scholarly journals Integrative analysis of long non-coding RNA (lncRNA) and mRNA expression in TLR4-primed MSCs of ankylosing spondylitis

2020 ◽  
Author(s):  
Yuxi Li ◽  
Ming Li ◽  
Ting Liu ◽  
Jiajun Huang ◽  
Yuwei Liang ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Fold Change ◽  
Signalling Pathway ◽  
Functional Networks ◽  
Potential Mechanism ◽  
Target Mrna ◽  
Qrt Pcr ◽  
Tlr4 Activation

Abstract Background: Ankylosing spondylitis (AS) is a chronic autoimmune disease, and the precise pathogenesis is largely unknown at present. Our previous study found that the expression of toll-like receptor 4 (TLR4) of mesenchymal stem cells from AS patients (AS-MSCs) was reduced and activation of TLR4 by lipopolysaccharide (LPS) could enhance the immunoregulatory ability of AS-MSCs. However, the potential mechanism by which TLR4 affect the immunoregulatory function of AS-MSCs remains unclear. Objective: The goal of this study was to explore the expression profiles and functional networks of lncRNAs and mRNAs in TLR4-primed AS-MSCs and to clarify the potential mechanisms by which TLR4-primed AS-MSCs exert immunoregulatory effects.Methods: Immunoregulatory effects of MSCs were determined after TLR4 activation. Then, the differentially expressed (DE) long non-coding RNAs (lncRNA) and messenger RNAs (mRNA) between AS-MSCs and TLR4-primed AS-MSCs (stimulated by LPS) were identified through high-throughput sequencing followed by qRT-PCR confirmation. Finally, bioinformatic analyses were performed to identify the critical biological functions, signalling pathways and associated functional networks involved in the TLR4-primed immunoregulatory function of AS-MSCs.Results: A total of 147 DE lncRNAs and 698 DE mRNAs were identified between TLR4-primed AS-MSCs and unstimulated AS-MSCs. Of total, 107 lncRNAs were upregulated and 40 were downregulated (fold change ≥2, P <0.05), while 504 mRNAs upregulated and 194 downregulated (fold change ≥2, P <0.05). 5 lncRNAs and 5 mRNAs with largest fold changes were respectively verified by qRT-PCR. GO and KEGG analysis demonstrated that the DE mRNAs and lncRNAs were highly associated with the inflammatory response, such as NOD-like receptor (NLR) signalling pathway, the TNF signalling pathway and the NF-kappa B signalling pathway. Cis-regulation prediction revealed 8 novel lncRNAs while trans-regulation prediction revealed 15 lncRNAs, respectively. 8 core pairs of LncRNA and target mRNA in the lncRNA-TF-mRNA network were: PACERR-PTGS2, LOC105378085-SOD2, LOC107986655-HIVEP2, MICB-DT-MICB, LOC105373925-SP140L, LOC107984251-IFIT5, LOC112268267-GBP2 and LOC101926887-IFIT3, respectively.Conclusion: In AS, TLR4 activation can enhance the immunoregulation ability of MSCs. Eight core pairs of lncRNA and target mRNA have been found in TLR4-primed AS-MSCs, which could contribute to elucidate the potential mechanism of immunoregulatory dysfunction of AS-MSCs.

scholarly journals Integrative analysis of long non-coding RNA (lncRNA) and mRNA expression in TLR4-primed MSCs of ankylosing spondylitis

2020 ◽  
Author(s):  
Yuxi Li ◽  
Ming Li ◽  
Ting Liu ◽  
Jiajun Huang ◽  
Yuwei Liang ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Fold Change ◽  
Signalling Pathway ◽  
Functional Networks ◽  
Potential Mechanism ◽  
Target Mrna ◽  
Qrt Pcr ◽  
Tlr4 Activation

