Attenuated palmitoylation of serotonin receptor 5-HT1A affects receptor function and contributes to depression-like behaviors.
Gorinski Nataliya,Bijata Monika,Prasad Sonal,Wirth Alexander,Abdel Galil Dalia,Zeug Andre,Bazovkina Daria,Kondaurova Elena,Kulikova Elizabeth,Ilchibaeva Tatiana,Zareba-Koziol Monika,Papaleo Francesco,Scheggia Diego,Kochlamazashvili Gaga,Dityatev Alexander,Smyth Ian,Krzystyniak Adam,Wlodarczyk Jakub,Richter Diethelm W,Strekalova Tatyana,Sigrist Stephan,Bang Claudia,Hobuß Lisa,Fiedler Jan,Thum Thomas,Naumenko Vladimir S,Pandey Ghanshyam,Ponimaskin Evgeni
Nature communications
The serotonergic system and in particular serotonin 1A receptor (5-HT1AR) are implicated in major depressive disorder (MDD). Here we demonstrated that 5-HT1AR is palmitoylated in human and rodent brains, and identified ZDHHC21 as a major palmitoyl acyltransferase, whose depletion reduced palmitoylation and consequently signaling functions of 5-HT1AR. Two rodent models for depression-like behavior show reduced brain ZDHHC21 expression and attenuated 5-HT1AR palmitoylation. Moreover, selective knock-down of ZDHHC21 in the murine forebrain induced depression-like behavior. We also identified the microRNA miR-30e as a negative regulator of Zdhhc21 expression. Through analysis of the post-mortem brain samples in individuals with MDD that died by suicide we find that miR-30e expression is increased, while ZDHHC21 expression, as well as palmitoylation of 5-HT1AR, are reduced within the prefrontal cortex. Our study suggests that downregulation of 5-HT1AR palmitoylation is a mechanism involved in depression, making the restoration of 5-HT1AR palmitoylation a promising clinical strategy for the treatment of MDD.
10.1038/s41467-019-11876-5
MicroRNA 135 is essential for chronic stress resiliency, antidepressant efficacy, and intact serotonergic activity.
Issler Orna,Haramati Sharon,Paul Evan D,Maeno Hiroshi,Navon Inbal,Zwang Rayya,Gil Shosh,Mayberg Helen S,Dunlop Boadie W,Menke Andreas,Awatramani Rajeshwar,Binder Elisabeth B,Deneris Evan S,Lowry Christopher A,Chen Alon
Neuron
The link between dysregulated serotonergic activity and depression and anxiety disorders is well established, yet the molecular mechanisms underlying these psychopathologies are not fully understood. Here, we explore the role of microRNAs in regulating serotonergic (5HT) neuron activity. To this end, we determined the specific microRNA "fingerprint" of 5HT neurons and identified a strong microRNA-target interaction between microRNA 135 (miR135), and both serotonin transporter and serotonin receptor-1a transcripts. Intriguingly, miR135a levels were upregulated after administration of antidepressants. Genetically modified mouse models, expressing higher or lower levels of miR135, demonstrated major alterations in anxiety- and depression-like behaviors, 5HT levels, and behavioral response to antidepressant treatment. Finally, miR135a levels in blood and brain of depressed human patients were significantly lower. The current results suggest a potential role for miR135 as an endogenous antidepressant and provide a venue for potential treatment and insights into the onset, susceptibility, and heterogeneity of stress-related psychopathologies.
10.1016/j.neuron.2014.05.042
Microarray Expression Profile of Circular RNAs in Plasma from Primary Biliary Cholangitis Patients.
