Differentially expressed circRNA and mRNA profiles of neural stem cells with radiation irradiation

2020 ◽  
Author(s):  
Zhaopeng Cai ◽  
Shan Wang ◽  
Zhongyu Xie ◽  
Peng Wang ◽  
Huiyong Shen ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Circular Rna ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Signal Pathways ◽  
Spine Metastasis ◽  
Radiation Induced ◽  
Differentially Expressed Mrna ◽  
Oncology Practice ◽  
Mapk Signal Pathway

Abstract Background Spine metastasis is common but highly problematic in clinical oncology practice. Radiotherapy plays an important role in the treatment of spine metastasis, but it at the same time damages the nervous tissue, especially the neural stem cell (NSC), and leads to radiation induced myelopathy. Circular RNA (circRNA) is a kind of non-coding RNA which responses to external stimulus and regulates cellular functions. However, the mechanism of radiotherapy affecting NSC and the role of circRNA in this process are still unclear. Methods The circRNA and mRNA of NSC treated with radiation or not were detect using next-generation sequencing. RT-PCR assays were preformed to confirm the sequencing results and the feature of differentially expressed circRNA. Bioinformation analyses were conducted to identified the critical circRNA and mRNA, as well as the enriched functions and pathways. Moreover, a circRNA-miRNA-mRNA network was constructed to investigate the possible regulatory mechanism. Results A total of 421 differentially expressed circRNA and 1602 differentially expressed mRNA of NSC were identified after radiotherapy. The GO and KEGG analysis of the differentially expressed mRNA as well as the host genes of the differentially expressed circRNA were performed and several key signal pathways such as MAPK signal pathway were identified. Moreover, a circRNA-miRNA-mRNA network focusing on MAPK signal pathway was shown and predicted that chr5:127160496|127165240 could be the critical circRNA in the regulatory mechanism of radiation treated NSCs. Conclusion Our finding showed the differentially expressed circRNA and mRNA profiles of NSC after radiotherapy, suggesting that circRNA may contribute to the pathogenesis of radiation induced myelopathy.

scholarly journals Identification of the circRNA-miRNA-mRNA Regulatory Network in Bladder Cancer by Bioinformatics Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-22
Author(s):  
Jiancheng Lv ◽  
Ping-an Chang ◽  
Xin Li ◽  
Xiao Yang ◽  
Jie Han ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Cancer Progression ◽  
Drug Targets ◽  
Regulatory Mechanism ◽  
Expression Profiles ◽  
Deep Understanding ◽  
Interaction Network ◽  
Circular Rna ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed

In recent years, increasing evidence shows that circular RNA (circRNA) disorder is closely related to tumorigenesis and cancer progression. However, the regulatory functions of most circRNAs in bladder cancer (BCa) remain unclear. This study was aimed at exploring the molecular regulatory mechanism of circRNAs in BCa. We obtained four datasets of circRNA, microRNA (miRNA), and messenger (mRNA) expression profiles from the Gene Expression Omnibus and The Cancer Genome Atlas microarray databases and identified 434, 367, and 4799/4841 differentially expressed circRNAs, miRNAs, and mRNAs, respectively. With these differentially expressed RNAs, we established a circRNA-miRNA-mRNA targeted interaction network. A total of 18, 24, and 51 central circRNAs, miRNAs, and mRNAs were identified, respectively. Among them, the top 10 mRNAs that had high connectivity with other circRNAs and miRNAs were regarded as hub genes. We detected the expression levels of these 10 mRNAs in 16 pairs of BCa tissues and adjacent normal tissues through quantitative real-time polymerase chain reaction. The differentially expressed mRNAs and central mRNAs were enriched in the processes and pathways that are associated with the growth, differentiation, proliferation, and apoptosis of tumor cells. The outstanding genes (CDCA4, GATA6, LATS2, RHOB, ZBTB4, and ZFPM2) also interacted with numerous drugs, indicating their potency as biomarkers and drug targets. The findings of this study provide a deep understanding of the circRNA-related competitive endogenous RNA regulatory mechanism in BCa pathogenesis.

scholarly journals Comparative analysis of the exosomal contents of DF-1 cells infected by ALV-J

