCLAF1 so as to repress the myogenic differentiation. Modulation of circZfp609 expression in muscle tissue may emerge as a potential target in breeding strategies attempting to control muscle development.

A comprehensive review of circRNA: from purification and identification to disease marker potential

Circular RNA (circRNA) is an endogenous noncoding RNA with a covalently closed cyclic structure. Based on their components, circRNAs are divided into exonic circRNAs, intronic circRNAs, and exon-intron circRNAs. CircRNAs have well-conserved sequences and often have high stability due to their resistance to exonucleases. Depending on their sequence, circRNAs are involved in different biological functions, including microRNA sponge activity, modulation of alternative splicing or transcription, interaction with RNA-binding proteins, and rolling translation, and are a derivative of pseudogenes. CircRNAs are involved in the development of a variety of pathological conditions, such as cardiovascular diseases, diabetes, neurological diseases, and cancer. Emerging evidence has shown that circRNAs are likely to be new potential clinical diagnostic markers or treatments for many diseases. Here we describe circRNA research methods and biological functions, and discuss the potential relationship between circRNAs and disease progression.

Assessment of myoblast circular RNA dynamics and its correlation with miRNA during myogenic differentiation

Myoblast differentiation is a highly complex process that is regulated by proteins as well as by non-coding RNAs. Circular RNAs have been identified as an emerging new class of non-coding RNA in the modulation of skeletal muscle development, whereas their expression profiles and functional regulation in myoblast differentiation remain unknown. In the present study, we performed deep RNA-sequencing of C2C12 myoblasts during cell differentiation and uncovered 37,751 unique circular RNAs derived from 6943 hosting genes. The ensuing qRT-PCR and RNA fluorescence in situ hybridization verification were carried out to confirm the RNA-sequencing results. An unbiased analysis demonstrated dynamic circular RNA expression changes in the process of myoblast differentiation, and the circular RNA abundances were independent from their cognate linear RNAs. Gene ontology analysis showed that many down-regulated circular RNAs were exclusive to cell division and the cell cycle, whereas up-regulated circular RNAs were related to the cell development process. Furthermore, interaction networks of circular RNA-microRNA were constructed. Several microRNAs well-known for myoblast regulation, such as miR-133, miR-24 and miR-23a, were in this network. In summary, this study showed that circular RNA expression dynamics changed during myoblast differentiation. Circular RNAs play a role in regulating the myoblast cell cycle and development by acting as microRNA binding sites to facilitate their regulation of gene expression during myoblast differentiation. These findings open a new avenue for future investigation of this emerging RNA class in skeletal muscle growth and development.

Circular RNAs function as ceRNAs to regulate and control human cancer progression

Circular RNAs (circRNAs) are connected at the 3′ and 5′ ends by exon or intron cyclization, forming a complete ring structure. circRNA is more stable and conservative than linear RNA and abounds in various organisms. In recent years, increasing numbers of reports have found that circRNA plays a major role in the biological functions of a network of competing endogenous RNA (ceRNA). circRNAs can compete together with microRNAs (miRNAs) to influence the stability of target RNAs or their translation, thus, regulating gene expression at the transcriptional level. circRNAs are involved in biological processes such as tumor cell proliferation, apoptosis, invasion, and migration as ceRNAs. circRNAs, therefore, represent promising candidates for clinical diagnosis and treatment. Here, we review the progress in studying the role of circRNAs as ceRNAs in tumors and highlight the participation of circRNAs in signal transduction pathways to regulate cellular functions.

Online Databases and Circular RNAs

circRNAs are a novel class of ncRNAs that unlike other ncRNAs are not linear and have a circular structure. These valuable ncRNAs have been detected in a wide range of organisms from plants to animals and in all cell lines and tissues. Commonly, circRNAs have several functions as gene expression regulation at transcriptional or posttranscriptional level, miRNA partnership, and splicing intercede. Currently, circRNAs are roughly remarked in a widespread collection of diseases, and circRNAs simply can be recognized in liquid samples for disease detection and progression assessment. Considering these features of circRNAs, these molecules are evolving the impeccable collection of original biomarkers for disease therapy and diagnosis. As the critical role of these molecules in different aspects medicine and biology, circRNAs are considered as key and critical class of ncRNA in the current ncRNA search field. To simplify the assessment of diverse features of circRNAs, several databases have been established such as circBase, CircInteractome, CircNet, Circ2Traits, CircR2Disease, TCSD, and CSCD. In this chapter, we have an overview on these main circRNA databases and introduce key features of each database.

Current Research on Non-Coding Ribonucleic Acid (RNA)

Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA. In small RNA, we discuss miRNA, transfer RNA, piwi-interacting RNA, small nucleolar RNA, small nuclear RNA, Y RNA, single recognition particle RNA, and 7SK RNA. We elaborate on the origin, detection method, and potential association with disease, putative functional mechanisms, and public resources for these non-coding RNAs. We aim to provide readers with a complete overview of non-coding RNAs and incite additional interest in non-coding RNA research.