A comprehensive evaluation of differentially expressed mRNAs and lncRNAs in cystitis glandularis with gene ontology, KEGG pathway, and ceRNA network analysis

Objective: MicroRNA (miR)-340-5p has been identified to play a key role in several cancers. However, the function of miR-340-5p in skin fibroblasts remains largely unknown. Methods: Gain of function experiments were performed by infecting normal skin fibroblast cells with a lentivirus carrying 22-bp miR-340-5p. Cell proliferation was detected by Cell Counting Kit-8 (CCK-8) assay. To uncover the mechanisms, mRNA-seq was used. Differentially expressed mRNAs were further determined by Gene Ontology and KEGG pathway analyses. The protein levels were analysed by Western blotting. A dual-luciferase reporter assay was used to detect the direct binding of miR-340-5p with the 3'UTR of Kruppel-like factor 2 (KLF2). Results: MiR-340-5p lentivirus infection suppressed normal skin fibroblast proliferation. The mRNAseq data revealed that 41 mRNAs were differentially expressed, including 22 upregulated and 19 downregulated transcripts in the miR-340-5p overexpression group compared with those in the control group. Gene Ontology and KEGG pathway analyses revealed that miR-340-5p overexpression correlated with the macromolecule biosynthetic process, cellular macromolecule biosynthetic process, membrane, and MAPK signalling pathway. Bioinformatics analysis and luciferase reporter assays showed that miR-340-5p binds to the 3'UTR of KLF2. Forced expression of miR-340-5p decreased the expression of KLF2 in normal skin fibroblasts. Overexpression of KLF2 restored skin fibroblast proliferation in the miR-340-5p overexpression group. Conclusion: This study demonstrates that miR-340-5p may suppress skin fibroblast proliferation, possibly through targeting KLF2. These findings could help us understand the function of miR-340-5p in skin fibroblasts. miR-340-5p could be a therapeutic target for preventing scarring.

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LINC01018 and SMIM25 sponged miR-182-5p in endometriosis revealed by the ceRNA network construction

International Journal of Immunopathology and Pharmacology ◽

10.1177/2058738420976309 ◽

2020 ◽

Vol 34 ◽

pp. 205873842097630

Author(s):

Li Jiang ◽

Mengmeng Zhang ◽

Sixue Wang ◽

Yuzhen Xiao ◽

Jingni Wu ◽

...

Keyword(s):

Messenger Rna ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Protein Protein Interaction ◽

Cerna Network ◽

Non Coding Rna ◽

Differentially Expressed Mirnas ◽

Long Non Coding Rna

The current study intended to explore the interaction of the long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) under the background of competitive endogenous RNA (ceRNA) network in endometriosis (EMs). The differentially expressed miRNAs (DEmiRs), differentially expressed lncRNA (DELs), and differentially expressed genes (DEGs) between EMs ectopic (EC) and eutopic (EU) endometrium based on three RNA-sequencing datasets (GSE105765, GSE121406, and GSE105764) were identified, which were used for the construction of ceRNA network. Then, DEGs in the ceRNA network were performed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) analysis. Besides, the DEmiRs in the ceRNA network were validated in GSE124010. And the target DELs and DEGs of verified DEmiRs were validated in GSE86534. The correlation of verified DEmiRs, DEGs, and DELs was explored. Moreover, gene set enrichment analysis (GSEA) was applied to investigate the function of verified DEmiRs, DEGs, and DELs. Overall, 1352 DEGs and 595 DELs from GSE105764, along with 27 overlapped DEmiRs between GSE105765 and GSE121406, were obtained. Subsequently, a ceRNA network, including 11 upregulated and 16 downregulated DEmiRs, 7 upregulated and 13 downregulated DELs, 48 upregulated and 46 downregulated DEGs, was constructed. The GO and KEGG pathway analysis showed that this ceRNA network probably was associated with inflammation-related pathways. Furthermore, hsa-miR-182-5p and its target DELs (LINC01018 and SMIM25) and DEGs (BNC2, CHL1, HMCN1, PRDM16) were successfully verified in the validation analysis. Besides, hsa-miR-182-5p was significantly negatively correlated with these target DELs and DEGs. The GSEA analysis implied that high expression of LINC01018, SMIM25, and CHL1, and low expression of hsa-miR-182-5p would activate inflammation-related pathways in endometriosis EU samples. LINC01018 and SMIM25 might sponge hsa-miR-182-5p to upregulate downstream genes such as CHL1 to promote the development of endometriosis.

