scholarly journals Abnormal expression of rno_circRNA_014900 and rno_circRNA_005442 induced by ketamine in the rat hippocampus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Mao ◽  
Tianmei Li ◽  
Di Fan ◽  
Hongli Zhou ◽  
Jianguo Feng ◽  
...  
Keyword(s):  
Target Genes ◽  
Circular Rna ◽  
Fold Change ◽  
Rat Hippocampus ◽  
Antidepressant Effect ◽  
Signal Pathways ◽  
Qrt Pcr ◽  
Abnormal Expression ◽  
Reverse Transcription Pcr ◽  
Pathway Analyses

Abstract Background Recent studies have shown that circular RNA (circRNA) is rich in microRNA (miRNA) binding sites. We have previously demonstrated that the antidepressant effect of ketamine is related to the abnormal expression of various miRNAs in the brain. This study determined the expression profile of circRNAs in the hippocampus of rats treated with ketamine. Methods The aberrantly expressed circRNAs in rat hippocampus after ketamine injection were analyzed by microarray chip, and we further validated these circRNAs by quantitative reverse-transcription PCR (qRT-PCR). The target genes of the different circRNAs were predicted using bioinformatic analyses, and the functions and signal pathways of these target genes were investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results Microarray analysis showed that five circRNAs were aberrantly expressed in rat hippocampus after ketamine injection (fold change > 2.0, p < 0.05). The results from the qRT-PCR showed that one of the circRNAs was significantly increased (rno_circRNA_014900; fold change = 2.37; p = 0.03), while one was significantly reduced (rno_circRNA_005442; fold change = 0.37; p = 0.01). We discovered a significant enrichment in several GO terms and pathways associated with depression. Conclusion Our findings showed the abnormal expression of ketamine-induced hippocampal circRNAs in rats.

scholarly journals Bioinformatics Analysis: The Regulatory Network of hsa_circ_0007843 and hsa_circ_0007331 in Colon Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Zeping Han ◽  
Huafang Chen ◽  
Zhonghui Guo ◽  
Jianxia Zhu ◽  
Xingyi Xie ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cell Communication ◽  
Circular Rna ◽  
Signal Pathways ◽  
Upregulated Genes

Objective. To analyze the molecular regulation network of circular RNA (circRNA) in colon cancer (CC) by bioinformatics method. Methods. hsa_circ_0007843 and hsa_circ_0007331 proved to be associated with CC in previous studies were chosen as the research object. ConSite database was used to predict the transcription factors associated with circRNA, and the CC-associated transcription factors were screened out after intersection. The CircInteractome database was used to predict the RNA-binding proteins (RBPs) interacting with circRNAs and screen out the CC-associated RBPs after an intersection. Furthermore, the CircInteractome database was used to predict the miRNAs interrelated with circRNAs, and the HMDD v3.2 database was used to search for miRNAs associated with CC. The target mRNAs of miRNA were predicted by the miRWalk v3.0 database. CC-associated target genes were screened out from the GeneCards database, and the upregulated genes were enriched and analyzed by the FunRich 3.1.3 software. Finally, the molecular regulatory network diagram of circRNA in CC was plotted. Results. The ConSite database predicted a total of 14 common transcription factors of hsa_circ_0007843 and hsa_circ_0007331, among which Snail, SOX17, HNF3, C-FOS, and RORα-1 were related to CC. The CircInteractome database predicted that the RBPs interacting with these two circRNAs were AGO2 and EIF4A3, and both of them were related to CC. A total of 17 miRNAs interacting with hsa_circ_0007843 and hsa_circ_0007331 were predicted by CircInteractome database. miR-145-5p, miR-21, miR-330-5p, miR-326, and miR-766 were associated with CC according to the HMDDv3.2 database. miR-145-5p and miR-330-5p, lowly expressed in CC, were analyzed in the follow-up study. A total of 676 common target genes of these two miRNAs were predicted by the miRWalk3.0 database. And 57 target genes were involved in the occurrence and development of CC from the GeneCards database, with 23 genes downregulated and 34 genes upregulated. Additionally, GO analysis showed that the 34 upregulated genes were mainly enriched in biological processes such as signal transduction and cell communication. KEGG pathway analysis showed that the upregulated genes were closely related to integrin, ErbB receptor, and ALK1 signal pathways. Finally, a complete regulatory network of hsa_circ_0007843 and hsa_circ_0007331 in CC was proposed, whereby each one of the participants was either directly or indirectly associated and whose deregulation may result in CC progression. Conclusion. Predicting the molecular regulatory network of circRNAs by bioinformatics provides a new theoretical basis for further occurrence and development pathogenesis of CC and good guidance for future experimental research.

