circRNA Transcripts Research Articles

CircRNA Expression Profiles and the Potential Role of CircZFP644 in Mice With Severe Acute Pancreatitis via Sponging miR-21-3p.

Severe acute pancreatitis (SAP) is the most serious type of pancreatitis with high morbidity and mortality. The underlying mechanism behind SAP pathogenesis is complex and remains elusive. Circular RNAs (circRNAs) are emerging as vital regulators of gene expression in various diseases by sponging microRNAs (miRNAs). However, the roles of circRNAs in the pathophysiology of SAP remain unknown. In the present study, next-generation RNA sequencing was utilized to identify circRNA transcripts in the pancreatic tissues from three SAP mice and three matched normal tissues. The differentially expressed circRNAs were confirmed by real-time PCR, and the biological functions of their interaction with miRNAs and mRNAs were analyzed. Our results demonstrate that 56 circRNAs were differentially expressed in SAP mice compared with normal controls. Six differentially expressed circRNAs were confirmed with the sequencing data. Importantly, we characterized a significantly downregulated circRNA derived from the ZFP664 gene in SAP. CircZFP644 was found to be negatively correlated with miR-21-3p, with a perfectly matched binding sequence to miR-21-3p. In conclusion, CircZFP644 may play an important role in the pathogenesis of SAP through sponging miR-21-3p. Our findings may provide novel insights regarding the workings of the pathophysiological mechanism of SAP and offer novel targets for SAP.

CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs

Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved. On the basis of the internal structural characteristics of circRNAs, we developed CircAST, a tool to assemble alternatively spliced circRNA transcripts and estimate their expression by using multiple splice graphs. Simulation studies showed that CircAST correctly assembled the full sequences of circRNAs with a sensitivity of 85.63%–94.32% and a precision of 81.96%–87.55%. By assigning reads to specific isoforms, CircAST quantified the expression of circRNA isoforms with correlation coefficients of 0.85–0.99 between theoretical and estimated values. We evaluated CircAST on an in-house mouse testis RNA-seq dataset with RNase R treatment for enriching circRNAs and identified 380 circRNAs with full-length sequences different from those of their corresponding cognate linear RNAs. RT-PCR and Sanger sequencing analyses validated 32 out of 37 randomly selected isoforms, thus further indicating the good performance of CircAST, especially for isoforms with low abundance. We also applied CircAST to published experimental data and observed substantial diversity in circular transcripts across samples, thus suggesting that circRNA expression is highly regulated. CircAST can be accessed freely at https://github.com/xiaofengsong/CircAST.

Circular RNA CircFndc3b modulates cardiac repair after myocardial infarction via FUS/VEGF-A axis

Circular RNAs are generated from many protein-coding genes, but their role in cardiovascular health and disease states remains unknown. Here we report identification of circRNA transcripts that are differentially expressed in post myocardial infarction (MI) mouse hearts including circFndc3b which is significantly down-regulated in the post-MI hearts. Notably, the human circFndc3b ortholog is also significantly down-regulated in cardiac tissues of ischemic cardiomyopathy patients. Overexpression of circFndc3b in cardiac endothelial cells increases vascular endothelial growth factor-A expression and enhances their angiogenic activity and reduces cardiomyocytes and endothelial cell apoptosis. Adeno-associated virus 9 -mediated cardiac overexpression of circFndc3b in post-MI hearts reduces cardiomyocyte apoptosis, enhances neovascularization and improves left ventricular functions. Mechanistically, circFndc3b interacts with the RNA binding protein Fused in Sarcoma to regulate VEGF expression and signaling. These findings highlight a physiological role for circRNAs in cardiac repair and indicate that modulation of circFndc3b expression may represent a potential strategy to promote cardiac function and remodeling after MI.

Long and Repeat-Rich Intronic Sequences Favor Circular RNA Formation under Conditions of Reduced Spliceosome Activity.

SummaryCircular RNAs (circRNAs), an important class of regulatory RNAs, have been shown to be the most prevalent in the brain compared with other tissues. However the processes governing their biogenesis in neurons are still elusive. Moreover, little is known about whether and how different biogenesis factors work in synchrony to generate neuronal circRNAs. To address this question, we pharmacologically inhibited the spliceosome and profiled rat neuronal circRNAs using RNA sequencing. We identified over 100 circRNAs that were up-regulated and a few circRNAs that were down-regulated upon spliceosome inhibition. Bioinformatic analysis revealed that up-regulated circRNAs possess significantly longer flanking introns compared with the un-changed circRNA population. Moreover, the flanking introns of up-regulated circRNAs harbor a higher number of distinct repeat sequences and more reverse complementary motifs compared with the unchanged circRNAs. Taken together, our data demonstrate that the biogenesis of circRNAs containing distinct intronic features becomes favored under conditions of limited spliceosome activity.

