circRNA-miRNA Interaction Network Research Articles

LncRNA and circRNA expression profiles in the hippocampus of Aβ25‑35‑induced AD mice treated with Tripterygium glycoside.

Tripterygium glycosides (TG) have been reported to ameliorate Alzheimer's disease (AD), although the mechanism involved remains to be determined. In the present study, the lncRNA and circRNA expression profiles of an AD mouse model treated with TG were assessed using microarrays. lncRNAs, mRNAs, and circRNAs in the hippocampi of 3 AD+normal saline (NS) mice and 3 AD+TG mice were detected using microarrays. The most differentially expressed lncRNAs, mRNAs, and circRNAs were screened between the AD+NS and AD+TG groups. The differentially expressed lncRNAs and circRNAs were analyzed using GO enrichment and KEGG analyses. Co-expression analysis of lncRNAs, circRNAs, and mRNAs was performed by calculating the correlation coefficients. Protein-protein interaction (PPI) network analysis was performed on mRNAs using STRING. The lncRNA-target-transcription factor (TF) network was analyzed using the Network software. In total, 661 lncRNAs, 64 circRNAs, and 503 mRNAs were found to be differentially expressed in AD mice treated with TG. Pou4f1, Egr2, Mag, and Nr4a1 were the hub genes in the PPI network. The KEGG results showed that the mRNAs that were co-expressed with lncRNAs were enriched in the TNF, PI3K-Akt, and Wnt signaling pathways. LncRNA-target-TF network analysis indicated that TFs, including Cebpa, Zic2, and Rxra, were the most likely to regulate the detected lncRNAs. The circRNA-miRNA interaction network indicated that 275 miRNAs may bind to the 64 circRNAs. In conclusion, these findings provide a novel perspective on AD pathogenesis, and the detected lncRNAs, mRNAs, and circRNAs may serve as novel therapeutic targets for the management of AD.

Identification and bioinformatic analysis of CircRNAs in the plasma of patients with very severe chronic obstructive pulmonary disease

BackgroundThe differential expression of circular RNAs (circRNAs) in individuals with very severe chronic obstructive pulmonary disease (COPD) and healthy individuals was screened using microarray technology. The related functions and mechanisms were analyzed using bioinformatic methods to explore the potential of target circRNAs as biomarkers of COPD and provide insights for future pathogenesis.Patients and methodsThirty patients with very severe COPD and thirty healthy controls were diagnosed at The Second People’s Hospital of Hefei from September 2021 to September 2022. The differential expression of circRNAs was compared and analyzed using a gene microarray and verified using quantitative real-time polymerase chain reaction (qRT-PCR) technology.ResultsA total of 90 upregulated and 29 downregulated circRNAs were screened in patients with very severe COPD and compared with those in healthy controls. qRT-PCR analysis showed that hsa_circ_0062683 of patients with very severe COPD was significantly upregulated, and hsa_circ_0089763 and hsa_circ_0008882 were significantly downregulated. By constructing the circRNA-miRNA interaction network, it was found that hsa-miR-612, hsa-miR-593-5p, hsa-miR-765, and hsa-miR-103a-2-5p are the miRNAs regulated by more differentially expressed circRNAs (DEcircRNAs). DEcircRNAs may participate in the development of COPD through hypoxia or regulation of various immune cells.ConclusionPlasma circRNAs may play a helpful role in the diagnosis and assessment of COPD and be valuable disease biomarkers.

The diagnostic potential of a circRNA-miRNA network in non-small cell lung cancer.