Zheng Jiajia,Li Zhenrong,Wang Tiancheng,Zhao Yang,Wang Yongfeng
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
BACKGROUND/AIMS:Circular RNAs (circRNAs) play a crucial role in the occurrence of several diseases, including autoimmune diseases. However, their role in primary biliary cholangitis (PBC) remains unclear. Here, we aimed to determine the circRNA expression profile in plasma from PBC patients and further explore the value of circRNA in diagnosing PBC. METHODS:CircRNA microarrays were used to determine circRNA expression profiles in plasma samples from 6 PBC patients and 6 healthy controls. Statistical analyses identified differentially expressed circRNAs, and these circRNAs were verified by qRT-PCR in 29 PBC patients and 30 healthy controls. MicroRNA (miRNA) target prediction software identified putative miRNA response elements (MREs), which were used to construct a map of circRNA-miRNA interactions for the differentially expressed circRNAs. RESULTS:Our results indicated that there were 18 up-regulated and 4 down-regulated circular RNAs in the plasma from PBC patients compared with that from healthy individuals. Among the differentially expressed circRNAs, hsa_circ_402458 (P=0.0033), hsa_circ_087631 and hsa_circ_406329 (P=0.0185) were up-regulated, and hsa_circ_407176 (P=0.0066) and hsa_circ_082319 were down-regulated in the PBC group versus the healthy group as demonstrated by qRT-PCR. In particular, hsa_circ_402458 was significantly higher in PBC patients not receiving UDCA treatment than in PBC patients receiving UDCA treatment (P=0.0338). The area under the receiver operating characteristic curve for hsa_circ_402458 for diagnosing PBC was 0.710 (P=0.005). For hsa_circ_402458, two putative miRNA targets, hsa-miR-522-3p and hsa-miR-943, were predicted. CONCLUSIONS:circRNA dysregulation may play a role in PBC pathogenesis, and hsa_circ_402458 shows promise as a candidate biomarker for PBC.
10.1159/000485487
Expression profile and bioinformatics analysis of circular RNAs in acute ischemic stroke in a South Chinese Han population.
Li Shenghua,Chen Lan,Xu Chen,Qu Xiang,Qin Zhenxiu,Gao Jinggui,Li Jinpin,Liu Jingli
Scientific reports
Recent studies have found that circular RNAs (circRNAs) play crucial roles not only in the normal growth and the development of different tissues and organs but also in the pathogenesis and progression of various disorders. However, the expression patterns and the function of circRNAs in acute ischemic stroke (AIS) in the South Chinese Han population are unclear. In the present study, RNA sequencing (RNA-seq) data was generated from 3 AIS patients and 3 healthy controls. The circRNAs were detected and identified by CIRI2 and Find_circ software. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were used to detect the expression of circRNAs. Meanwhile, the potential diagnostic value of the selected circRNAs for AIS was assessed by generating receiver operating characteristic (ROC) curve with area under curve (AUC). The bioinformatic analysis of the host genes of differentially expressed (DE) circRNAs was performed by gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, KOBAS for pathway analysis and regulatory network analysis. miRNA-circRNA and miRNA-mRNA interactions were predicted by using TargetScan, miRanda and starBase. CircRNA-miRNA-mRNA interaction networks were created with Cytoscape. Our result showed that there were 2270 DE circRNAs between AIS patients and healthy controls. Among them, 659 were found upregulated and 1611 were downregulated. Bioinformatic analysis showed that the DE circRNAs were related to the following biological processes: endocytosis, energy metabolism, apoptosis, FoxO signaling pathway, platelet activation, neurotrophin signaling pathway and VEGF signaling pathway, which may be associated with the pathological of AIS. Three randomly selected circRNAs were successfully validated by qRT-PCR. The results show that hsa_circ_0005548 was significantly upregulated, while hsa_circ_0000607 and hsa_circ_0002465 were significantly downregulated in AIS. Furthermore, the AUC values for hsa_circ_005548, hsa_circ_0000607 and hsa_circ_0002465 were 0.51, 0.75 and 0.69, respectively, suggesting that hsa_circ_0000607 and hsa_circ_0002465 could be potential biomarkers for AIS. In addition, Bcl2 was predicted to be a direct target of miR-337-3p, and hsa_circRNA_0000607 was predicted to act as a sponge for miR-337-3p. Thus, hsa_circ_0000607 may be involved in AIS by regulating the miR-337-3p/Bcl2 axis. Collectively, our findings indicate that numerous dysregulated circRNAs may play pivotal functional roles in AIS and hsa_circ_0000607 may play a crucial role in the pathogenesis and progression of AIS by regulating the miR-337-3p/Bcl2 axis.
10.1038/s41598-020-66990-y
RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer.