Oxygen-induced circRNA profiles and coregulatory networks in a retinopathy of prematurity mouse model.

Retinopathy of prematurity (ROP) is a leading cause of childhood blindness. At present, the molecular mechanisms underlying ROP are still far from being clearly understood. Circular RNAs (circRNAs), a novel class of noncoding RNAs, have been reported to serve vital regulatory roles in several human diseases. However, it is still unclear how circRNAs are involved in ROP. In the present study, oxygen-induced retinopathy (OIR) murine retinal samples and paired normal tissues were chosen for high-throughput transcriptome RNA sequencing and bioinformatic analyses. As a result, a total of 236 differentially expressed circRNAs, 14 differentially expressed miRNAs, and 9,756 differentially expressed mRNAs were identified in the OIR samples. Gene ontology analysis showed that angiogenesis ranked in the top five upregulated biological processes associated with differential mRNA expression. Then, 66 co-expression pairs of circRNA-mRNA were predicted according to the mRNAs that were enriched in angiogenesis. Furthermore, coregulation prediction was separately performed to identify the differentially expressed miRNAs that targeted angiogenesis-associated circRNAs or mRNAs. Finally, nine differentially expressed circRNAs were predicted to be competing endogenous RNAs by constructing a circRNA-miRNA-mRNA network followed by reverse transcription-quantitative PCR validation. The results of the present study suggest that the identified set of circRNA transcripts and the potential regulatory mechanisms for the development of ROP are worthy of functional studies.

Changes in the Circular RNA Transcriptome During Inorganic Arsenic‐Induced Epithelial‐to‐Mesenchymal Transition

Inorganic arsenic (iAs) found in the environment is associated with diseases such as cancer. Chronic, low dose exposure to iAs induces cellular transformation and epithelial‐to‐mesenchymal transition (EMT), a hallmark of metastasis. Since iAs is not genotoxic, we hypothesize that iAs drives carcinogenesis by altering gene expression though epigenetic mechanisms. One class of epigenetic gene regulators recently discovered are circular RNAs (circRNAs), which are covalently closed and highly stable isoforms derived from precursor messenger RNAs (mRNAs). They are generated from actively transcribed genes and their biogenesis competes with that of mRNA. circRNAs are highly conserved across eukaryotes however the function of this new class of regulators is still unclear. Our lab and others have shown alterations to the epigenome as driving iAs‐mediated carcinogenesis. However the relevance of the expression of circRNAs in this process is not understood. Interestingly, our preliminary data suggest that circRNAs are differentially expressed during this process. We therefore aim to identify and profile the changes in circRNA expression that occur during iAs‐induced EMT. We have treated BEAS‐2B cells with iAs over a time‐course, measuring changes in EMT‐markers over time. We already have shown that cells move from pre‐EMT to mid EMT to late‐EMT and finally back through MET during iAs‐mediated carcinogenesis. This model was used to profile differential expression of circRNAs. To accomplish this, total RNA was isolated and enriched for circRNAs with an RNase R digest. For gene‐specific analyses, divergent primers designed to amplify across the circRNA backsplice junctions were used in reverse transcription quantitative polymerase chain reaction to identify differentially expressed circRNA transcripts. In our preliminary gene‐specific approach, we have identified a circRNA containing the 3′ untranslated region of neural cell adhesion molecule 2 (NCAM2) in BEAS‐2B cells. NCAM2 is a cell‐to‐cell adhesion molecule involved in neuronal growth and migration, and is known to be upregulated during EMT. We observed that during iAs‐mediated EMT, while the expression of the linear NCAM2 transcript increased, there was a concurrent decrease in the expression of the 3′ untranslated region. These results indicate that circRNA expression is altered during iAs‐induced EMT and suggests that iAs promotes carcinogenesis by altering steady state competition between linear and circular RNA production. We are currently using next generation sequencing to fully profile the circRNA transcriptome as cells undergo iAs‐induced EMT to gain a broader understanding of the functional significance of circRNA in iAs‐induced EMT.Support or Funding InformationThis work was supported by NIEHS grant (R01‐ES024478).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Characterization of circRNA‑associated ceRNA networks in patients with nonvalvular persistent atrial fibrillation.