scholarly journals Identification of miRNAs Associated with Graft Union Development in Pecan [Carya illinoinensis (Wangenh.) K. Koch]

Forests ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 472 ◽  
Author(s):  
Zhenghai Mo ◽  
Gang Feng ◽  
Wenchuan Su ◽  
Zhuangzhuang Liu ◽  
Fangren Peng
Keyword(s):  
Target Genes ◽  
Callus Formation ◽  
Expression Profiles ◽  
Regulation Of Gene Expression ◽  
Carya Illinoinensis ◽  
Juvenile Period ◽  
Graft Union ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Gene Regulations

Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a high-value fruit tree with a long juvenile period. The fruiting process of pecan seedlings can be largely accelerated through grafting. As non-coding small RNAs, plant miRNAs participate in various biological processes through negative regulation of gene expression. To reveal the roles of miRNAs in the graft union development of pecan, four small RNA libraries were constructed from the graft union at days 0, 8, 15, and 30 after grafting. A total of 47 conserved miRNAs belonging to 31 families and 39 novel miRNAs were identified. For identified miRNAs, 584 target genes were bioinformatically predicted, and 266 of them were annotated; 29 miRNAs (including 16 conserved and 13 novel miRNAs) were differentially expressed during the graft process. The expression profiles of 12 miRNA were further validated by quantitative reverse transcription PCR (qRT-PCR). In addition, qRT-PCR revealed that the expression levels of 3 target genes were negatively correlated with their corresponding miRNAs. We found that miRS26 might be involved in callus formation; miR156, miR160, miR164, miR166, and miRS10 might be associated with vascular bundle formation. These results indicate that the miRNA-mediated gene regulations play important roles in the graft union development of pecan.

scholarly journals Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets towards Prediction of Novel Serum Biomarkers

2013 ◽  
Vol 7 ◽  
pp. BBI.S10501 ◽  
Author(s):  
Madhu Beta ◽  
Nalini Venkatesan ◽  
Madavan Vasudevan ◽  
Umashankar Vetrivel ◽  
Vikas Khetan ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Target Genes ◽  
Mirna Gene ◽  
Target Prediction ◽  
Fold Change ◽  
Serum Samples ◽  
Gene Target ◽  
Qrt Pcr ◽  
Serum Microrna ◽  
Oncogenic Mirnas

Retinoblastoma (RB) is a malignant tumor of the retina seen in children, and potential non invasive biomarkers are in need for rapid diagnosis and for prognosticating the therapy. This study was undertaken to identify the differentially expressed miRNAs in the serum of children with RB in comparison with the normal age matched serum, to analyze its concurrence with the existing RB tumor miRNA profile, to identify its novel gene targets specific to RB, and to study the expression of a few of the identified oncogenic miRNAs in the advanced stage primary RB patient's serum sample. MiRNA profiling was performed on 14 pooled serum from children with advanced RB and 14 normal age matched serum samples, wherein 21 miRNAs were found to be upregulated (fold change ≥ +2.0, P ≤ 0.05) and 24 to be downregulated (fold change ≤ –2.0, P ≤ 0.05). Furthermore, intersection of 59 significantly deregulated miRNAs identified from RB tumor profiles with that of miRNAs detected in serum profile revealed that 33 miRNAs had followed a similar deregulation pattern in RB serum. Later we validated a few of the miRNAs (miRNA 17-92) identified by microarray in the RB patient serum samples (n = 20) by using qRT-PCR. Expression of the oncogenic miRNAs, miR-17, miR-18a, and miR-20a by qRT-PCR was significant in the serum samples exploring the potential of serum miRNAs identification as noninvasive diagnosis. Moreover, from miRNA gene target prediction, key regulatory genes of cell proliferation, apoptosis, and positive and negative regulatory networks involved in RB progression were identified in the gene expression profile of RB tumors. Therefore, these identified miRNAs and their corresponding target genes could give insights on potential biomarkers and key events involved in the RB pathway.

