An increasing number of studies have indicated the crucial involvement of long non-coding RNAs (lncRNAs) in the onset and progression of malignancies. However, a complete understanding of the molecular mechanism underlying the effect of abnormally expressed lncRNAs on breast cancer (BC) remains elusive. This study aimed to elucidate the influence of the lncRNA small nucleolar RNA host gene 1 (SNHG1) on BC progression and its underlying mechanism. Our findings revealed a conspicuous up-regulation of SNHG1 in both BC tissues and cells. The downregulation of SNHG1 was observed to inhibit BC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) processes, while simultaneously promoting apoptosis. Furthermore, dual-luciferase reporter gene and RNA pull-down assays established that SNHG1 targeted miR-641 expression, while miR-641 targeted RRS1. Rescue studies demonstrated that in vitro SNHG1 silencing could be reversed by the miR-641 inhibitor, as well as by RRS1 upregulation. Moreover, in vivo downregulation of SNHG1 was found to inhibit BC growth. Through the inhibition of the miR-641 level, SNHG1 elevated the level of the downstream target RRS1, thereby fostering BC growth, migration, and invasion while inhibiting apoptosis. These findings suggest that SNHG1 may represent a potential therapeutic target for BC treatment.

The development of gene therapies for the treatment of diseases of the central nervous system has been hindered by the limited availability of adeno-associated viruses (AAVs) that efficiently traverse the blood-brain barrier (BBB). Here, we report the rational design of AAV9 variants displaying cell-penetrating peptides on the viral capsid and the identification of two variants, AAV.CPP.16 and AAV.CPP.21, with improved transduction efficiencies of cells of the central nervous system on systemic delivery (6- to 249-fold across 4 mouse strains and 5-fold in cynomolgus macaques, with respect to the AAV9 parent vector). We also show that the neurotropism of AAV.CPP.16 is retained in young and adult macaques, that this variant displays enhanced transcytosis at the BBB as well as increased efficiency of cellular transduction relative to AAV9, and that it can be used to deliver antitumour payloads in a mouse model of glioblastoma. AAV capsids that can efficiently penetrate the BBB will facilitate the clinical translation of gene therapies aimed at the central nervous system.

Circular ribonucleic acids (RNAs) (circRNAs) are formed by covalently linking the downstream splice donor and the upstream splice acceptor. One of the most important functions of circRNAs is mainly exerted through binding RNA-binding proteins (RBPs). However, there is no efficient algorithm for identifying genome-wide circRNA-RBP interactions. Here, we developed a unique algorithm, circRIP, for identifying circRNA-RBP interactions from RNA immunoprecipitation sequencing (RIP-Seq) data. A simulation test demonstrated the sensitivity and specificity of circRIP. By applying circRIP, we identified 95 IGF2BP3-binding circRNAs based on the IGF2BP3 RIP-Seq dataset. We further identified 2823 and 1333 circRNAs binding to >100 RBPs in K562 and HepG2 cell lines, respectively, based on enhanced cross-linking immunoprecipitation (eCLIP) data, demonstrating the significance to survey the potential interactions between circRNAs and RBPs. In this study, we provide an accurate and sensitive tool, circRIP (https://github.com/bioinfolabwhu/circRIP), to systematically identify RBP and circRNA interactions from RIP-Seq and eCLIP data, which can significantly benefit the research community for the functional exploration of circRNAs.