Circular RNAs (circRNAs) are non-coding RNAs forming closed-loop structures, and their aberrant expression may lead to disease. However, the potential network of circRNA‑associated competing endogenous RNA (ceRNA) involved in nonvalvular persistent atrial fibrillation (NPAF) has not been previously reported. In the present study, four left atrial appendages (LAA) of patients with NPAF and four normal LAAs were examined via RNA sequencing, and their potential functions were investigated via bioinformatics analysis. The circRNA‑enriched genes were analyzed using Gene Ontology (GO) categories, while the enrichment of circRNAs was detected via the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 296 significantly dysregulated circRNA transcripts were obtained, with 238 upregulated and 58 downregulated. A number of circRNAs were further confirmed using reverse transcription‑quantitative polymerase chain reaction analysis. Furthermore, the more comprehensive circRNA‑associated ceRNA networks were examined in patients with NPAF. GO categories and KEGG annotation analysis of circRNAs revealed that the circRNA‑associated ceRNA networks were likely to influence AF though alterations in calcium and cardiac muscle contraction. The circRNA‑associated ceRNA networks revealed that dysregulated circRNAs in NPAF may be involved in regulating hsa‑microRNA (miR)‑208b and hsa‑miR‑21. To the best of our knowledge, this study presents the circRNA‑associated ceRNA networks in NPAF for the first time, which may have potential implications for the pathogenesis of AF. This study reveals a potential perspective from which to investigate circRNAs in circRNA‑associated ceRNA networks (hsa_circRNA002085, hsa_circRNA001321) in NPAF, and provides a potential biomarker for AF.

Abstract 288: Circular RNA CircFNDC3b Modulates Cardiac Repair After Myocardial Infarction via FUS-1/VEGF-A Axis

Circular RNA (circRNA) is a new addition to the list of growing body of non-coding RNAs.Recent studies highlighted that circRNA are dysregulated in cardiovascular disease. However,knowledge of the role of circRNAs in ischemic cardiac injury is limited. Using global circRNAexpression profiling, we identified several circRNA transcripts that were differentially regulatedpost-MI in mice, including circFNDC3b (derived from 2 and 3 exons of cognate FNDC3b gene)which is significantly down regulated. Cell fractionation experiments revealed that circFNDC3bis highly enriched in endothelial cells of post-MI mice. Notably, we found a circFNDC3b orthologin humans, which was also significantly down regulated in ischemic cardiomyopathy patients.Further, gene profile analysis of circFNDC3b overexpression in cardiac endothelial cellsdemonstrated an increase in angiogenic genes. Among them, vascular endothelial growthfactor-A (VEGF-A) was significantly elevated concomitant with reduced in vitro apoptosis ofcardiomyoblasts and endothelial cells, which also exhibited enhanced tube formation. Forcardiac overexpression of circFNDC3b, we generated AAV9 viral particles and found that in vivoover expression attenuated LV dysfunction post-MI and enhanced neovascularization.Mechanistically, circFNDC3b interacts with its potential target RNA binding protein FUS-1 (fusedin sarcoma) and regulate VEGF signaling, thereby reducing cardiomyocyte apoptosis andenhancing neovascularization and cardiac function post-MI. These results indicatethat circFNDC3b is a novel potential target to prevent cardiac remodeling and highlight theimportance of circRNAs in cardiovascular diseases.