scholarly journals Increased levels of circulating circular RNA (hsa_circ_0013587) may serve as a novel biomarker for pancreatic cancer

2021 ◽  
Author(s):  
Kaiwei Xu ◽  
Zhoujian Qiu ◽  
Liu Xu ◽  
Xuedan Qiu ◽  
Lu Hong ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Early Diagnosis ◽  
Circular Rna ◽  
Circular Rnas ◽  
Plasma Samples ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Pancreatic Cancer Cells ◽  
Clinical Stages ◽  
Cancer Tissues

Aim: Circular RNA can serve as a biomarker for early diagnosis of pancreatic cancer. Materials & methods: Analyzed the expression of various differentially expressed circular RNAs in the pancreatic cancer tissues by gene chip and identified the expression of hsa_circ_0013587 in pancreatic cancer cells, tissues and plasma by quantitative reverse transcription PCR (qRT-PCR). Results: Hsa_circ_0013587 was highly expressed in the pancreatic cancer tissues, cell lines and plasma samples from patients with pancreatic cancer. Notably, hsa_circ_0013587 was upregulated in pancreatic cancer patients with later clinical stages III–IV as compared with those detected in early clinical stages I–II. Conclusion: A high expression of hsa_circ_0013587 may serve as a novel diagnostic and therapeutic biomarker for pancreatic cancer.

scholarly journals MiRNAs expression profiling of rat ovaries displaying PCOS with insulin resistance

2020 ◽  
Vol 302 (5) ◽  
pp. 1205-1213
Author(s):  
Chunren Zhang ◽  
Chuyi Yu ◽  
Zengxian Lin ◽  
Haixia Pan ◽  
Kunyin Li ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Target Genes ◽  
Kegg Pathway ◽  
Polycystic Ovary ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Real Time Quantitative Pcr ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses

Abstract Purpose The present study established microRNA (miRNA) expression profiles for rat ovaries displaying polycystic ovary syndrome (PCOS) with insulin resistance and explored the underlying biological functions of differentially expressed miRNAs. Methods A PCOS with insulin resistance rat model was created by administering letrozole and a high-fat diet. Total RNA was extracted from the ovaries of PCOS with insulin resistance rats and normal rats. Three ovaries from each group were used to identify differentially expressed miRNAs by deep sequencing. A hierarchical clustering heatmap and volcano plot were used to display the pattern of differentially expressed miRNAs. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the potential target genes of the differentially expressed miRNAs and identify their putative biological function. Nine of the differentially expressed miRNAs were selected for validation by Real-time Quantitative PCR (qRT-PCR). Results A total of 58 differentially expressed miRNAs were identified in the rat ovaries exhibiting PCOS with insulin resistance compared with control ovaries, including 23 miRNAs that were upregulated and 35 miRNAs that were downregulated. GO and KEGG pathway analyses revealed that the predicted target genes were related to metabolic processes, cellular processes, and metabolic pathways. Furthermore, qRT-PCR confirmed that miR-3585-5p and miR-30-5p were significantly upregulated and miR-146-5p was downregulated in the ovaries of PCOS with insulin resistance rats compared with the controls. Conclusion These results indicate that differentially expressed miRNAs in rat ovaries may be involved in the pathophysiology of insulin resistance in PCOS. Our study may be beneficial in establishing miRNAs as novel diagnostic and therapeutic biomarkers for insulin resistance in PCOS.

scholarly journals Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke

2021 ◽  
Vol 8 ◽  
Author(s):  
Shuai Zhang ◽  
Jing Wang ◽  
Mei Jie Qu ◽  
Kun Wang ◽  
Ai Jun Ma ◽  
...  
Keyword(s):  
Differential Expression ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Diagnostic Value ◽  
Diagnostic Tools ◽  
Large Artery ◽  
Qrt Pcr ◽  
Validation Set ◽  
Pathway Analyses