Abstract Background: Ankylosing spondylitis (AS) is a chronic autoimmune disease, and the precise pathogenesis is largely unknown at present. Our previous study found that the expression of toll-like receptor 4 (TLR4) of mesenchymal stem cells from AS patients (AS-MSCs) was reduced and activation of TLR4 by lipopolysaccharide (LPS) could enhance the immunoregulatory ability of AS-MSCs. However, the potential mechanism by which TLR4 affect the immunoregulatory function of AS-MSCs remains unclear. Objective: The goal of this study was to explore the expression profiles and functional networks of lncRNAs and mRNAs in TLR4-primed AS-MSCs and to clarify the potential mechanisms by which TLR4-primed AS-MSCs exert immunoregulatory effects.Methods: Immunoregulatory effects of MSCs were determined after TLR4 activation. Then, the differentially expressed (DE) long non-coding RNAs (lncRNA) and messenger RNAs (mRNA) between AS-MSCs and TLR4-primed AS-MSCs (stimulated by LPS) were identified through high-throughput sequencing followed by qRT-PCR confirmation. Finally, bioinformatic analyses were performed to identify the critical biological functions, signalling pathways and associated functional networks involved in the TLR4-primed immunoregulatory function of AS-MSCs.Results: A total of 147 DE lncRNAs and 698 DE mRNAs were identified between TLR4-primed AS-MSCs and unstimulated AS-MSCs. Of total, 107 lncRNAs were upregulated and 40 were downregulated (fold change ≥2, P <0.05), while 504 mRNAs upregulated and 194 downregulated (fold change ≥2, P <0.05). 5 lncRNAs and 5 mRNAs with largest fold changes were respectively verified by qRT-PCR. GO and KEGG analysis demonstrated that the DE mRNAs and lncRNAs were highly associated with the inflammatory response, such as NOD-like receptor (NLR) signalling pathway, the TNF signalling pathway and the NF-kappa B signalling pathway. Cis-regulation prediction revealed 8 novel lncRNAs while trans-regulation prediction revealed 15 lncRNAs, respectively. 8 core pairs of LncRNA and target mRNA in the lncRNA-TF-mRNA network were: PACERR-PTGS2, LOC105378085-SOD2, LOC107986655-HIVEP2, MICB-DT-MICB, LOC105373925-SP140L, LOC107984251-IFIT5, LOC112268267-GBP2 and LOC101926887-IFIT3, respectively.Conclusion: In AS, TLR4 activation can enhance the immunoregulation ability of MSCs. Eight core pairs of lncRNA and target mRNA have been found in TLR4-primed AS-MSCs, which could contribute to elucidate the potential mechanism of immunoregulatory dysfunction of AS-MSCs.

scholarly journals Integrating the lncRNA and mRNA expression profiles of TLR4-primed mesenchymal stem cells in ankylosing spondylitis

2020 ◽  
Author(s):  
Yuxi Li ◽  
Ming Li ◽  
Jiajun Huang ◽  
Yuwei Liang ◽  
Junshen Huang ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
Mrna Expression ◽  
High Throughput Sequencing ◽  
Mononuclear Cells ◽  
Expression Profiles ◽  
Functional Networks ◽  
Control Group ◽  
Mrna Levels ◽  
Peripheral Blood Mononuclear ◽  
Qrt Pcr

Abstract Background Our previous study found that the toll-like receptor 4 (TLR4) expression of ankylosing spondylitis (AS) patients was significantly different from that of healthy donors. The goals of this study were to explore the expression profiles and functional networks of lncRNAs and mRNAs in TLR4-primed mesenchymal stromal cells from AS patients (AS-MSCs) and to clarify the mechanisms by which TLR4-primed MSCs exert immunoregulatory effects in AS. Methods Firstly, the immunoregulatory effects of MSCs were determined after TLR4 activation. Then, the differentially expressed (DE) lncRNAs and mRNAs between the control group (AS-MSCs without stimulation) and experimental group (AS-MSCs stimulated with lipopolysaccharide) were identified through high-throughput sequencing followed by qRT-PCR confirmation. Finally, bioinformatic analyses were performed to identify the critical biological functions, signalling pathways and associated functional networks involved in the TLR4-primed immunoregulatory function of AS-MSCs. Results TLR4-primed AS-MSCs showed a strong ability to inhibit the proliferation of peripheral blood mononuclear cells (PBMCs) with 1 µg/ml LPS stimulation for 4 hours. A total of 147 DE lncRNAs and 698 DE mRNAs were identified between TLR4-primed AS-MSCs and unstimulated AS-MSCs. Significant fold changes in lncRNA and mRNA levels were confirmed by qRT-PCR. GO and KEGG analysis demonstrated that the DE mRNAs and lncRNAs were highly associated with the inflammatory response. Cis-regulation prediction revealed 9 novel lncRNAs while trans-regulation prediction revealed 15 lncRNAs, respectively. Conclusions Our research describes the lncRNA and mRNA expression profiles and functional networks in TLR4-primed AS-MSCs, which is supposed to enhance the understanding of the pathogenesis of AS-MSC immunoregulatory dysfunction.

Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽  
2021 ◽  
pp. 096120332110614
Author(s):  
Yan Liang ◽  
Ji Zhang ◽  
Wenxian Qiu ◽  
Bo Chen ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Signaling Pathway ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Pcr Analysis ◽  
Clinical Indicators ◽  
Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

Differential Expression Profiles of Long Noncoding RNA and mRNA of Osteogenically Differentiated Mesenchymal Stem Cells in Ankylosing Spondylitis

2016 ◽  
Vol 43 (8) ◽  
pp. 1523-1531 ◽  
Author(s):  
Zhongyu Xie ◽  
Jinteng Li ◽  
Peng Wang ◽  
Yuxi Li ◽  
Xiaohua Wu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Ankylosing Spondylitis ◽  
Osteogenic Differentiation ◽  
Noncoding Rna ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Pcr Assays

Objective.We previously demonstrated that mesenchymal stem cells (MSC) from patients with ankylosing spondylitis (AS; ASMSC) have a greater osteogenic differentiation capacity than MSC from healthy donors (HDMSC) and that this difference underlies the pathogenesis of pathological osteogenesis in AS. Here we compared expression levels of long noncoding RNA (lncRNA) and mRNA between osteogenically differentiated ASMSC and HDMSC and explored the precise mechanism underlying abnormal osteogenic differentiation in ASMSC.Methods.HDMSC and ASMSC were induced with osteogenic differentiation medium for 10 days. Microarray analyses were then performed to identify lncRNA and mRNA differentially expressed between HDMSC and ASMSC, which were then subjected to bioinformatics analysis and confirmed by quantitative real-time PCR (qRT-PCR) assays. In addition, coding-non-coding gene co-expression (CNC) networks were constructed to examine the relationships between the lncRNA and mRNA expression patterns.Results.A total of 520 lncRNA and 665 mRNA were differentially expressed in osteogenically differentiated ASMSC compared with HDMSC. Bioinformatics analysis revealed 64 signaling pathways with significant differences, including transforming growth factor-β signaling. qRT-PCR assays confirmed the reliability of the microarray data. The CNC network indicated that 4 differentially expressed lncRNA, including lnc-ZNF354A-1, lnc-LIN54-1, lnc-FRG2C-3, and lnc-USP50-2 may be involved in the abnormal osteogenic differentiation of ASMSC.Conclusion.Our study characterized the differential lncRNA and mRNA expression profiles of osteogenically differentiated ASMSC and identified 4 lncRNA that may participate in the abnormal osteogenic differentiation of ASMSC. These results provide insight into the pathogenesis of pathological osteogenesis in AS.

scholarly journals High-Throughput Sequencing Reveals the Differential MicroRNA Expression Profiles of Human Gastric Cancer SGC7901 Cell Xenograft Nude Mouse Models Treated with Traditional Chinese Medicine Si Jun Zi Tang Decoction

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Junfu Guo ◽  
Xiangnan Li ◽  
Lanying Miao ◽  
Hongwei Sun ◽  
Xia Gao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Human Gastric Cancer ◽  
Model Group ◽  
Sgc7901 Cell ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

Objective. The present study aimed to investigate the potential mechanism underlying the antitumor effect of Si Jun Zi Tang (SJZT) decoction on gastric cancer. Methods. Twelve human gastric cancer SGC7901 cell xenograft nude mouse models were established. The mice were randomly divided into the Model group and SJZT group. SJZT exerted significant antitumor effects after 21 days of decoction administration. High-throughput sequencing was used to analyze the microRNA (miRNA) expression profiles of tumor tissues. Bioinformatics analysis was performed to provide further information regarding the differentially expressed miRNAs. Five representative differentially expressed miRNAs and four predicted target genes were further validated using quantitative real-time reverse transcription PCR (qRT-PCR). Results. We identified 33 miRNAs that were differentially expressed in the SJZT group compared with the Model group. Among them, 32 miRNAs were upregulated and 1 miRNA was downregulated. Bioinformatic analysis showed that most of miRNAs acted as tumor suppressors and their target genes participated in multiple signaling pathways, including the PI3K/Akt signaling pathway, microRNAs in cancer, and Wnt signaling pathway. The qRT-PCR result confirmed that miR-223-3p, miR-205-5p, miR-147b-3p, and miR-223-5p were overexpressed and their respective paired target genes FUT9, POU2F1, MUC4, and RAB14 mRNA were obviously downregulated in the SJZT group compared with those in the Model group. Network analysis revealed that miR-223-3p and miR-205-5p shared two targets POU2F1 (encoding POU class 2 homeobox 1) and FUT9 (encoding fucosyltransferase 9), suggesting they have a common role in certain pathways. Conclusion. This study provided novel insights into the anticancer mechanism of SJZT against gastric cancer, which might be partly related to the modulation of miRNA expression and their target pathways in tumors.