Abstract The significant function of circRNAs in cancer was recognized in recent work, so a well-organized resource is required for characterizing the interactions between circRNAs and other functional molecules (such as microRNA and RNA-binding protein) in cancer. We previously developed cancer-specific circRNA database (CSCD), a comprehensive database for cancer-specific circRNAs, which is widely used in circRNA research. Here, we updated CSCD to CSCD2 (http://geneyun.net/CSCD2 or http://gb.whu.edu.cn/CSCD2), which includes significantly more cancer-specific circRNAs identified from a large number of human cancer and normal tissues/cell lines. CSCD2 contains >1000 samples (825 tissues and 288 cell lines) and identifies a large number of circRNAs: 1 013 461 cancer-specific circRNAs, 1 533 704 circRNAs from only normal samples and 354 422 circRNAs from both cancer and normal samples. In addition, CSCD2 predicts potential miRNA–circRNA and RBP–circRNA interactions using binding motifs from >200 RBPs and 2000 microRNAs. Furthermore, the potential full-length and open reading frame sequence of these circRNAs were also predicted. Collectively, CSCD2 provides a significantly enhanced resource for exploring the function and regulation of circRNAs in cancer.

Circular RNA is a newly discovered member of non-coding RNA (ncRNA) and regulates the target gene by acting as a micro-RNA sponge. It plays vital roles in various diseases. However, the functions of circular RNA in non-small cell lung cancer (NSCLC) remain still unclear. Our data showed that circ-WHSC1 was highly expressed in NSCLC cells and tissues. Both in vitro and in vivo experiments showed that circ-WHSC1 promoted NSCLC proliferation. circ-WHSC1 also promoted the migration and invasion of lung cancer cells. Through bioinformatic analysis and functional experiments, we showed that circ-WHSC1 could act as a sponge for micro-RNA-7 (miR-7) and regulate the expression of TAB2 (TGF-beta activated kinase one binding protein two). Inhibition of the circ-WHSC1/miR-7/TAB2 pathway could effectively attenuate lung cancer progression. In summary, this study confirmed the existence and oncogenic function of circ-WHSC1 in NSCLC. The research suggests that the circ-WHSC1/miR-7/TAB2 axis might be a potential target for NSCLC therapy.

BackgroundNowadays, the diagnosis of small-cell lung cancer (SCLC) remains a great challenge. Changes in the chromosome 3p (chr3) gene are usually observed in the pathogenesis of lung cancer, which seems to imply that these chr3 genes may be a diagnostic marker in the early stage of SCLC. MethodsBased on Differentially expressed genes (DEGs) screening analysis, Weighted gene co-expression network analysis, and Receiver operating characteristic (ROC) curves, this study explored the diagnostic value of the chr3 gene obtained from the University of California Santa Cruz Genome Browser Database in SCLC. Meanwhile, quantitative real-time Polymerase Chain Reaction (qRT-PCR) was used to reveal the expression patterns of diagnostic biomarkers in Human pulmonary alveolar epithelial cells and the SCLC cell line NCI-H146. The potential pathways involved in the diagnostic biomarkers were investigated by a single-gene Gene Set Enrichment Analysis (GSEA). Furthermore, drugs regulating the expression levels of diagnostic biomarkers were predicted by the Comparative Toxicogenomics Database (CTD).ResultsWe identified a total of 33 differentially expressed chr3 (DE-chr3) genes and 1156 hub genes associated with clinical features of SCLC, and functional enrichment analysis showed that all of these genes were significantly enriched in the cell cycle terms. Ultimately, the area under curve of the ROC curve demonstrated that the overlapping genes of the DE-chr3 genes and the hub genes, CDC25A , FYCO1 , and RFTN1 , were relatively accurate in distinguishing normal from SCLC samples, which were considered to be diagnostic biomarkers. CDC25A was overexpressed in SCLC samples, while FYCO1 and RFTN1 were highly expressed in normal samples, as evidenced by qRT-PCR results. Single-gene GSEA showed that diagnostic biomarkers were significantly associated with cell cycle, ABC transporter, immune cell differentiation, immune response, and multiple respiratory disease pathways. Further, a total of 141 drugs were predicted by the CTD to modulate the expression of diagnostic biomarkers, of which 8 drugs were the shared drugs for 3 diagnostic biomarkers.ConclusionsThis project provided 3 novel and powerful diagnostic biomarkers for SCLC based on the chr3 genes. Meanwhile, a guideline for the development and selection of drugs for clinical treatment based on diagnostic biomarkers was also included.