Exosomes show diagnostic and therapeutic promise as carriers of ncRNAs in diseases. LncRNAs in exosomes have been identified as being stable and avoided degradation by nucleolytic enzymes. Although lncRNAs have been confirmed to be important in cancers, no studies for exo-lncRNAs have been reported in LAA stroke. High-throughput sequencing was performed to detect the differential expression profiles of lncRNAs in five paired plasma-derived exosome samples from patients with LAA stroke and controls (matched on vascular risk factors). Exo-lncRNA-associated networks were predicted with a combination of multiple databases. The expression of the selected genes in the networks was confirmed by qRT-PCR in a validation set (LAA vs. controls = 30:30). Furthermore, ROC analysis was used to evaluate the diagnostic performance of the lncRNA-related networks. A total of 1,020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. qRT-PCR confirmed that the expression trend of differential expressed genes was consistent with RNA-seq. Furthermore, the AUCs of the lnc_002015-related network and lnc_001350-related network were 0.959 and 0.97, respectively, in LAA stroke. Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic networks for LAA stroke for the first time. The results suggested that exosomal lncRNA-related networks could be potential diagnostic tools in LAA stroke.

scholarly journals Circ-ANAPC7 is Upregulated in Acute Myeloid Leukemia and Appears to Target the MiR-181 Family

2018 ◽  
Vol 47 (5) ◽  
pp. 1998-2007 ◽  
Author(s):  
Hongli Chen ◽  
Tian Liu ◽  
Jing Liu ◽  
Yuandong Feng ◽  
Baiyan Wang ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Reverse Transcription ◽  
Myeloid Leukemia ◽  
Target Genes ◽  
Deficiency Anemia ◽  
Circular Rnas ◽  
Quantitative Reverse Transcription Pcr ◽  
Reverse Transcription Pcr ◽  
Pathway Analyses ◽  
Acute Myeloid

Background/Aims: Circular RNAs (circRNAs) are a family of novel non-coding RNAs associated with various diseases, especially cancer. Recent studies have demonstrated that circRNAs participate in pathogenesis mainly by acting as microRNA (miRNA) sponges. The expression profile of circRNAs in acute myeloid leukemia (AML) has rarely been reported. Methods: Profiles of circRNAs were analyzed using an Arraystar human circRNA microarray with 5 bone marrow samples from patients with newly diagnosed AML and 5 from patients with iron-deficiency anemia. Quantitative reverse transcription PCR was used to validate the expression pattern of circRNAs. Furthermore, circRNA–miRNA network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were applied. Results: CircRNA microarray analysis revealed that 698 circRNAs were differentially expressed in AML patients, with 282 circRNAs found to be upregulated and 416 to be downregulated. Quantitative reverse transcription PCR showed that circ-ANAPC7 was significantly upregulated in AML. Bioinformatics analysis predicted that circ-ANAPC7 acts as a sponge for the miR-181 family, KEGG analysis revealed that it is associated with cancer-related pathways, and GO analysis indicated that most of its target genes are involved in biological processes. Conclusions: These findings show that circ-ANAPC7 is a promising biomarker for AML, and that it might participate in AML pathogenesis by acting as a sponge for the miR-181 family.

scholarly journals Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aijun Sun ◽  
Rui Wang ◽  
Shuaikang Yang ◽  
Xiaojing Zhu ◽  
Ying Liu ◽  
...  
Keyword(s):  
Disease Virus ◽  
Cultured Cells ◽  
Circular Rna ◽  
Marek's Disease Virus ◽  
Marek's Disease ◽  
Circular Rnas ◽  
Marek’S Disease Virus ◽  
Marek’S Disease ◽  
Pathway Analyses ◽  
Profiling Analysis