Increasing studies demonstrate the significant contributions of circRNA-related competitive endogenous RNA (ceRNA) regulatory networks to tumorigenesis and cancer progression. Here, we aimed to construct a non-small cell lung cancer (NSCLC)-specific circRNA-miRNA network and evaluate its diagnostic potential in NSCLC. MiRNA deep sequencing was performed to screen differentially-expressed serum miRNAs in NSCLC. Four bioinformatics databases (TargetScan, miRanda, starBase, and RNAhybrid) were used to analyze the integrated circRNA-miRNA interaction network. The circRNA-miRNA network, including hsa-miR-4482-3p, hsa-miR-146a-3p, hsa_circ_0008167 and hsa_circ_0003317 was constructed based on their interactions and preliminary testing in NSCLC cells. The relative levels of the selected non-coding RNAs (ncRNAs) were quantified using quantitative real-time polymerase chain reaction (qRT-PCR) in the healthy, pneumonia, benign lung tumor and NSCLC cohorts. The diagnostic power of the circRNA-miRNA network was evaluated using receiver operating characteristic (ROC) analyses. The serum levels of hsa-miR-4482-3p, hsa-miR-146a-3p, hsa_circ_0008167, and hsa_circ_0003317 were dysregulated in NSCLC. The combination of the four ncRNAs showed the highest diagnostic value to discriminate between benign lung tumors and NSCLC. Additionally, the upregulated levels of hsa_circ_0008167 were correlated to more aggressive features of NSCLC, such as lymph node metastasis, distant metastasis, and higher stage. Furthermore, the combination of hsa_circ_0008167 + hsa-miR-4482-3p, and hsa_circ_0008167 + hsa-miR-4482-3p + hsa-miR-146a-3p had the greatest diagnostic power to differentiate between lymph node +/- metastases and higher/lower stages, respectively, compared to circRNAs or miRNAs alone, and traditional tumor markers. In conclusion, we identified a specific circRNA-miRNA network with higher sensitivity and specificity to diagnose NSCLC, thereby providing a new strategy for further development of ceRNA-related tumor markers in other cancers. KEY MESSAGES: Serum miR-4482-3p, miR-146a-3p, circ_0008167 and circ_0003317 are dysregulated in NSCLC. Higher levels of serum circ_0008167 are associated with more malignant NSCLC. Multiple combinations of circRNAs and miRNAs show higher value to diagnose NSCLC.

Key circRNAs from goat: discovery, integrated regulatory network and their putative roles in the differentiation of intramuscular adipocytes

BackgroundThe procession of preadipocytes differentiation into mature adipocytes involves multiple cellular and signal transduction pathways. Recently. a seirces of noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) were proved to play important roles in regulating differentiation of adipocytes.ResultIn this study, we aimed to identificate the potential circRNAs in the early and late stages of goat intramuscular adipocytes differentiation. Using bioinformatics methods to predict their biological functions and map the circRNA-miRNA interaction network. Over 104 million clean reads in goat intramuscular preadipocytes and adipocytes were mapped, of which16 circRNAs were differentially expressed (DE-circRNAs). Furthermore, we used real-time fluorescent quantitative PCR (qRT-PCR) technology to randomly detect the expression levels of 8 circRNAs among the DE-circRNAs, and our result verifies the accuracy of the RNA-seq data. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the DE-circRNAs, two circRNAs, circ_0005870 and circ_0000946, were found in Focal adhesion and PI3K-Akt signaling pathway. Then we draw the circRNA-miRNA interaction network and obtained the miRNAs that possibly interact with circ_0005870 and circ_0000946. Using TargetScan, miRTarBase and miR-TCDS online databases, we further obtained the mRNAs that may interact with the miRNAs, and generated the final circRNA-miRNA-mRNA interaction network. Combined with the following GO (Gene Ontology) and KEGG enrichment analysis, we obtained 5 key mRNAs related to adipocyte differentiation in our interaction network, which are FOXO3(forkhead box O3), PPP2CA (protein phosphatase 2 catalytic subunit alpha), EEIF4E (eukaryotic translation initiation factor 4), CDK6 (cyclin dependent kinase 6) and ACVR1 (activin A receptor type 1).ConclusionsBy using Illumina HiSeq and online databases, we generated the final circRNA-miRNA-mRNA interaction network that have valuable functions in adipocyte differentiation. Our work serves as a valuable genomic resource for in-depth exploration of the molecular mechanism of ncRNAs interaction network regulating adipocyte differentiation.