Xie Yan,Li Juan,Li Peilong,Li Ning,Zhang Ying,Binang Helen,Zhao Yinghui,Duan Weili,Chen Yingjie,Wang Yunshan,Du Lutao,Wang Chuanxin
Frontiers in oncology
Circular RNAs (circRNAs) are emerging as cardinal areas of focus in the non-coding RNA field. Growing evidences have revealed exosomal circRNAs as potential biomarkers for detection of various cancers. However, the clinical importance of most serum exosomal circRNAs in colorectal cancer (CRC) have rarely been investigated. In this study, we examined the possible clinical application of serum exosomal circRNAs in the diagnosis of CRC. Firstly, we conducted RNA sequencing (RNA-seq) analysis using fifty CRC and fifty healthy control serum samples to identify CRC-related circRNAs. The sequencing data showed 122 differentially expressed circRNAs including 100 up-regulated and 22 down-regulated circRNA transcripts in CRC patients. Then, eight most dysregulated circRNAs were selected for validation by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay. Validation analysis revealed that the serum exosomal circ-PNN (hsa_circ_0101802) levels were significantly up-regulated in CRC cases compared with those in the healthy control groups. Receiver operating characteristic curve (ROC) analysis suggested that circ-PNN had significant value in CRC diagnosis with areas under the ROC curve (AUC) of 0.855 and 0.826 in the training and validation sets, respectively. We also found that the AUC of serum exosomal circ-PNN for early-stage CRC was 0.854. Finally, a network map based on circ-PNN was constructed to determine its potential miRNA-mRNAs binding. We also demonstrated that the expression of hsa-miR-6833-3P, hsa-let-7i-3p and hsa-miR-1301-3P were negatively correlated with circ-PNN in CRC patients. Collectively, our findings indicated that serum exosomal circ-PNN might be a potential non-invasive biomarker for the detection of CRC and may play a crucial role in the pathogenesis of CRC.
10.3389/fonc.2020.00982
Identification of the Potential Key Circular RNAs in Elderly Patients With Postoperative Cognitive Dysfunction.
Frontiers in aging neuroscience
BACKGROUND:Postoperative cognitive dysfunction (POCD) is one of the severe complications after surgery, inducing low life quality and high mortality, especially in elderly patients. However, the underlying molecular mechanism of POCD remains largely unknown, and the ideal biomarker for clinical diagnosis and prognosis is lacking. Circular RNAs (circRNAs), as a unique class of non-coding RNAs, were characterized by its stability and conservativeness, serving as novel biomarkers in various diseases. Nevertheless, the role of circRNAs in the occurrence of POCD remains elusive. METHODS:To investigate the differentially expressed circRNAs in the serum of POCD patients and its potential role in the development of POCD, we performed a circRNA microarray to screen the differentially expressed circRNAs in the serum samples from three patients of the POCD group and three paired patients of the non-POCD group. Subsequently, quantitative real-time polymerase chain reaction analysis (qRT-PCR) was utilized to verify the microarray data with the serum samples from 10 paired patients. Cytoscape software was used to construct the circRNA-miRNA-mRNA network for circRNAs with different expression levels as well as the target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed the biological functions of the differentially expressed circRNAs target genes. RESULTS:In total, we have analyzed 10,198 circRNAs through the microarray. Compared with the non-POCD patient group, there were 210 differentially expressed circRNAs with 133 upregulated and 77 downregulated in the POCD group (≥2-fold differential expression, ≤ 0.05). The qRT-PCR confirmed 10 circRNAs with different expressed levels, and the results were consistent with the microarray findings. Among them, hsa_circRNA_001145, hsa_circRNA_101138, and hsa_circRNA_061570 had the highest magnitude of change. The GO analysis showed that the differentially expressed circRNAs were associated with the regulation of the developmental process, cell-to-cell adhesion, and nervous system development. The KEGG analysis showed that the target genes of circRNAs were enriched in the MAPK signaling pathway and RAS signaling pathway. According to the targetscan7.1 and mirdbV5 databases, the circRNA-miRNA-mRNA network was constructed, and these results provided a vital landscape of circRNA expression profile in POCD. CONCLUSIONS:Our study provides an essential perspective for the differential expression of circRNAs in POCD patients. Further studies need to be performed to explore their potential therapeutic roles in the development of POCD.
10.3389/fnagi.2020.00165
Serum circular RNAs act as blood-based biomarkers for hypertrophic obstructive cardiomyopathy.