Abstract 1299: Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer

Abstract Background: Due to their stability, specificity, and accessibility, circular RNAs (circRNAs) may represent an attractive new class of biomarkers in early-stage bladder cancer (BC) and possess regulatory functions. Experimental procedures: We characterize circRNA transcripts using whole transcriptome RNA-Seq data from 457 non-muscle-invasive bladder cancer (NMIBC) samples (348 Ta and 109 T1). We identify backsplice-spanning reads by using a modified version of the find_circ pipeline with an increased filtering stringency on both anchor sequences. Same pipeline is used to identify circRNAs in publicly available tissue samples obtained from ENCODE (n = 113) and in locally generated RNA-Seq data from unfractionated BC cell lines (n = 8) as well as from the nucleic and cytoplasmic fractions of three BC cell lines. Results and limitations: Here, we identify more than 15,000 unique circRNAs supported by at least two reads in at least two different samples. We show that a set of highly expressed circRNAs have conserved core splice sites, are likely to be surrounded by inverted homologous Alu repeats, and are enriched with Synonymous Constraint Elements as well as microRNA target sites. Moreover, we identify 113 abundant circRNAs that are differentially expressed between high and low-risk tumor subtypes. Analysis of progression-free survival reveals 13 circRNAs that are associated with BC progression independently of the linear transcript and parent gene. We point to circHIPK3 and circCDYL as important candidates because they possess strong clinical and biological associations. The progression-free survival analyses reveal a significantly lower risk of progression for patients with high circHIPK3 and circCDYL expression levels compared to patients with low levels. Correspondingly, both circRNA candidates are found at higher levels in non-malignant BC cell lines than metastatic BC cell lines. We are currently conducting knockdown and overexpression studies in BC cell lines to reveal their biological role. Future studies should address whether circRNAs that correlate with BC progression are present in urine and plasma samples, and importantly, validation in independent cohorts should be performed in order to confirm their clinical relevance. Conclusions: We demonstrate that abundant circRNAs possess key biological characteristics, distinguishing them from low-expressed circRNAs and non-circularized exons, and suggest that circRNAs might serve as a new class of prognostic biomarkers in NMIBC. Citation Format: Trine Line H. Okholm, Morten M. Nielsen, Mark P. Hamilton, Lise-Lotte Christensen, Søren Vang, Jakob Hedegaard, Thomas B. Hansen, Jørgen Kjems, Lars Dyrskjøt, Jakob S. Pedersen. Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1299.

S188. DYSREGULATION OF CIRCULAR RNA EXPRESSION IN SCHIZOPHRENIA OBSERVED IN POSTMORTEM DORSOLATERAL PREFRONTAL CORTEX

BackgroundThe last few years has witnessed the emergence of a novel class of long non-coding RNA known as circular RNA (circRNA). These molecules are characterised by their circularity formed through the back splicing of 3’ and 5’ ends of transcript segments produced by one or more of its exons. CircRNAs function as transcriptional modulators, microRNA regulators, as well as template for translation. In our current study, we profiled circRNA expression in post-mortem brain samples from Schizophrenia (SZ) and control subjects using next-generation sequencing technology to discover the association of these novel RNA molecules with the pathogenesis of SZ.MethodsTotal RNA from cerebral cortex (BA46) of 17 SZ patients and 18 healthy controls were subjected to ribosomal RNA depletion and then RNase R treatment to further deplete linear RNA and enrich for exonuclease resistant circRNA transcripts. Sequencing libraries were constructed using Illumina TruSeq RNA Library Prep Kit (LT) (150 cycles) and sequenced by an Illumina NexSeq500. Sequencing data was analysed by the CIRCexplorer2 pipeline to identify circRNA transcripts. To validate the sequencing findings, real-time PCR was performed using outward primers sets designed to specifically amplify circular transcripts.ResultsWe discovered a large number of distinct circRNAs (95,212), many of which were highly expressed throughout the cohort. Surprisingly, a large proportion (52%) of the identified circRNAs sequences were novel or not previously reported. Differential expression analysis suggested that there was substantial alteration in circRNA expression in SZ. More than two thirds of these molecules displayed decreased expression, whereas the remainder were upregulated. Functional annotation of the host genes was significantly enrichment for terms-related to neurobiology and neurocognitive impairment including clusters such as neurogenesis, differentiation and synapse. Many of these circRNAs were also predicted to interact with miRNAs, supporting a potential miRNA sponging function for these circRNA.DiscussionRNA sequencing in the human postmortem DLPFC revealed dysregulation of circRNA expression in schizophrenia. This alteration was characterized by a substantial decrease in circRNA expression in the disorder. Bioinformatic predictions of circRNA interaction suggest they function as miRNA regulators and may have a broader role in etiology or pathophysiology of the disorder.

Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing.