Comprehensive analysis of dysregulated circular RNAs and construction of a ceRNA network involved in the pathology of Alzheimer's disease in a 5 × FAD mouse model.

Alzheimer's disease (AD) causes a decline in cognitive function that poses a significant hazard to human health. However, the exact pathogenesis of AD and effective treatment have both proven elusive. Circular RNAs (circRNAs), which were initially deemed as meaningless non-coding RNAs, have been shown to participate in a variety of physiological and pathological processes. However, the variations and characteristics of circRNAs are not fairly well understood during the occurrence and development of AD. In this study, we performed RNA sequencing analyses, identified circRNA expression profiles, and explored the circRNA-associated competing endogenous RNA (ceRNA) relationship in the hippocampus of five familial AD (5 × FAD) mice with cognitive dysfunction. The RNA sequencing results identified 34 dysregulated circRNAs in the hippocampus of 5 × FAD mice, including 17 upregulated and 17 downregulated circRNAs. The circRNA-miRNA interaction network for the dysregulated circRNAs was generated, and it was found to include 34 circRNAs and 711 miRNAs. Next, 2067 mRNAs potentially modulated by upregulated circRNA-interacting miRNAs and 2297 mRNAs potentially modulated by downregulated circRNA-interacting miRNAs were identified. Pathway enrichment analyses revealed that the circRNA-miRNA-mRNA network modulated AD development via multiple pathways, such as axon guidance, mitogen-activated protein kinase, and neurotrophin. The associated biological processes were mainly related to neuron projection development, cell morphogenesis, and head development. Their corresponding distributions were especially high in the axon, postsynapse, and neuronal body. We constructed a ceRNA network that included five circRNAs, four miRNAs, and 188 mRNAs. In this network, the differential expressions of three circRNAs (circRNA04655, circRNA00723, and circRNA01891), two miRNAs (miR-3470b and miR-6240), and 13 mRNAs (Vgll3, Nhsl2, Rab7, Tardbp, Vps33b, Fam107a, Tacr1, Ankrd40, Creb1, Snap23, Csnk1a1, Bmi1, and Bfar) in the hippocampus of 5 × FAD mice using qRT-PCR analyses were consistent with the RNA sequencing results. Another one circRNAs (circRNA00747) and two mRNAs (Zfp37 and Polr1e) had similar expression trends to the sequencing data, while circRNA03723 and Mapk10 had deviated expression trends to the sequencing data. In conclusion, our study uncovered dysregulated circRNA expression profiles in the hippocampus of 5 × FAD mice, stretched comprehension of ceRNA biology, investigated the potential role of this ceRNA network in pathogenesis and progression, and identified potential biomarkers and therapeutic targets for AD.

Differential expression and functional analysis of circRNA in the ovaries of Yili geese at different egg-laying stages.

Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. Circular RNA (circRNA) has been proven to play a significant role in the regulation of animal reproduction. Studying the expression characteristics of circRNAs in goose ovaries at various egg-laying stages can provide a reference for the molecular regulation mechanism of ovary development in geese that is mediated by circRNAs. In this study, the expression profiles of circRNAs were compared in ovary tissues from Yili geese in three different breeding periods, namely the prelaying period (KL), laying period (CL), and ceased period (XL), and differentially expressed circRNAs related to ovarian development in Yili geese were screened. The potential biological functions of differential circRNAs were predicted by bioinformatics, and the differential circRNA-miRNA regulatory network was constructed. The results showed that a total of 4483 circRNAs were identified in 12 ovarian tissue samples from Yili geese at different laying stages. In the KL vs. CL, XL vs. CL, and XL vs. KL groups, 159, 455, and 383 differentially expressed circRNAs were identified, respectively. The host genes of the differential circRNAs were mostly enriched in the signal transduction, metabolism, and other related pathways, such as those for phototransduction, glycerophospholipid metabolism, aminoacyl-tRNA biosynthesis, and retinol metabolism. Finally, we constructed circRNA-miRNA regulation networks. Nine differential circRNAs were randomly selected for qRT-PCR verification, and the expression trends were consistent with the sequencing results. Our results indicated that significant differences in the expression profiles of circRNAs in the ovaries of Yili geese at different egg-laying stages. Meanwhile, through analyzing the differential circRNA-miRNA interaction network, core regulators such as circRNA NW_013186107.1:36835|52,574 and gga-miR-34b-5p were screened. This study provides a reference for the further analysis of the molecular regulatory mechanism of the circRNAs regulating goose ovary development and enriches the theory of genetic regulation during goose ovary development.

Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury.

Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNAs can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rats was established and comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done. As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA's host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and Sanger sequencing. This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

The circular RNA expression profile in ovarian serous cystadenocarcinoma reveals a complex circRNA\u2013miRNA regulatory network

BackgroundOvarian serous cystadenocarcinoma is one of the most serious gynecological malignancies. Circular RNA (circRNA) is a type of noncoding RNA with a covalently closed continuous loop structure. Abnormal circRNA expression might be associated with tumorigenesis because of its complex biological mechanisms by, for example, functioning as a microRNA (miRNA) sponge. However, the circRNA expression profile in ovarian serous cystadenocarcinoma and their associations with other RNAs have not yet been characterized. The main purpose of this study was to reveal the circRNA expression profile in ovarian serous cystadenocarcinoma.MethodsWe collected six specimens from three patients with ovarian serous cystadenocarcinoma and adjacent normal tissues. After RNA sequencing, we analyzed the expression of circRNAs with relevant mRNAs and miRNAs to characterize potential function.Results15,092 unique circRNAs were identified in six specimens. Approximately 46% of these circRNAs were not recorded in public databases. We then reported 353 differentially expressed circRNAs with oncogenes and tumor-suppressor genes. Furthermore, a conjoint analysis with relevant mRNAs revealed consistent changes between circRNAs and their homologous mRNAs. Overall, construction of a circRNA–miRNA network suggested that 4 special circRNAs could be used as potential biomarkers.ConclusionsOur study revealed the circRNA expression profile in the tissues of patients with ovarian serous cystadenocarcinoma. The differential expression of circRNAs was thought to be associated with ovarian serous cystadenocarcinoma in the enrichment analysis, and co-expression analysis with relevant mRNAs and miRNAs illustrated the latent regulatory network. We also constructed a complex circRNA–miRNA interaction network and then demonstrated the potential function of certain circRNAs to aid future diagnosis and treatment.

Expression Profiles and Bioinformatics Analysis of Full-length circRNA Isoforms in Gliomas

Background: Circular RNAs (circRNAs) are a newly discovered type of non-coding RNA, which have been demonstrated to act as microRNA (miRNA) “sponges” to modulate gene expression. Emerging evidence has confirmed that circRNAs take part in many biological processes in a variety of malignant tumors, including gliomas, suggesting that they could serve as biomarkers or therapeutic targets for tumors. The purpose of this study was to explore the roles of circRNAs in gliomas and to provide valuable clues for clinical diagnosis and treatment. Methods: RNA-seq data with poly(A)-/RNase R treatment was employed to investigate the expression profiles of circRNAs in tumor and paracancerous tissues derived from glioma patients. CircAST was used for full-length circRNA reconstruction and quantification. Bioinformatics analyses, including GO enrichment and KEGG pathway analyses, were performed to reveal the potential biological process and pathways of their host genes. A circRNA-miRNA interaction network was constructed to depict the interactions of the dysregulated circRNA transcripts with miRNAs. Results: A total of 20,474 circular transcripts that originated from 16,022 circRNAs were successfully reconstructed in the samples. We detected 646 upregulated and 112 downregulated circular transcripts in tumor tissues compared with paracancerous tissues. GO analysis revealed that their host genes may be related to positive regulation of GTPase activity, regulation of synaptic transmission, and glutamatergic and dendrite morphogenesis in the cytoplasm and cytosol. KEGG pathway analysis showed that the glutamatergic synapse, neurotrophin signaling pathway, and ErbB signaling pathway may be linked to the occurrence and development of gliomas. Conclusion: Our study revealed a comprehensive profile of differentially expressed circRNA transcripts in gliomas, indicating that aberrantly expressed circRNAs might play important roles in the occurrence and development of human gliomas.