2021 ◽  
Author(s):  
J Yang ◽  
P Zhuang ◽  
Z Cheng ◽  
G Wang
Keyword(s):  
Target Genes ◽  
Viral Pathogenesis ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Signal Pathways ◽  
Differentially Expressed Proteins ◽  
Detection Technology ◽  
Subgroup J ◽  
Avian Leukosis Virus Subgroup

Exploration of the abnormal expression of exosomal molecules during the infection of avian leukosis virus subgroup J (ALV-J) is essential to provide a deeper understanding of the exosome’s role in the viral pathogenesis involved. The study aimed to investigate the differentially expressed proteins and miRNAs of the exosomes derived from DF-1 cells infected by ALV-J, their gene function and involved signal pathways. We isolated exosomes from DF-1 cells infected by ALV-J. The differentially expressed proteins and miRNAs of the exosomes were determined by proteomics and transcription detection technology. A Gene Ontology (GO) analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis identified the miRNAs target genes and the signal pathways regulated by the different proteins or/and miRNAs. A total of 116 proteins (58 upregulated and 58 downregulated) and 3 miRNAs (all upregulated) were determined. These proteins were involved in 155 signal pathways, in which the highest number of proteins involved in the cancer pathway was (up to) seven. The target genes of the miRNAs were involved in 3 signal pathways. Both the proteins and target genes of the miRNAs were involved in the Ribosome pathway and ECM-receptor interaction pathway. The results suggested that the ALV-J infection changed the proteins and miRNAs of the exosomes significantly.

scholarly journals Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds

2019 ◽  
Vol 20 (5) ◽  
pp. 1107 ◽  
Author(s):  
Jing Wang ◽  
Qiaoling Ren ◽  
Liushuai Hua ◽  
Junfeng Chen ◽  
Jiaqing Zhang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Myogenic Differentiation ◽  
Wnt Signaling Pathway ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Longissimus Dorsi Muscle ◽  
Dorsi Muscle ◽  
Non Coding Rna ◽  
Differentially Expressed Mrna

Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and ｜log2FoldChange｜>1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.

scholarly journals MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 468 ◽  
Author(s):  
Xiangfei Ma ◽  
Junwei Sun ◽  
Shuaipeng Zhu ◽  
Zhenwei Du ◽  
Donghua Li ◽  
...  
Keyword(s):  
Production Efficiency ◽  
Target Genes ◽  
Strong Association ◽  
Abdominal Fat ◽  
Signal Pathway ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Signal Pathways ◽  
Abdominal Fat Deposition

The excessive deposition of abdominal fat has become an important factor in restricting the production efficiency of chickens, so reducing abdominal fat deposition is important for improving growth rate. It has been proven that miRNAs play an important role in regulating many physiological processes of organisms. In this study, we constructed a model of adipogenesis by isolating preadipocytes (Ab-Pre) derived from abdominal adipose tissue and differentiated adipocytes (Ab-Ad) in vitro. Deep sequencing of miRNAs and mRNAs expressed in Ab-Pre and Ab-Ad groups was conducted to explore the effect of miRNAs and mRNAs on fat deposition. We identified 80 differentially expressed miRNAs (DEMs) candidates, 58 of which were up-regulated and 22 down-regulated. Furthermore, six miRNAs and six mRNAs were verified by qRT-PCR, and the results showed that the expression of the DEMs and differentially expressed genes (DEGs) in the two groups was consistent with our sequencing results. When target genes of miRNA were combined with mRNA transcriptome data, a total of 891 intersection genes were obtained, we predicted the signal pathways of cross genes enrichment to the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, and ECM–receptor interaction. Meanwhile, we constructed miRNA and negatively correlated mRNA target networks, including 12 miRNA–mRNAs pairs, which showed a strong association with the abdominal adipocyte differentiation (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Overall, these findings provide a background for further research on lipid metabolism. Thus, we can better understand the molecular genetic mechanism of chicken abdominal fat deposition.

scholarly journals Antiepileptic Effect ofUncaria rhynchophyllaandRhynchophyllineInvolved in the Initiation of c-Jun N-Terminal Kinase Phosphorylation of MAPK Signal Pathways in Acute Seizures of Kainic Acid-Treated Rats

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Hsin-Cheng Hsu ◽  
Nou-Ying Tang ◽  
Chung-Hsiang Liu ◽  
Ching-Liang Hsieh
Keyword(s):  
Kainic Acid ◽  
Epileptic Seizures ◽  
Signal Pathway ◽  
Mitogen Activated Protein Kinase ◽  
Signal Pathways ◽  
Sprague Dawley ◽  
Acute Seizures ◽  
Anticonvulsive Effect ◽  
Kinase Phosphorylation ◽  
Mapk Signal Pathway