From gene expression to serum proteins: biomarker discovery in ankylosing spondylitis

2008 ◽  
Vol 69 (01) ◽  
pp. 297-300 ◽  
Author(s):  
N Haroon ◽  
F W L Tsui ◽  
F D O’Shea ◽  
B Chiu ◽  
H W Tsui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ankylosing Spondylitis ◽  
Biomarker Discovery ◽  
Serum Proteins ◽  
Activity Index ◽  
Disease Activity Index ◽  
Fold Change ◽  
Reactive Protein ◽  
Qrt Pcr ◽  
Significant Difference

Objectives:Studying post-infliximab gene expression changes could provide insights into the pathogenesis of ankylosing spondylitis (AS).Methods:Gene expression changes were screened by microarray on peripheral blood RNA of 16 AS patients at baseline and 2 weeks post-infliximab, and selected results were confirmed by quantitative real-time (qRT)–PCR. Corresponding serum-soluble LIGHT (sLIGHT) was estimated by ELISA and the fold change in sLIGHT was correlated to the fold change in erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and the Bath AS disease activity index.Results:Post-infliximab, 69% of the patients (11/16) achieved an ASAS20 response. Six candidate genes were differentially expressed by microarray; four of which were validated by qRT–PCR. sLIGHT showed the most significant difference. There was good correlation of baseline sLIGHT with CRP (R  =  0.60; p = 0.01) and ESR (R  =  0.51; p = 0.04). The fold change in sLIGHT correlated with change in both CRP (R  =  0.71, p = 0.002) and ESR (R  =  0.77, p<0.001).Conclusion:LIGHT is significantly downregulated by infliximab. sLIGHT correlated well with changes in inflammatory markers.

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.

Differentially Expressed Circular RNAs in Stenosed Arteriovenous Fistula Tissues of Uremia Patients

2021 ◽  
Author(s):  
Lili Lan ◽  
Yu Liu ◽  
Menglin Zou ◽  
Yihang Xie ◽  
Yiye Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Effective Management ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Vascular Stenosis ◽  
Polymerase Chain

Abstract BackgroundArteriovenous fistula (AVF) is the most common renal replacement therapy for uremic patients. However, stenosis in AVF may lead to AVF failure, hence prevention and effective management of AVF failure is an issue to be addressed. circular RNAs (circRNAs) dysregulation may be pivotal for the development and progression of AVF stenosis. MethodsFour stenosed tissues from AVF outflow veins and four normal venous tissues without vascular stenosis were collected for RNA-sequencing (RNA-seq). The circRNAs expression profiles were identified by high-throughput sequencing, and the functions and pathways of differentially expressed (DE) circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Gene Genomes (KEGG) enrichment analyses. Seven DE circRNAs were screened for quantitative real‐time polymerase chain reaction (qRT-PCR) validation. circRNA-miRNA interaction network was constructed. ResultsA total of 17,620 circRNA transcripts were examined by RNA-seq, and 208 DE circrRNAs were identified between AG and CG, of which 92 were upregulated and 116 were downregulated. The expression trend in the four selected circRNAs was validated by qRT-PCR, which was consistent with the RNA-seq results. Dysregulated circRNAs may be involved in stenosis by mediating focal adhesion kinase (FAK) pathway. ConclusionOur study revealed abnormal circRNA expression in stenosed tissues of the AVF outflow vein, which was functionally classified. The results indicated that DE circRNAs in the stenosed tissues of AVF and their related FAK pathway have potential to be targets for the prevention and treatment of AVF failure.

scholarly journals Differential Expression Profiles and Functional Prediction of Circular RNAs in Pediatric Dilated Cardiomyopathy

2020 ◽  
Vol 7 ◽  
Author(s):  
Wei Sun ◽  
Bo Han ◽  
Dongxiao Cai ◽  
Jing Wang ◽  
Diandong Jiang ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Healthy Volunteers ◽  
Expression Profiles ◽  
Interaction Network ◽  
Fold Change ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Down Regulation ◽  
Non Invasive ◽  
Qrt Pcr

Circular RNAs (circRNAs) have emerged as essential regulators and biomarkers in various diseases. To assess the different expression levels of circRNAs in pediatric dilated cardiomyopathy (PDCM) and explore their biological and mechanistic significance, we used RNA microarrays to identify differentially expressed circRNAs between three children diagnosed with PDCM and three healthy age-matched volunteers. The biological function of circRNAs was assessed with a circRNA–microRNA (miRNA)–mRNA interaction network constructed from Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Differentially expressed circRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in 25 children with PDCM and 25 healthy volunteers. We identified 257 up-regulated (fold change ≤ 0.5, P &lt; 0.05) and 899 down-regulated (fold change ≥2, P &lt; 0.05) circRNAs in PDCM patients when compared to healthy volunteers. The qRT-PCR experiments confirmed has_circ_0067735 down-regulation (0.45-fold, P &lt; 0.001), has_circ_0070186 up-regulation (2.82-fold, P &lt; 0.001), and has_circ_0069972 down-regulation (0.50-fold, P &lt; 0.05). A functional analysis of these differentially expressed circRNAs suggests that they are associated with hypertrophy, remodeling, fibrosis, and autoimmunity. CircRNAs have been implicated in PDCM through largely unknown mechanisms. Here we report differentially expressed circRNAs in PDCM patients that may illuminate the mechanistic roles in the etiology of PDCM that could serve as non-invasive diagnostic biomarkers.

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.

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