CircRNA expression profiling and bioinformatics analysis indicate the potential biological role and clinical significance of circRNA in influenza A virus-induced lung injury

Circular RNA (circRNA) plays an important role in the regulation of multiple biological processes. However, circRNA profiling and the potential biological role of circRNA in influenza A virus (IAV)-induced lung injury have not been investigated. In the present study, circRNA expression profiles in lung tissues from mice with and without IAV-induced lung injury were analyzed using high-throughput sequencing, and differentially expressed circRNAs were verified by quantitative PCR. The gene homology of candidate circRNAs was investigated and the expression of plasma circRNAs from patients with IAV-induced acute respiratory distress syndrome (ARDS) was detected. The target microRNAs (miRNAs) of circRNAs were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. In total, 781 circRNAs were differentially expressed between ARDS mice and control (467 were up-regulated and 314 were down-regulated). Moreover, the candidate circRNAs (Slco3a1, Nfatc2, Wdr33, and Dmd) expression showed the same trend with the sequencing results. The isoforms of circRNA Slco3a1 and Wdr33 were highly conserved between humans and mice. Plasma circRNA Slco3a1 and Wdr33 presented differential expression in patients with IAV-induced ARDS compared to control. The circRNA-miRNA interaction network and GO and KEGG analyses indicated the potential biological role of circRNAs in the development of IAV-induced lung injury. Taken together, a large number of differentially expressed circRNAs were identified in our study. CircRNA Slco3a1 and Wdr33 had significantly different expression in specimens from mice and humans, and showed a potential biological role in IAV-induced lung injury by bioinformatics analysis.Electronic supplementary materialThe online version contains supplementary material available at 10.1007/s12038-021-00152-8.

Altered circular RNA expression profiles in an ovalbumin-induced murine model of allergic rhinitis.

Emerging evidence shows that circular RNAs (circRNAs) participate in the pathogenesis of multiple immune diseases. However, few studies have focused on the mechanisms of circRNAs involved in allergic rhinitis (AR). This study performed an RNA sequence (RNA-seq) profiling to identify the expression of circRNAs in nasal mucosa from ovalbumin-induced AR murine models and normal controls. Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) was then conducted to validate the differential expression of circRNAs. Bioinformatics analysis was applied to demonstrate the biological functions of the dysregulated circRNAs. A total of 86 distinct circRNA candidates were sequenced, of which 51 were upregulated and 35 were downregulated. The T cell receptor, B cell receptor, and calcium signaling pathways may be involved in the pathology of AR. Furthermore, a circRNA-miRNA interaction network was constructed via miRNA response elements analysis. Some circRNAs were correlated with miRNAs that are involved in T cell polarization and activation, thereby highlighting their potential role in the pathogenesis of AR. This study demonstrates a number of aberrantly expressed circRNAs related to AR, and offers a novel perspective into AR pathogenesis and future therapeutic strategies.

Differentially expressed circular RNAs in orbital adipose/connective tissue from patients with thyroid-associated ophthalmopathy