Seizures cause inflammation of the central nervous system. The extent of the inflammation is related to the severity and recurrence of the seizures. Cell surface receptors are stimulated by stimulators such as kainic acid (KA), which causes intracellular mitogen-activated protein kinase (MAPK) signal pathway transmission to coordinate a response. It is known thatUncaria rhynchophylla(UR) andrhynchophylline(RP) have anticonvulsive effects, although the mechanisms remain unclear. Therefore, the purpose of this study is to develop a novel strategy for treating epilepsy by investigating how UR and RP initiate their anticonvulsive mechanisms. Sprague-Dawley rats were administered KA (12 mg/kg, i.p.) to induce seizure before being sacrificed. The brain was removed 3 h after KA administration. The results indicate that pretreatment with UR (1.0 g/kg), RP (0.25 mg/kg), and valproic acid (VA, 250 mg/kg) for 3 d could reduce epileptic seizures and could also reduce the expression of c-Jun aminoterminal kinase phosphorylation (JNKp) of MAPK signal pathways in the cerebral cortex and hippocampus brain tissues. Proinflammatory cytokines interleukin (IL)-1β, IL-6, and tumor necrosis factor-αremain unchanged, indicating that the anticonvulsive effect of UR and RP is initially involved in the JNKp MAPK signal pathway during the KA-induced acute seizure period.

Genome-Wide Identification of differently expressed lncRNAs, mRNAs, and circRNAs in patients with osteoarthritis

2020 ◽  
Vol 15 ◽  
Author(s):  
Yeqing Sun ◽  
Lei Chen ◽  
Yingqi Zhang ◽  
Jincheng Zhang ◽  
Shashi Ranjan Tiwari
Keyword(s):  
Regulatory Networks ◽  
Expression Profiles ◽  
Interleukin 1 ◽  
Interaction Network ◽  
Circular Rna ◽  
Negative Regulation ◽  
Differentially Expressed ◽  
Positive Regulation ◽  
Proteinprotein Interaction ◽  
Differently Expressed Genes

Background: Osteoarthritis (OA), one of the most important causes leading to joint disability, was considered as an untreatable disease. A series of genes were reported to regulate the pathogenesis of OA, including microRNAs, Long non-coding RNAs and Circular RNA. So far, the expression profiles and functions of lncRNAs, mRNAs, and circRNAs in OA are not fully understood. Objective: The present study aimed to identify differently expressed genes in OA. Methods: The present study conducted RNA-seq to identify differently expressed genes in OA. Ontology (GO) analysis was used to analysis the Molecular Function and Biological Process. KEGG pathway analysis was used to perform the differentially expressed lncRNAs in biological pathways. Results: Hierarchical clustering revealed a total of 943 mRNAs, 518 lncRNAs, and 300 circRNAs were dysregulated in OA compared to normal samples. Furthermore, we constructed differentially expressed mRNAs mediated proteinprotein interaction network, differentially expressed lncRNAs mediated trans regulatory networks, and competitive endogenous RNA (ceRNA) to reveal the interaction among these genes in OA. Bioinformatics analysis revealed these dysregulated genes were involved in regulating multiple biological processes, such as wound healing, negative regulation of ossification, sister chromatid cohesion, positive regulation of interleukin-1 alpha production, sodium ion transmembrane transport, positive regulation of cell migration, and negative regulation of inflammatory response. To the best of our knowledge, this study for the first time revealed the expression pattern of mRNAs, lncRNAs and circRNAs in OA. Conclusion: This study provided novel information to validate these differentially expressed RNAs may be as possible biomarkers and targets in OA.