MOTIVATION:Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5' and 3' termini of exon(s) can be covalently ligated to form circRNAs through back-splicing (head-to-tail splicing). CircRNAs can be conserved across species, show tissue- and developmental stage-specific expression patterns, and may be associated with human disease. However, the mechanism of circRNA formation is still unclear although some sequence features have been shown to affect back-splicing. RESULTS:In this study, by applying the state-of-art machine learning techniques, we have developed the first deep learning model, DeepCirCode, to predict back-splicing for human circRNA formation. DeepCirCode utilizes a convolutional neural network (CNN) with nucleotide sequence as the input, and shows superior performance over conventional machine learning algorithms such as support vector machine and random forest. Relevant features learnt by DeepCirCode are represented as sequence motifs, some of which match human known motifs involved in RNA splicing, transcription or translation. Analysis of these motifs shows that their distribution in RNA sequences can be important for back-splicing. Moreover, some of the human motifs appear to be conserved in mouse and fruit fly. The findings provide new insight into the back-splicing code for circRNA formation. AVAILABILITY AND IMPLEMENTATION:All the datasets and source code for model construction are available at https://github.com/BioDataLearning/DeepCirCode. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

Metabolic abnormality is one of the hallmarks of cancer cells, and limiting material supply is a potential breakthrough approach for cancer treatment. Increasing researchers have been involved in the study of glioma cell metabolism reprogramming since the significance of IDH1 was confirmed in glioma. However, the molecular mechanisms underlying metabolic reprogramming induced by methionine deprivation regulates glioma cell proliferation remain unclear. Here we demonstrated that methionine deprivation inhibited glioma cell proliferation via downregulating interleukin 1 receptor antagonist (IL1RN) both in vitro and in vivo, methionine deprivation or knocking down IL1RN induced glioma cell cycle arrest. Moreover, we confirmed that IL1RN is a tumor associated gene and its expression is negatively correlated with the survival time of glioma patients. Altogether these results demonstrate a strong rationale insight that targeting amino acid metabolism such as methionine deprivation/IL1RN related gene therapy may offer novel direction for glioma treatment.

Circular RNAs (circRNAs) are a novel class of RNAs with mostly unknown function, and their biogenesis is still unclear. CircRNAs often show tissue and developmental stage-specific expression, and have been reported to be associated with human diseases such as cancer. During the pre-RNA processing, the 5' and 3' termini of one or more exons can be joined together to form circRNAs, and this process is called back-splicing. However, not all RNA splicing sites can participate in back-splicing. To understand the mechanism of circRNA formation, we used two different machine learning algorithms, random forest (RF) and support vector machine (SVM), to predict back-splicing sites from sequence compositional features. Our results indicate that both RF and SVM models can accurately predict back-splicing sites. Moreover, informative sequence features have been selected using RF, and the identified sequence motifs provide new insight into the mechanism of circRNA formation. To our knowledge, this work represents the first published study to utilize machine learning techniques to model RNA back-splicing sites, and the novel method can be useful for understanding circRNA biogenesis and regulation.

LncRNAs have emerged as a novel class of critical regulators of cancer. We aimed to construct a landscape of lncRNAs and their potential target genes in lung adenocarcinoma. Genome-wide expression of lncRNAs and mRNAs was determined using microarray. qRT-PCR was performed to validate the expression of the selected lncRNAs in a cohort of 42 tumor tissues and adjacent normal tissues. R and Bioconductor were used for data analysis. A total of 3045 lncRNAs were differentially expressed between the paired tumor and normal tissues (1048 up and 1997 down). Meanwhile, our data showed that the expression NONHSAT077036 was associated with N classification and clinical stage. Further, we analyzed the potential co-regulatory relationship between the lncRNAs and their potential target genes using the 'cis' and 'trans' models. In the 25 related transcription factors (TFs), our analysis of The Cancer Genome Atlas database (TCGA) found that patients with lower expression of POU2F2 and higher expression of TRIM28 had a shorter overall survival time. The POU2F2 and TRIM28 co-expressed lncRNA landscape characterized here may shed light into normal biology and lung adenocarcinoma pathogenesis, and be valuable for discovery of biomarkers.

Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. However, there is no existing tool to visualize and explore circRNAs. Therefore, we introduce CircView, a user-friendly visualization tool for circRNAs detected from existing tools. CircView enables users to visualize circRNAs and to quantify number of samples with detected circRNAs. CircView allows users to explore circRNAs detected by unique or multiple tools. Furthermore, CircView allows users to view the regulatory elements, such as microRNA response elements and RNA-binding protein binding sites. CircView is a unique tool to visualize and explore circRNAs, which helps users to better understand potential functions of circRNAs and design the functional experiments.

Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and mouse tissue-specific (TS) circRNAs. We identified in total 302 853 TS circRNAs in the human and mouse genome, and showed that the brain has the highest abundance of TS circRNAs. We further confirmed the existence of circRNAs by reverse transcription polymerase chain reaction (RT-PCR). We also characterized the genomic location and conservation of these TS circRNAs and showed that the majority of TS circRNAs are generated from exonic regions. To further understand the potential functions of TS circRNAs, we identified microRNAs and RNA binding protein, which might bind to TS circRNAs. This process suggested their involvement in development and organ differentiation. Finally, we constructed an integrated database TSCD (Tissue-Specific CircRNA Database: http://gb.whu.edu.cn/TSCD) to deposit the features of TS circRNAs. This study is the first comprehensive view of TS circRNAs in human and mouse, which shed light on circRNA functions in organ development and disorders.

Inflammation is extremely important in the development of cerebral ischemia/reperfusion injury. Pannexin 1 (Panx1) channel has been reported to activate inflammasome in astrocytes and be involved in ischemic injury, but this damage effect is reversed by a Panx1 inhibitor—probenecid. However, the mechanism of probenecid protects against cerebral ischemia/reperfusion injury remains unclear. In present study, we hypothesized that probenecid protected astrocytes from ischemia/reperfusion injury in vitro by modulating the inflammasome. Primary cultured neocortical astrocytes were exposed to oxygen–glucose deprivation/reoxygenation (OGD/RX) and probenecid was added in this model. Viability and nuclear morphology of astrocytes, production of reactive oxygen species (ROS), protein expressions of NLRP3 (NOD-like receptor protein 3), caspase-1, and AQP4 (Aquaporins 4), as well as release of cellular HMGB1 and IL-1β were observed to evaluate the effect and mechanisms of probenecid on OGD/reoxygenated astrocytes. Probenecid did not affect cell viability at concentrations of 1, 5, 10, and 100μM but induced significant astrocytes death at 500μM. Probenecid inhibited cell death and ROS generation in astrocytes subjected to 6h of OGD and 24h of reoxygenation. The expression levels of NLRP3, caspase-1, and AQP4 increased after 6h of OGD, but probenecid treatment attenuated this increase. Moreover, the extracellular release of IL-1β and HMGB1 from OGD/reoxygenated astrocytes increased significantly. However, treatment by probenecid resulted in substantial reduction of these proteins levels in extracellular space. In conclusion, The Panx1 inhibitor, probenecid, which was administered before OGD, provided protective effects on the OGD/reoxygenation model of cultured astrocytes by modulating inflammasome activity and downregulating AQP4 expression.