Sonnenschein Kristina,Wilczek Adriana Luisa,de Gonzalo-Calvo David,Pfanne Angelika,Derda Anselm Arthur,Zwadlo Carolin,Bavendiek Udo,Bauersachs Johann,Fiedler Jan,Thum Thomas
Scientific reports
Hypertrophic cardiomyopathy (HCM) is one of the most common hereditary heart diseases and is associated with a high risk of sudden cardiac death. HCM is characterized by pronounced hypertrophy of cardiomyocytes, fiber disarray and development of fibrosis and can be divided into a non-obstructive (HNCM) and obstructive form (HOCM) therefore requiring personalized therapeutic therapies. In the present study, we investigated the expression patterns of several circulating circular RNAs (circRNAs) as potential biomarkers in patients with HCM. We included 64 patients with HCM and 53 healthy controls to the study and quantitatively measured the expression of a set of circRNAs already known to be associated with cardiac diseases (circDNAJC6) and/or being highly abundant in blood (circTMEM56 and circMBOAT2). Abundancy of circRNAs was then correlated to relevant clinical parameters. Serum expression levels of circRNAs DNAJC6, TMEM56 and MBOAT2 were downregulated in patients with HCM. The inverse association between circRNA levels and HCM remained unchanged even after adjusting for confounding factors. All circRNAs, evaluated separately or in combination, showed a robust discrimination capacity when comparing control subjects with HCM, HNCM or HOCM patients (AUC from 0.722 to 0.949). Two circRNAs, circTMEM56 and circDNAJC6, significantly negatively correlated with echocardiographic parameters for HOCM. Collectively, circulating circRNAs DNAJC6, TMEM56 and MBOAT2 can distinguish between healthy and HCM patients. In addition, circTMEM56 and circDNAJC6 could serve as indicators of disease severity in patients with HOCM. Thus, circRNAs emerge as novel biomarkers for HCM facilitating the clinical decision making in a personalized manner.
10.1038/s41598-019-56617-2
CircMTO1 inhibits liver fibrosis via regulation of miR-17-5p and Smad7.
Wang Wei,Dong Ruiling,Guo Yong,He Jianan,Shao Chaopeng,Yi Pin,Yu Fujun,Gu Dayong,Zheng Jianjian
Journal of cellular and molecular medicine
Circular RNAs (circRNAs), often dysregulated in a variety of human diseases, participate in the initiation and development of cancers. Recently, circMTO1 (a circRNA derived from MTO1 gene), identified as a tumor suppressor, has been shown to contribute to the suppression of hepatocellular carcinoma. The present study aimed to explore the clinical significance and roles of circMTO1 in liver fibrosis. Here, we found that serum circMTO1 was significantly down-regulated in chronic hepatitis B (CHB) patients. Interestingly, serum circMTO1 was negatively correlated with fibrosis stages as well as HAI scores. Receiver operating characteristic curve analysis revealed that serum circMTO1 may serve as a diagnostic biomarker for liver fibrosis in CHB patients. Notably, overexpression of circMTO1 led to the suppression of transforming growth factor-β1-induced hepatic stellate cells (HSCs) activation. Bioinformatic analysis and luciferase activity assays indicated that circMTO1 was a target of mircoRNA-17-5p (miR-17-5p). Data from RNA pull-down assay further confirmed that circMTO1 interacted with miR-17-5p. The inhibitory effects of circMTO1 on HSC activation were suppressed by miR-17-5p mimics. Further studies showed that Smad7 was a target of miR-17-5p. Moreover, circMTO1-inhibited HSC activation was also blocked down by loss of Smad7. Taken together, we demonstrate that circMTO1 inhibits liver fibrosis via regulation of miR-17-5p and Smad7, and serum circMTO1 may be a novel promising biomarker of liver fibrosis.
10.1111/jcmm.14432
Evaluation of circ_100219 and miR-135b in serum and exosomes of healthy pregnant women.