AbstractMarek’s disease virus (MDV) induces severe immunosuppression and lymphomagenesis in the chicken, its natural host, and results in a condition that investigated the pathogenesis of MDV and have begun to focus on the expression profiling of circular RNAs (circRNAs). However, little is known about how the expression of circRNAs is referred to as Marek’s disease. Previous reports have is regulated during MDV replication. Here, we carried out a comprehensive profiling analysis of N6-methyladenosine (m6A) modification on the circRNA transcriptome in infected and uninfected chicken embryonic fibroblast (CEF) cells. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) revealed that m6A modification was highly conserved in circRNAs. Comparing to the uninfected group, the number of peaks and conserved motifs were not significantly different in cells that were infected with MDV, although reduced abundance of circRNA m6A modifications. However, gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses revealed that the insulin signaling pathway was associated with the regulation of m6A modified circRNAs in MDV infection. This is the first report to describe alterations in the transcriptome-wide profiling of m6A modified circRNAs in MDV-infected CEF cells.

scholarly journals miR-373-3p Regulates Invasion and Migration Abilities of Trophoblast Cells via Targeted CD44 and Radixin

2021 ◽  
Vol 22 (12) ◽  
pp. 6260
Author(s):  
Hyun-Jung Lee ◽  
Seung Mook Lim ◽  
Hee Yeon Jang ◽  
Young Ran Kim ◽  
Joon-Seok Hong ◽  
...  
Keyword(s):  
Preterm Labor ◽  
Target Genes ◽  
Gene Array ◽  
Migration And Invasion ◽  
Trophoblast Cells ◽  
Invasion And Migration ◽  
Mirna Array ◽  
Qrt Pcr ◽  
Putative Target ◽  
And Migration

Preterm labor (PTL) is one of the obstetric complications, and is known to be associated with abnormal maternal inflammatory response and intrauterine inflammation and/or infection. However, the expression of specific miRNAs associated with PTL is not clear. In this study, we performed combination analysis of miRNA array and gene array, and then selected one miRNA (miR-373-3p) and its putative target genes (CD44 and RDX) that exhibited large expression differences in term and PTL placentas with or without inflammation. Using qRT-PCR and luciferase assays, we confirmed that miR-373-3p directly targeted CD44 and RDX. Overexpression of miR-373-3p reduced the migration and invasion of trophoblast cells, while inhibition of miR-373-3p restored the migration and invasion abilities of trophoblast cells. Finally, we validated the expression of miR-373-3p and its target genes in clinical patients’ blood. miR-373-3p was increased in PTL patients’ blood, and was the most expressed in PTL patients’ blood with inflammation. In addition, by targeting the miR-373-3p, CD44 and RDX was decreased in PTL patients’ blood, and their expression were the lowest in PTL patients’ blood with inflammation. Taken together, these findings suggest that miR-373-3p and its target genes can be potential biomarkers for diagnosis of PTL.

scholarly journals Data Integration Reveals the Potential Biomarkers of Circulating MicroRNAs in Osteoarthritis

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 412
Author(s):  
Thuan Duc Lao ◽  
Thuy Ai Huyen Le
Keyword(s):  
Target Genes ◽  
Potential Implication ◽  
Circulating Micrornas ◽  
Abnormal Expression ◽  
Online Databases ◽  
Socioeconomic Burden ◽  
Therapeutic Tools ◽  
Potential Use ◽  
Potential Biomarkers

The abnormal expression of circulating miRNAs (c-miRNAs) has become an emerging field in the development of miRNAs-based diagnostic and therapeutic tools for human diseases, including osteoarthritis (OA). OA is the most common form of arthritis leading to disability and a major socioeconomic burden. The abnormal expression of miRNAs plays important roles in the pathogenesis of OA. Unraveling the role of miRNAs in the pathogenesis of OA will throw light on the potential for the development of miRNAs-based diagnostic and therapeutic tools for OA. This article reviews and highlights recent advances in the study of miRNAs in OA, with specific demonstration of the functions of miRNA, especially c-miRNA, in OA pathogenesis as well as its potential implication in the treatment of OA. Based on a systematic literature search using online databases, we figured out the following main points: (1) the integrative systematic review of c-mRNAs and its target genes related to OA pathogenesis; (2) the potential use of c-miRNAs for OA diagnosis purposes as potential biomarkers; and (3) for therapeutic purposes, and we also highlight certain remedies that regulate microRNA expression based on its target genes.

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