Our study aimed to investigate the differentially expressed circRNAs and their potential roles in orbital adipose/connective tissue from patients with thyroid-associated ophthalmopathy (TAO). The orbital adipose/connective tissue samples from three TAO patients and three control individuals were collected for RNA sequencing after depletion of ribosomal RNA. Differentially expressed mRNAs and up-regulated circRNAs were used for co-expression analysis. Functional and pathway enrichment analysis were conducted for the up- and down-regulated mRNAs in the circRNA-mRNA co-expression network. Meanwhile, circRNA-miRNA interaction network was established by miRanda software. The expression levels of mRNAs and circRNAs in control and TAO samples were determined by qRT-PCR. Among all the 16,329 circRNAs predicted from RNA sequencing data, 163 circRNAs (95 down-regulated and 68 up-regulated) were differentially expressed in TAO samples. Besides, 607 differentially expressed mRNAs were identified. The co-expression analysis showed circRNA_14940 was correlated with CCND1 and TNXB, while circRNA_10135 was correlated with PTGFR, and circRNA_14936 was correlated with TNFRSF19. The up-regulated CCND1 participated in Wnt signaling pathway. The down-regulated TNXB was involved in the ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling pathway. PTGFR participated in neuroactive ligand-receptor interaction and calcium signaling pathway. TNFRSF19 was involved in cytokine-cytokine receptor interaction. In the interaction network, circRNA_14936 could interact with hsa-miR-10392–3p, and circRNA_12367 could interact with hsa-miR-1228–3p. Moreover, the expression changes of MMP2, TNXB, PTGFR, CCND1, and TNFRSF19, as well as circRNA_14936, circRNA_14940, and circRNA_12367 were validated by qRT-PCR. In conclusion, the differentially expressed circRNAs might participate in pathogenesis of TAO, and we speculated that circRNA_14940-CCND1-Wnt signaling pathway might be an important regulatory axis.

Analysis of the Molecular Mechanism of Acute Coronary Syndrome Based on circRNA-miRNA Network Regulation.

Background With the development of biological technology, biomarkers for the prevention and diagnosis of acute coronary syndrome (ACS) have become increasingly evident. However, the study of novel circular RNAs (circRNAs) in ACS is still in progress. This study aimed to investigate whether the regulation of circRNA-miRNA networks is involved in ACS pathogenesis. Methods We used microarray analysis to detect significantly expressed circRNAs and miRNAs in the peripheral blood of patients in the control group (CG) and ACS groups, including an unstable angina pectoris (UAP) group and an acute myocardial infarction (AMI) group. A circRNA-miRNA interaction network analysis was carried out with open-source bioinformatics. The gene ontology (GO), pathway, and disease enrichment analyses for differentially expressed circRNAs were further analysed with hierarchical clustering. Results A total of 266 circRNAs (121 upregulated and 145 downregulated, P < 0.05, fold change FC ≥2) and 3 miRNAs (1 upregulated and 2 downregulated, P < 0.05, FC ≥ 1.2) were differentially expressed in the ACS groups compared with those in the CG. In addition, among these expressed circRNAs and miRNAs, a single circRNA could bind to more than 1–100 miRNAs, and vice versa. Next, an AMI-UAP network, an AMI-CG network, a UAP-CG network, and an AMI-CG-UAP network were constructed. The top 30 enriched GO terms among the three groups were emphasized as differentially expressed. Disease enrichment analysis showed that these differentially expressed circRNAs are involved in the pathogenesis of cardiovascular diseases. KEGG pathway analysis was performed to identify pathways associated with circRNAs targeting mRNAs. Conclusion CircRNAs are closely related to the pathological process of ACS via a mechanism that may be related to the up- or down-regulation of circRNAs and miRNAs and circRNA-miRNA coexpression. The metabolic pathways, signalling pathways, and diseases affected by these circRNAs can be predicted by enrichment analysis.

Circular RNA expression profiles in extracellular vesicles from the plasma of patients with pancreatic ductal adenocarcinoma.

Tumor‐derived extracellular vesicles (EVs) and their contents are involved in the development of human malignancies. Circular RNAs (circRNAs), enriched in EVs, can regulate diverse cellular processes by acting as microRNA (miRNA) sponges or through other mechanisms. In the present study, we explored the potential roles of circRNAs in EVs in the development of pancreatic ductal adenocarcinoma (PDAC). First, plasma was obtained from patients with PDAC (n = 8) and healthy volunteers (n = 8), and EVs were isolated by the ultracentrifugation method. Nanoparticle tracking analysis and transmission electron microscopy confirmed the size and form of the isolated EVs. The circRNA expression profiles of EVs were investigated by high‐throughput whole transcriptome sequencing. We then further validated the accuracy of the circRNA sequencing data by quantitative real‐time PCR analysis using plasma samples and PC cell lines, and subsequently performed bioinformatics analysis to reveal the potential functional roles of the differentially expressed circRNAs and to construct a circRNA‐miRNA interaction network to predict the target miRNAs of these circRNAs. Our work provides novel targets for further studies concerning the pathogenesis of PDAC.