The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians
AIM:Circular RNAs (circRNAs) are recently discovered and highly stable noncoding RNAs acting as gene regulators. These circRNAs can function as miRNA sponges, thereby upregulating or downregulating miRNA target gene expression. MiR-135b is expressed in placenta tissue and can be found in maternal circulation, thus playing a functional role in pregnancy. This miR is a target of circ_100219. This preliminary study was aimed to evaluate circ_100219 and miR-135b expression in pregnant and nonpregnant women, and explore the relationship between circ_100219 and miR-135b in serum and exosomes. METHODS:Total RNA was isolated from serum and exosomes of 30 healthy pregnant women (32.9 ± 5.1 years) between 23-27 gestational weeks and 30 healthy nonpregnant women (31.3 ± 5.4 years). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to quantify circ_100219 and miR-135b expression. GAPDH and U6 snRNA were chosen as reference for normalizing expression levels. The differences between pregnant and nonpregnant women were assessed with Mann-Whitney test and correlation with Spearman's test. RESULTS:The circ_100219 expression levels were significantly lower both in serum and exosomes of second trimester pregnant women compared to the control group ( < .0001), whilst Mir-135b expression levels were significantly higher in pregnant than in the control group ( < .0001). A significant negative correlation was observed between circ_100219 and miR-135b expression levels in both serum and exosomes ( = -0.34 and = .009; = -0.31 and = .01, respectively). The circ_100219:miR-135b ratio was significantly increased in nonpregnant women compared to the pregnant group, in both serum and exosomes (49.0 versus 1.1, < .0001 and 2042.4 versus 28.5, < .0001, respectively). CONCLUSIONS:Our results confirm a role for circ_100219 and miR-135b in physiological pregnancy. Further studies are needed to investigate the circ_100219:miR-135b ratio in pregnancy complications.
10.1080/14767058.2019.1689556
Elevated serum circ_0068481 levels as a potential diagnostic and prognostic indicator in idiopathic pulmonary arterial hypertension.
Pulmonary circulation
Circular RNAs have continuous, stable, and covalently closed circular structures and are not easily degraded by nucleases, thus they are ideal serum biomarkers for detecting diseases. However, research is still lacking on circular RNAs as diagnostic and prognostic markers for idiopathic pulmonary arterial hypertension. This study investigated the potential role of serum circ_0068481 levels in idiopathic pulmonary arterial hypertension diagnosis and prognosis. This prospective cohort study enrolled 82 patients with idiopathic pulmonary arterial hypertension between January 2016 and July 2018 at Guangdong Provincial People's Hospital. Serum circ_0068481 levels were measured using quantitative reverse transcription-polymerase chain reaction. Baseline data, including clinical background, hemodynamic variables, and biochemical variables, were collected. Receiver operating characteristic curves were used to investigate diagnostic effect, the Kaplan-Meier method was used to estimate survival rates, and univariate analysis of prognostic factors was performed with a Cox proportional hazard model. We found that serum circ_0068481 expression levels were significantly higher in patients with idiopathic pulmonary arterial hypertension and had higher sensitivity and specificity for predicting idiopathic pulmonary arterial hypertension. Additionally, we found that circ_0068481 expression correlated significantly with heart function, 6-min walk distance, serum N-terminal pro-B-type natriuretic peptide, serum HS, the 6th World Symposium on Pulmonary Hypertension risk stratification, right heart failure, and patient death. Moreover, serum circ_0068481 levels were elevated in patients with idiopathic pulmonary arterial hypertension and right heart failure and were able to predict right heart failure. Serum circ_0068481 levels were also elevated in patients who died with idiopathic pulmonary arterial hypertension and were able to predict poorer clinical outcomes. Circ_0068481 is a novel and noninvasive biomarker for diagnosing idiopathic pulmonary arterial hypertension and predicting poor clinical outcome in patients with idiopathic pulmonary arterial hypertension.
10.1177/2045894019888416
LncRNA UCA1, Upregulated in CRC Biopsies and Downregulated in Serum Exosomes, Controls mRNA Expression by RNA-RNA Interactions.