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 DEBKS: A Tool to Detect Differentially Expressed Circular RNA

2021 ◽  
Author(s):  
Zelin Liu ◽  
Huiru Ding ◽  
Jianqi She ◽  
Chunhua Chen ◽  
Weiguang Zhang ◽  
...  
Keyword(s):  
Circular Rna ◽  
Differentially Expressed

scholarly journals The circular RNA circSlc7a11 promotes bone cancer pain pathogenesis in rats by modulating LLC-WRC 256 cell proliferation and apoptosis

2021 ◽  
Author(s):  
Han-Wen Chen ◽  
Xiao-Xia Zhang ◽  
Zhu-Ding Peng ◽  
Zu-Min Xing ◽  
Yi-Wen Zhang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cancer Pain ◽  
Expression Profiles ◽  
Bone Cancer ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Bone Cancer Pain ◽  
Circular Rnas ◽  
Altered Expression ◽  
Proliferation And Apoptosis

AbstractTreatment of bone cancer pain (BCP) caused by bone metastasis in advanced cancers remains a challenge in clinical oncology, and the underlying mechanisms of BCP are poorly understood. This study aimed to investigate the pathogenic roles of circular RNAs (circRNAs) in regulating cancer cell proliferation and BCP development. Eight differentially expressed circRNAs in the rat spinal cord were validated by agarose gel electrophoresis and Sanger sequencing. Expression of circRNAs and mRNAs was detected by quantitative RT-PCR. MTS assay and flow cytometry were performed to analyze cell proliferation and apoptosis, respectively. Differentially expressed mRNA profiles were characterized by deep RNA sequencing, hierarchical clustering, and functional categorization. The interactions among circRNAs, microRNAs (miRNAs), and mRNAs were predicted using TargetScan. Additionally, western blot was performed to determine the protein levels of Pax8, Isg15, and Cxcl10. Multiple circRNAs were differentially expressed in the spinal cords of BCP model rats; of these, circSlc7a11 showed the greatest increase in expression. The overexpression of circSlc7a11 significantly promoted cell proliferation and repressed apoptosis of LLC-WRC 256 and UMR-106 cells, whereas circSlc7a11 silencing produced the opposite effects. Altered expression of circSlc7a11 also induced substantial changes in the mRNA expression profiles of LLC-WRC 256 cells; these changes were linked to multiple apoptotic processes and signaling pathways, such as the chemokine signaling pathway, and formed a complex circRNA/miRNA/mRNA network. Additionally, Pax8, Isg15, and Cxc110 protein level in LLC-WRC 256 cells was consistent with the mRNA results. The circRNA circSlc7a11 regulates rat BCP development by modulating LLC-WRC 256 cell proliferation and apoptosis through multiple-signaling mechanisms.

scholarly journals Activation of IGF-1 pathway and suppression of atrophy related genes are involved in Epimedium extract (icariin) promoted C2C12 myotube hypertrophy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi-An Lin ◽  
Yan-Rong Li ◽  
Yi-Ching Chang ◽  
Mei-Chich Hsu ◽  
Szu-Tah Chen
Keyword(s):  
Mtor Inhibitor ◽  
Signal Pathway ◽  
C2c12 Cells ◽  
Signal Pathways ◽  
Heavy Chains ◽  
Regenerative Effect ◽  
Ampk Phosphorylation ◽  
Pre Treatment ◽  
Myotube Hypertrophy ◽  
C2c12 Myotube

AbstractThe regenerative effect of Epimedium and its major bioactive flavonoid icariin (ICA) have been documented in traditional medicine, but their effect on sarcopenia has not been evaluated. The aim of this study was to investigate the effects of Epimedium extract (EE) on skeletal muscle as represented by differentiated C2C12 cells. Here we demonstrated that EE and ICA stimulated C2C12 myotube hypertrophy by activating several, including IGF-1 signal pathways. C2C12 myotube hypertrophy was demonstrated by enlarged myotube and increased myosin heavy chains (MyHCs). In similar to IGF-1, EE/ICA activated key components of the IGF-1 signal pathway, including IGF-1 receptor. Pre-treatment with IGF-1 signal pathway specific inhibitors such as picropodophyllin, LY294002, and rapamycin attenuated EE induced myotube hypertrophy and MyHC isoform overexpression. In a different way, EE induced MHyC-S overexpression can be blocked by AMPK, but not by mTOR inhibitor. On the level of transcription, EE suppressed myostatin and MRF4 expression, but did not suppress atrogenes MAFbx and MuRF1 like IGF-1 did. Differential regulation of MyHC isoform and atrogenes is probably due to inequivalent AKT and AMPK phosphorylation induced by EE and IGF-1. These findings suggest that EE/ICA stimulates pathways partially overlapping with IGF-1 signaling pathway to promote myotube hypertrophy.

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