The integrative regulatory network of circRNA and microRNA in keloid scarring.

Circular RNA (circRNA), a novel type of non-coding RNA that consists of a circular loop, has been demonstrated to act as a "sponge" for microRNAs (miRNAs). However, the role of circRNAs in keloid remains unknown. In this study, we investigated circRNA expression profiles in keloid to identify potential diagnostic and therapeutic circRNAs. We performed a circRNA microarray assay to determine circRNA expression in keloid and paired normal skin tissues. Quantitative reverse transcription polymerase chain reaction was used to evaluate the expression levels of candidate circRNAs. The most significantly over-expressed circRNA was used to predict putative miRNA targets and the binding sites of miRNAs with this circRNA. Finally, we constructed a circRNA-miRNA interaction network and carried out gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. We found 52 significantly upregulated and 24 downregulated circRNAs in keloid compared with normal skin tissue. We confirmed that hsa_circ_0057452, hsa_circ_0007482, hsa_circ_0020792, hsa_circ_0057342, and hsa_circ_0043688 were significantly upregulated in keloid tissues. Analysis of the circRNA-miRNA interaction network revealed that circRNAs could interact with miRNAs, including miRNA-29a, miRNA-23a-5p and miRNA-1976. GO and KEGG analyses indicated that these target genes were involved in biological functions and signaling pathways that may play vital roles in the pathogenesis of keloid. This study revealed that circRNAs are potentially implicated in the development of keloid and could serve as novel diagnostic and therapeutic targets.

Analyses of circRNA profiling during the development from pre-receptive to receptive phases in the goat endometrium

BackgroundRecent studies have revealed that noncoding RNAs play important regulatory roles in the formation of endometrial receptivity. Circular RNAs (circRNAs) are a universally expressed noncoding RNA species that have been recently proposed to act as miRNA sponges that directly regulate expression of target genes or parental genes.ResultsWe used Illumina Solexa technology to analyze the expression profiles of circRNAs in the endometrium from three goats at gestational day 5 (pre-receptive endometrium, PE) and three goats at gestational day 15 (receptive endometrium, RE). Overall, 21,813 circRNAs were identified, of which 5,925 circRNAs were specific to the RE and 9,078 were specific to the PE, which suggested high stage-specificity. Further analysis found 334 differentially expressed circRNAs in the RE compared with PE (P < 0.05). The analysis of the circRNA-miRNA interaction network further supported the idea that circRNAs act as miRNA sponges to regulate gene expression. Moreover, some circRNAs were regulated by estrogen (E2)/progesterone (P4) in endometrial epithelium cell lines (EECs) and endometrial stromal cell line (ESCs), and each circRNA molecule exhibited unique regulation characteristics with respect to E2 and P4.ConclusionsThese data provide an endometrium circRNA expression atlas corresponding to the biology of the goat receptive endometrium during embryo implantation.

Expression patterns of novel circular RNAs in chicken cells after avian leukosis virus subgroup J infection

Avian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus that causes severe economic losses to the poultry industry worldwide. Circular RNAs (circRNAs) are a class of non-coding RNAs that has been described in various biological systems and pathogenic processes. However, the immune mechanisms in response to circRNAs remain unknown. In this study, high-throughput transcriptome sequencing was used to detect circRNAs present in chicken macrophage (HD11) and chick embryo fibroblast (CEF) cells infected with ALV-J. We identified 7684 circRNAs from diverse genomic locations in CEF and HD11 after ALV-J infection, these RNAs showed complex expression patterns that differed based on the cells type and infection time. In total, 302 differentially expressed (DE) circRNAs and 164 DE circRNAs were identified in CEF and HD11 after ALV-J infection, respectively. CircRNA7419—associated with KDM4C— and circRNA6679 and circRNA6680—associated with TNFAIP6— were involved in the immune response upon ALV-J infection in CEF. Host genes were analyzed through further bioinformatics analysis. The result confirmed that a large number of DE circRNAs corresponded to several immune-associated or tumor-associated terms and pathways, such as Mucin type O-Glycan biosynthesis, MAPK signaling pathway, B cell receptor signaling, and Wnt signaling pathway in CEF, as well as Jak-STAT signaling pathway, apoptosis, and MAPK signaling pathway in HD11. CircRNAs related to the B cell receptor signaling pathway in CEF, and the Jak-STAT signaling pathway in HD11, were selected for circRNA-miRNA interaction network analyses. Our study indicates that circRNAs expression was altered by ALV-J infection in both CEF and HD11, and may play a key role in the progression of ALV-J infection.