Noncoding RNA play important roles in various biological processes and diseases, including cancer. The expression profile of circular RNA (circRNA) has not been systematically investigated in lung adenocarcinoma (LUAD). In this study, we performed genomewide transcriptome profiling of coding genes, long noncoding RNA (lncRNA), and circRNA in paired LUAD and nontumor tissues by ribosomal RNA‐depleted RNA sequencing. The detected reads were first mapped to the human genome to analyze expression of coding genes and lncRNA, while the unmapped reads were subjected to a circRNA prediction algorithm to identify circRNA candidates. We identified 1282 differentially expressed coding genes in LUAD. Expression of 19 023 lncRNA was detected, of which 244 lncRNAs were differentially expressed in LUAD. AFAP1‐AS1, BLACAT1, LOC101928245, and FENDRR were most differentially expressed lncRNAs in LUAD. Also identified were 9340 circRNA candidates with ≥ 2 backspliced, including 3590 novel circRNA transcripts. The median length of circRNA was ~ 530 nt. CircRNA are often of low abundance, and more than half of circRNAs we identified had < 10 reads. Agarose electrophoresis and Sanger sequencing were used to confirm that four candidate circRNA were truly circular. Our results characterized the expression profile of coding genes, lncRNA, and circRNA in LUAD; 9340 circRNAs were detected, demonstrating that circRNA are widely expressed in LUAD.DatabaseThe raw RNA sequencing data have been submitted to Gene Expression Omnibus (GEO) database and can be accessed with the ID GEO: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104854.

Circular RNAs of the nucleophosmin (NPM1) gene in acute myeloid leukemia.

In acute myeloid leukemia, there is growing evidence for splicing pattern deregulation, including differential expression of linear splice isoforms of the commonly mutated gene nucleophosmin (NPM1). In this study, we detect circular RNAs of NPM1 and quantify circRNA hsa_circ_0075001 in a cohort of NPM1 wild-type and mutated acute myeloid leukemia (n=46). Hsa_circ_0075001 expression correlates positively with total NPM1 expression, but is independent of the NPM1 mutational status. High versus low hsa_circ_0075001 expression defines patient subgroups characterized by distinct gene expression patterns, such as lower expression of components of the Toll-like receptor signaling pathway in high hsa_circ_0075001 expression cases. Global evaluation of circRNA expression in sorted healthy hematopoietic controls (n=10) and acute myeloid leukemia (n=10) reveals circRNA transcripts for 47.9% of all highly expressed genes. While circRNA expression correlates globally with parental gene expression, we identify hematopoietic differentiation-associated as well as acute myeloid leukemia subgroup-specific circRNA signatures.

The Circular RNA Landscape of Periodontal Ligament Stem Cells During Osteogenesis.

The present study aims to investigate the distinct expression pattern of circular RNAs (circRNAs) in periodontal ligament stem cells (PDLSCs) during osteogenesis. PDLSCs were isolated and cultured in osteogenic medium. Total RNA was extracted from cells at day 0 (D0), day 3 (D3), day 7 (D7), and day 14 (D14) and submitted to RNA-sequencing to detect expression profiles of circRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs). Real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to validate expression of circRNAs and miRNAs. Differential expression analysis and gene ontology analysis were performed. A circRNA-miRNA-mRNA network was constructed to reveal the potential regulatory role of circRNAs. A total of 12,693 circRNA transcripts were detected, and circRNAs displayed stage-specific expression. Expression of four well-known circRNAs was validated by qRT-PCR. In total, 118 circRNAs were differentially expressed at D3, 128 circRNAs were differentially expressed at D7, and 139 circRNAs were differentially expressed at D14 compared with D0. Host genes of differentially expressed circRNAs were enriched in cytoplasmic or membrane-bound vesicles and extracellular matrix, indicating their potential roles in modulating biogenesis of extracellular vesicles. Moreover, mRNAs that were potentially regulated by circRNAs were enriched in bone-formation-associated processes, including extracellular matrix organization, cell differentiation, and bone morphogenetic protein signaling pathway. Expression profiles of circRNAs were significantly altered during osteogenic differentiation of PDLSCs, providing a clue for future studies on the role of circRNAs in osteoblast differentiation.

A map of human circular RNAs in clinically relevant tissues

Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far. Recently, circRNAs have emerged as a large class of RNA which can function as post-transcriptional regulators. It has also been shown that many circRNAs are tissue- and stage-specifically expressed. Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research. Here, we present a circRNA expression resource of 20 human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein cells (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation. In eight different samples from a single donor, we found highly tissue-specific circRNA expression. Circular-to-linear RNA ratios revealed that many circRNAs were expressed higher than their linear host transcripts. Among the 71 validated circRNAs, we noticed potential biomarkers. In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients’ samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes. Our findings underscore the need to assess circRNAs in mechanisms of human disease.Key messagescircRNA resource catalog of 20 clinically relevant tissues.circRNA expression is highly tissue-specific.circRNA transcripts are often more abundant than their linear host RNAs.circRNAs can be differentially expressed in disease-associated genes.