Barbagallo Cristina,Brex Duilia,Caponnetto Angela,Cirnigliaro Matilde,Scalia Marina,Magnano Antonio,Caltabiano Rosario,Barbagallo Davide,Biondi Antonio,Cappellani Alessandro,Basile Francesco,Di Pietro Cinzia,Purrello Michele,Ragusa Marco
Molecular therapy. Nucleic acids
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) contribute to the onset of many neoplasias through RNA-RNA competitive interactions; in addition, they could be secreted by cancer cells into biological fluids, suggesting their potential diagnostic application. By analyzing the expression of 17 lncRNAs and 31 circRNAs in biopsies and serum exosomes from colorectal cancer (CRC) patients through qRT-PCR, we detected CCAT1, CCAT2, HOTAIR, and UCA1 upregulation and CDR1AS, MALAT1, and TUG1 downregulation in biopsies. In serum exosomes, UCA1 was downregulated, while circHIPK3 and TUG1 were upregulated. Combined receiver operating characteristic (ROC) curves of TUG1:UCA1 and circHIPK3:UCA1 showed high values of sensitivity and specificity. Through in vitro (i.e., RNA silencing and mitogen-activated protein kinase [MAPK] inhibition) and in silico analyses (i.e., expression correlation and RNA-RNA-binding prediction), we found that UCA1 could (1) be controlled by MAPKs through CEBPB; (2) sequester miR-135a, miR-143, miR-214, and miR-1271, protecting ANLN, BIRC5, IPO7, KIF2A, and KIF23 from microRNA (miRNA)-induced degradation; and (3) interact with mRNA 3'-UTRs, preventing miRNA binding. UCA1 and its co-regulated antisense LINC01764 could interact and reciprocally mask their own miRNA-binding sites. Functional enrichment analysis of the RNA-RNA network controlled by UCA1 suggested its potential involvement in cellular migration. The UCA1 regulatory axis would represent a promising target to develop innovative RNA-based therapeutics against CRC.
10.1016/j.omtn.2018.05.009
Hsa_circRNA_0054633 is highly expressed in gestational diabetes mellitus and closely related to glycosylation index.
Wu Hangyu,Wu Siyang,Zhu Yingchao,Ye Mei,Shen Jun,Liu Yan,Zhang Yisheng,Bu Shizhong
Clinical epigenetics
BACKGROUND:Circular RNA (circRNA) is involved in the pathological processes of various diseases. CircRNA is more stable than linear RNAs and is expressed in high levels in tissues, making it a better biomarker candidate than linear RNAs. In this study, we aimed to identify potential circRNA biomarkers of gestational diabetes mellitus (GDM). METHODS:A retrospective case-control study was conducted using data and samples from women treated at a hospital in China between July 10, 2017, and February 15, 2018. We collected serum samples from 40 healthy pregnant women (controls) and 40 women with GDM (cases) during the second trimester as well as 65 controls and 65 cases during the third trimester of pregnancy. Placenta tissues and neonatal cord blood were each from another 20 cases and 20 controls. We selected six circRNAs (hsa_circRNA_0054633, hsa_circRNA_103410, hsa_circRNA_063981, hsa_circRNA_102682, hsa_circRNA_0018508, and hsa_circRNA_406918) as candidate biomarkers and used quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) to measure their concentrations in the serum and placental tissues. The Pearson correlation test was used to assess the correlation between various circRNAs and between circRNA and clinical variables. The area under the receiver operating characteristic (ROC) curve was used to assess the diagnostic value of circRNAs for GDM at each stage. RESULTS:Hsa_circRNA_0054633 was highly expressed in the blood during the second and third trimesters; its expression was also high in the placenta but low in the cord blood (P < 0.05). Hsa_cirRNA_0054633 was highly correlated with GHBA1 and GHBA1c levels in maternal blood samples at various stages of the GDM group (including placental tissue and umbilical cord blood) (P < 0.05). Hsa_circRNA_063981, hsa_circRNA_102682, and hsa_circRNA_103410 were also differentially expressed between the case and control groups at different stages (P < 0.05). There was a strong correlation between hsa_circRNA_0054633 and hsa_circRNA_103410 levels in third-trimester maternal blood (P = 0.000, r = 0.554) and in neonatal umbilical cord blood (P = 0.000, r = 0.866). Hsa_circRNA_0054633 showed a significant diagnostic value in the second and third trimesters of pregnancy, placenta, and cord blood (AUC = 0.793, 0.664, 0.747, and 0.783, respectively, P < 0.001). CONCLUSION:This study suggests that hsa_cirRNA_0054633 is abnormally expressed in GDM patients and may play a potential role in the development of GDM. The possibility of using circRNAs for the diagnosis of GDM requires additional investigation in future studies.
10.1186/s13148-019-0610-8
Circular RNA expression in extracellular vesicles isolated from serum of patients with endometrial cancer.