Characterisation of the circular RNA landscape in mesenchymal stem cells from psoriatic skin lesions.

Circular RNAs (circRNAs) have recently emerged as novel non-coding regulatory RNAs, reportedly involved in many biological processes and human diseases. However, the role of circRNAs in the pathogenesis of psoriasis is unclear. Additionally, mesenchymal stem cells (MSCs) are involved in pathological processes associated with immune diseases, including psoriasis. In this study, we determined the circRNA expression profile of MSCs from psoriatic skin lesions and investigated possible mechanisms associated with psoriasis. RNA sequencing was used to detect circRNA expression in MSCs from psoriatic skin lesions and normal skin, and detailed bioinformatic analysis was performed. Our results allowed us to predict a circRNA-microRNA (miRNA) interaction network and subsequently validate seven differentially expressed circRNAs and three miRNAs by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we analysed circRNA expression in plasma to determine the extent of abnormal circRNA circulation in patients with psoriasis. In total, 6,323 circRNAs were detected, of which 3,227 constituted previously unreported circRNAs. We identified 129 circRNAs that exhibited significantly different expression patterns between the psoriasis and control groups, and established a circRNA-miRNA interaction network through bioinformatic analysis that indicated circRNA interaction with miRNAs associated with psoriasis. Additionally, qRT-PCR results confirmed the differential expression of seven circRNAs as well as the stable expression of three circRNAs in plasma from psoriasis patients, consistent with trends observed in cells. This is the first study of circRNA expression in psoriasis, indicating possible circRNA involvement in the pathogenesis of psoriasis.

Profile analysis of circRNAs induced by porcine endemic diarrhea virus infection in porcine intestinal epithelial cells

The circRNA is a newly defined noncoding RNA and characterized by its unique splicing reactions to form circles. However, the function of circRNAs during viral infection remains largely unknown. In this study, the circRNA expression profile during porcine endemic diarrhea virus (PEDV) infection in IPEC-J2 cell line was investigated using the next-generation sequencing technology. A total of 26670 circRNA candidates were identified. The functional annotation analysis revealed that the parent genes of differentially expressed circRNAs might be associated with host response to PEDV infection. Further analysis verified the existence of eight selected circRNAs and confirmed that PEDV infection alerted the expression patterns of circRNAs and their linear parent genes in IPEC-J2 cell line. The circRNA-miRNA interaction network was also constructed to elucidate their potential targets. Our results provided not only the first large-scale profile analysis of circRNAs associated with PEDV infection but also a novel direction to elucidate host-PEDV interactions.

Identification and characterization of circular RNAs in rapid atrial pacing dog atrial tissue

Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues. Moreover, we found 146 differentially expressed circRNAs between control and RAP dogs. Five circRNAs were selected for subsequent RT-PCR validation, and four circRNAs confirmed with the high throughput sequencing analysis. GO analysis showed that the differentially expressed circRNAs might involve in the process of “structural constituent of cytoskeleton, ion channel activity”. We explored the circRNA-miRNA interaction network, and found extensive interaction among differentially expressed circRNAs and AF related miRNAs and mRNAs. Our work firstly identified the characterization of circRNAs in the dog atrial, and revealed the differentially expressed circRNAs in the RAP dog, this might lay a solid foundation on the function of circRNA in the mechanisms of AF.