Abstract 298: Circular Rna Mmu_circ_008396 Attenuates Cardiac Remodeling After Myocardial Infarction in Mice

Recent studies highlighted that circular RNAs (circRNA) can play an important role in cardiac hypertrophy. However, the circRNAs in cardiac diseases is still limited. Using global circRNA expression profiling, we identified several circRNA transcripts that were differentially regulated post-MI in mice, including mmu_circ_008396 that is significantly down regulated. Cell fractionation experiments indicated that mmu_circ_008396 is highly enriched in endothelial cells in post-MI mice. Interestingly, we found a mmu_circ_008396 circRNA ortholog in humans, which was also significantly down regulated in ischemic cardiomyopathy patients. Further, overexpression of mmu_circ_008396 significantly enhanced tube formation and reduced apoptosis of human umbilical vein endothelial cells. For cardiac overexpression of mmu_circ_008396 circRNA, we created AAV9 viral particles and found that in vivo over expression attenuated LV dysfunction post-MI and enhanced neovascularization. Mechanistically, mmu_circ_008396 binds to its potential target miRNAs (mmu-miR-93-3p, mmu-miR-412-3p and mmu-miR-298-5p) and regulate hemeoxygenase-1/ VEGF signaling, thereby enhancing neovascularization and cardiac repair post-MI. These results indicate that mmu_circ_008396 circRNA might be a novel potential target to prevent cardiac remodeling and also highlight the significance of circRNAs in cardiovascular diseases.

Characterization of circRNA-Associated-ceRNA Networks in a Senescence-Accelerated Mouse Prone 8 Brain

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases. Although many researchers have attempted to explain the origins of AD, developing an effective strategy in AD clinical therapy is difficult. Recent studies have revealed a potential link between AD and circRNA-associated-ceRNA networks. However, few genome-wide studies have identified the potential circRNA-associated-ceRNA pairs involved in AD. In this study, we systematically explored the circRNA-associated-ceRNA mechanism in a 7-month-old senescence-accelerated mouse prone 8 (SAMP8) model brain through deep RNA sequencing. We obtained 235 significantly dysregulated circRNA transcripts, 30 significantly dysregulated miRNAs, and 1,202 significantly dysregulated mRNAs. We then constructed the most comprehensive circRNA-associated-ceRNA networks in SAMP8 brain. GO analysis revealed that these networks were involved in regulating the development of AD from various angles, for instance, axon terminus (GO: 0043679) and synapse (GO: 0045202). Following rigorous selection, we discovered that the circRNA-associated-ceRNA networks in this AD mouse model were mainly involved in the regulation of Aβ clearance (Hmgb2) and myelin function (Dio2). This research is the first to provide a systematic dissection of circRNA-associated-ceRNA profiling in SAMP8 mouse brain. The selected circRNA-associated-ceRNA networks can profoundly affect the diagnosis and therapy of AD in the future.

Novel circular RNA expression profiles reflect progression of patients with hypopharyngeal squamous cell carcinoma.

Circular RNAs (circRNAs), a novel class of endogenous noncoding RNAs, have been shown to have important roles in a number of diseases, including several types of cancers. We hypothesized that circRNAs are involved in the pathogenesis of hypopharyngeal squamous cell carcinoma (HSCC). To test our hypothesis, we initially compared the expression profiles of circRNAs in 4 paired HSCC and adjacent normal tissue samples by using a circRNA microarray. The microarray data showed that 2392 circRNAs, including 1304 upregulated and 1088 downregulated circRNA transcripts, were significantly dysregulated in the HSCC tissues. The 10 most dysregulated circRNAs from the microarray analysis were further validated in another 32 pairs of specimens using quantitative real-time polymerase chain reaction assays. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. Bioinformatics analysis was also performed to predict possible pathways in which these networks might be involved. Finally, we analyzed the interaction between validated circRNAs and their potential cancer-related miRNA targets. We are the first to comprehensively delineate the expression profiles of circRNAs in HSCC and to provide potential candidates for future mechanism studies. Our study is potentially of critical significance in uncovering the roles of circRNAs in HSCC.