Xu Hanzi,Gong Zhen,Shen Yang,Fang Yichen,Zhong Shanliang
Epigenomics
AIM:We aimed to explore the roles of circular RNAs (circRNAs) in extracellular vesicles (EVs) isolated from serum of patients with endometrial cancer. MATERIALS & METHODS:EVs were isolated from serum samples of three patients with stage III adenocarcinoma aged 50-60 years and three matched healthy controls. RNA was extracted from the EVs and analyzed using RNA-seq technique. RESULTS:We got 209 upregulated circRNAs and 66 downregulated circRNAs. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the differentially expressed circRNAs were enriched in five pathways. The expression level of hsa_circ_0109046 and hsa_circ_0002577 was confirmed using real-time quantitative PCR. CONCLUSION:We identified 275 differentially expressed circRNAs and the expression level of two circRNAs was confirmed using real-time quantitative PCR.
10.2217/epi-2017-0109
Identification of Altered Circular RNA Expression in Serum Exosomes from Patients with Papillary Thyroid Carcinoma by High-Throughput Sequencing.
Yang Chunjiang,Wei Youchun,Yu Leitao,Xiao Yong
Medical science monitor : international medical journal of experimental and clinical research
BACKGROUND This study aimed to identify altered exosome circular RNA (circRNA) in the serum of patients with papillary thyroid carcinoma using high-throughput sequencing. MATERIAL AND METHODS Serum was collected from three patients with papillary thyroid carcinoma and three patients with a benign thyroid goiter. Exosomes were isolated using an exosome isolation kit and confirmed by transmission electron microscopy. Exosome circRNAs were analyzed by high-throughput sequencing using the HiSeq 4000 sequencer. The differentially expressed circRNAs were confirmed by fluorescence quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS Twenty-two differentially expressed circRNAs were screened, which included three that were upregulated and 19 that were down-regulated in serum from patients with papillary thyroid carcinoma compared with controls. Gene Ontology (GO) enrichment analysis showed that these differentially expressed circRNAs were associated with 16 signaling pathways, including the thyroid hormone signaling pathway, the PI3K-Akt signaling pathway, and the AMPK signaling pathway. Three differentially regulated circRNAs included hsacirc_007293, hsacirc_031752, and hsacirc_020135 were confirmed by qRT- PCR. The expression trends were consistent between the high-throughput sequencing technique and qRT-PCR. CONCLUSIONS The findings from this study have shown that gene regulation can be studied from exosomes obtained from serum samples in patients with papillary thyroid carcinoma, and supports the need for further studies on the role of exosome circRNAs in thyroid cancer.
10.12659/MSM.915658
Microarray is an efficient tool for circRNA profiling.
Li Shasha,Teng Shuaishuai,Xu Junquan,Su Guannan,Zhang Yu,Zhao Jianqing,Zhang Suwei,Wang Haiyan,Qin Wenyan,Lu Zhi John,Guo Yong,Zhu Qianyong,Wang Dong
Briefings in bioinformatics
Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. In this study, we integrated 87 935 circRNAs sequences that cover most of circRNAs identified till now represented in circBase to design microarray probes targeting back-splice site of each circRNA to profile expression of those circRNAs. By comparing the circRNA detection efficiency of RNA-seq with this circRNA microarray, we revealed that microarray is more efficient than RNA-seq for circRNA profiling. Then, we found ∼80 000 circRNAs were expressed in cervical tumors and matched normal tissues, and ∼25 000 of them were differently expressed. Notably, many of these circRNAs detected by this microarray can be validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) or RNA-seq. Strikingly, as many as ∼18 000 circRNAs could be robustly detected in cell-free plasma samples, and the expression of ∼2700 of them differed after surgery for tumor removal. Our findings provided a comprehensive and genome-wide characterization of circRNAs in paired normal tissues and tumors and plasma samples from multiple individuals. In addition, we also provide a rich resource with 41 microarray data sets and 10 RNA-seq data sets and strong evidences for circRNA expression in cervical cancer. In conclusion, circRNAs could be efficiently profiled by circRNA microarray to target their reported back-splice sites in interested samples.
10.1093/bib/bby006
A plasma circulating miRNAs profile predicts type 2 diabetes mellitus and prediabetes: from the CORDIOPREV study.