Background: microRNAs are small noncoding RNAs that modulate a variety of cellular processes by regulating multiple targets, which can promote or inhibit the development of malignant behaviors. Accumulating evidence suggests that miR-675-5p plays important roles in human carcinogenesis. However, its precise biological role remains largely elusive. This study examined the role of miR-675-5p in non-small cell lung cancer (NSCLC).Methods: The expression of miR-675-5p was analyzed by real-time quantitative PCR (qRT-PCR). The effect of miR-675-5p on proliferation was evaluated through MTT and colony formation assays, and cell migration and invasion were evaluated through transwell assays. The expression of target proteins and downstream molecules was analyzed by western blotting and immunohistochemical staining. The luciferase reporter assay was used to assess the target genes of miR-675-5p in non-small cell lung cancer cells.Results: The expression levels of miR-675-5p in NSCLC tissues were significantly reduced compared to those in adjacent non-cancerous tissues (P < 0.001). The expression of miR-675-5p in patients with non-small cell lung cancer had a negative correlation with lymph node metastasis (P < 0.01) and TNM stage (P < 0.05). Down-regulation of miR-675-5p promoted cell growth, proliferation, colony formation, invasion and migration, and promoted the tumorigenicity graft growth of nude mice in vivo (P < 0.01); whereas up-regulation of miR-675-5p had the contrary effects. The luciferase reporter assay showed that GPR55 was a direct target gene of miR-675-5p. Overexpression of miR-675-5p can lead to the down-regulation of GPR55 and its signaling pathway, whereas the effect can be reversed by down-regulation of miR-675-5p expression.Conclusions: miR-675-5p functions as a novel tumor suppressor in NSCLC and the anti-oncogenic activity may involve its inhibition of the target gene GPR55. These findings suggest the possibility for miR-675-5p as a therapeutic target in NSCLC.

The intra-arterial (IA) model by microcatheter administration was an effective way to deliver drugs or cells to the brain. All of these models were carried out introduced in rat rather than mice for the difficult and technically challenging due to their small caliber. In 2014, Alejandro Santillan first introduced this model in mice and we found that most of the operational steps were similar with the middle cerebral artery occlusion and reperfusion (MCAO/R) model. We attempted to combine these two techniques into a single model in mice and discovered that this technique was indeed possible. In our work, 12C57B1/6J male mice were carried on middle cerebral artery occlusion for 60 min and then the intra-arterial microcatheter was placed into the internal carotid artery (ICA) from the external carotid artery (ECA). GFP-Luc-Pro labeled mNSCs were infused through the microcatheter and then the blood flow perfusion was reestablished subsequently. The results showed that all 12 mice were carried on successfully the model of middle cerebral artery occlusion, and the placement of the microcatheter and the mNSCs perfusion were completed smoothly without exception. Which means that it is logical to combine the two models into one in order to facilitate studying of stroke. Meanwhile, during the dissection, we found the variation of occipital artery (OA) was noticeable and we classified first time this variation into four categories to attempt to protect the OA. (C) 2015 Elsevier Ireland Ltd. All rights reserved.

MicroRNAs (miRNAs) are 20–24 nucleotide long non-coding RNAs that play critical regulatory roles during plant development, organ morphogenesis, and cell fate determination and differentiation. In this study, miRNA microarray chips were used to explore the expression profile of ramie miRNAs between the bast of fiber elongation phase and those of cell wall thickening and end wall dissolving phase. There are 150 and 148 credible miRNAs in the bast of fiber elongation phase and cell wall thickening and end wall dissolving phase, respectively. These miRNAs distributed in 27 species and mainly concentrated in nine species. Analysis showed that 51 miRNAs were differentially expressed: 27 up-regulated (miR166, miR172, miR396, miR482, miR894 and miR2911 families) and 24 down-regulated (miR156, miR159, miR164, miR319 and miR1450 families) in the bast of fiber elongation phase compared with the bast of cell wall thickening and end wall dissolving phase. To further confirm our results, we examined the expression of three miRNAs (zma-miR172b*, pvu-miR482 and vvi-172a) by quantitative real-time reverse transcriptase-PCR. Our results will provide a molecular basis for future research miRNA function on ramie genetics and breeding.