Jiménez-Lucena Rosa,Camargo Antonio,Alcalá-Diaz Juan Francisco,Romero-Baldonado Cristina,Luque Raúl Miguel,van Ommen Ben,Delgado-Lista Javier,Ordovás Jose María,Pérez-Martínez Pablo,Rangel-Zúñiga Oriol Alberto,López-Miranda Jose
Experimental & molecular medicine
We aimed to explore whether changes in circulating levels of miRNAs according to type 2 diabetes mellitus (T2DM) or prediabetes status could be used as biomarkers to evaluate the risk of developing the disease. The study included 462 patients without T2DM at baseline from the CORDIOPREV trial. After a median follow-up of 60 months, 107 of the subjects developed T2DM, 30 developed prediabetes, 223 maintained prediabetes and 78 remained disease-free. Plasma levels of four miRNAs related to insulin signaling and beta-cell function were measured by RT-PCR. We analyzed the relationship between miRNAs levels and insulin signaling and release indexes at baseline and after the follow-up period. The risk of developing disease based on tertiles (T1-T2-T3) of baseline miRNAs levels was evaluated by COX analysis. Thus, we observed higher miR-150 and miR-30a-5p and lower miR-15a and miR-375 baseline levels in subjects with T2DM than in disease-free subjects. Patients with high miR-150 and miR-30a-5p baseline levels had lower disposition index (p = 0.047 and p = 0.007, respectively). The higher risk of disease was associated with high levels (T3) of miR-150 and miR-30a-5p (HR = 4.218 and HR = 2.527, respectively) and low levels (T1) of miR-15a and miR-375 (HR = 3.269 and HR = 1.604, respectively). In conclusion, our study showed that deregulated plasma levels of miR-150, miR-30a-5p, miR-15a, and miR-375 were observed years before the onset of T2DM and pre-DM and could be used to evaluate the risk of developing the disease, which may improve prediction and prevention among individuals at high risk for T2DM.
10.1038/s12276-018-0194-y
Comprehensive expression profiles and bioinformatics analysis reveal special circular RNA expression and potential predictability in the peripheral blood of humans with idiopathic membranous nephropathy.
Jin Xuefeng,Deng Bi,Ye Kun,Ye Dongmei,Huang Yiyun,Chen Xiaoyu,Yang Zhousheng,Chen Ying
Molecular medicine reports
The etiology of idiopathic membranous nephropathy (IMN) is considered to be closely associated with immunoregulation and genetic factors. Circular RNAs (circRNAs) have been found to regulate gene expression in various organisms, and to play an important role in multiple physiological and pathological processes, which may be involved in the pathogenesis of IMN. The purpose of the present study was to investigate the potential relationship between circRNAs in peripheral blood and disease. The diagnoses of IMN were confirmed using electron microscopy and immunofluorescence. Total RNA was isolated and microarray analysis was used to detect the expression levels of circRNAs in the peripheral blood of patients with IMN and in normal subjects. Selected genes from the microarray were selected and verified by reverse transcription‑quantitative (RT‑q)PCR. Bioinformatics tools were applied for further functional evaluation, and the potential disease predictability of circRNAs was determined using receiver‑operating characteristic (ROC) curves. The results showed that a total of 955 differentially expressed circRNAs were found in blood samples, 645 of which were upregulated and 310 which were downregulated. In total, five candidate circRNAs were validated using RT‑qPCR analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified numerous types of target genes and their corresponding microRNAs (miRNAs). The miRNAs identified were involved in biological processes and enriched in multiple important pathways, including the mitogen‑activated protein kinase, transforming growth factor‑β and Ras signaling pathways. The levels of circ_101319 were significantly higher (P<0.001) and exhibited promising diagnostic value in patients with IMN (area under ROC =0.89). The co‑expression network constructed for circ_101319 indicated that it may be associated with membranous nephropathy‑related pathways by mediating miRNAs. In conclusion, the present study revealed the expression and functional profile of differentially expressed circRNAs in the peripheral blood of patients with IMN, and provided new perspectives to predict and elucidate the development of IMN.
10.3892/mmr.2019.10671
A comprehensive profile of circulating RNAs in human serum.
Umu Sinan Uğur,Langseth Hilde,Bucher-Johannessen Cecilie,Fromm Bastian,Keller Andreas,Meese Eckart,Lauritzen Marianne,Leithaug Magnus,Lyle Robert,Rounge Trine B
RNA biology
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.
10.1080/15476286.2017.1403003