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Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma

BioMed Research International ◽

10.1155/2019/8308694 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14 ◽

Cited By ~ 1

Author(s):

Jiacheng Wu ◽

Shui Liu ◽

Yien Xiang ◽

Xianzhi Qu ◽

Yingjun Xie ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Pathway Analysis ◽

Target Genes ◽

Kegg Pathway ◽

Interaction Network ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Qrt Pcr ◽

Cerna Network ◽

Kegg Pathway Analysis

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910–miR-1261–UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.

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Construction of a circRNA - Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

10.21203/rs.3.rs-1059642/v1 ◽

2021 ◽

Author(s):

De-Bin Liu ◽

You-Fu He ◽

Gui-Jian Chen ◽

Hua Huang ◽

Xu-Ling Xie ◽

...

Keyword(s):

Aortic Dissection ◽

Regulatory Network ◽

Molecular Mechanisms ◽

Kegg Pathway ◽

Expression Profiles ◽

Differentially Expressed ◽

Receptor Interaction ◽

Qrt Pcr ◽

Cerna Network ◽

Arterial Blood

Abstract Background Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circular RNAs (circRNAs) play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed to elucidate the underlying molecular mechanisms of circRNAs regulation in aortic dissection based on the circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network. Methods Expression profiles of circRNAs (GSE97745), miRNAs (GSE92427), and mRNAs (GSE52093) were downloaded from Gene Expression Omnibus (GEO) databases, and the differentially expressed RNAs (DERNAs) were subsequently identified in AD by bioinformatics analysis. Further bioinformatics analyses, including circRNA-miRNA-mRNA ceRNA network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, were used to predict the potential functions of circRNA-associated ceRNA regulatory network. RNA was isolated from human arterial blood samples after which quantitative real-time PCR (qRT-PCR) was performed to confirm the DERNAs. Results We identified 14 (5 up-regulated and 9 down-regulated) differentially expressed circRNAs (DEcircRNAs), 17 (8 up-regulated and 9 down-regulated) differentially expressed miRNAs (DEmiRNAs) and 527 (297 up-regulated and 230 down-regulated) differentially expressed mRNAs (DEmRNAs) when AD samples were compared with normal ascending aorta samples (adjusted P-value < 0.05 and | log2FC |> 1.0). KEGG pathway analysis indicated that DEmRNAs were related to focal adhesion and extracellular matrix (ECM) receptor interaction signaling pathways. Simultaneously, the present study successfully constructed a ceRNA regulatory network based on 1 circRNAs (hsa_circRNA_082317), 1 miRNAs (hsa-miR-149-3p) and 10 mRNAs (MLEC, ENTPD7, SLC16A3, SLC7A8, TBC1D16, PAQR4, MAPK13, PIK3R2, ITGA5, SERPINA1) in AD. Furthermore, qRT-PCR demonstrated that hsa_circRNA_082317 andα5 integrin (ITGA5) were significantly up-regulated in AD (n = 3), and hsa-miR-149-3p was dramatically down-regulated in AD (n = 3). The expression of hsa-miR-149-3p target mRNA, ITGA5, was positively modulated by hsa_circRNA_082317. Conclusion This is the first study to demonstrate the circRNA-associated ceRNA regulatory network is altered in AD, implying that circRNAs may play important roles in regulating the onset and progression of AD and thus may serve as potential biomarkers for the diagnosis and treatment of AD.

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Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis

PeerJ ◽

10.7717/peerj.6425 ◽

2019 ◽

Vol 7 ◽

pp. e6425 ◽

Cited By ~ 13

Author(s):

Yang Fang ◽

Pingping Wang ◽

Lin Xia ◽

Suwen Bai ◽

Yonggang Shen ◽

...

Keyword(s):

Gene Expression ◽

Gene Ontology ◽

Differentially Expressed Genes ◽

Kegg Pathway ◽

Interaction Network ◽

Differentially Expressed ◽

Hub Genes ◽

Protein Protein Interaction ◽

Highly Expressed Genes ◽

Protein Protein Interaction Network

Background The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance. Methods Gene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein–protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app. Results In total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix–receptor interaction, and focal adhesion. The top 10 hub genes in the protein–protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA. Conclusion After comprehensive bioinformatics analysis, we found aberrantly hydroxymethylated differentially expressed genes and pathways in OA. The top 10 hub genes may be useful hydroxymethylation analysis biomarkers to provide more accurate OA diagnoses and target genes for treatment of OA.

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Comprehensive Analysis of Competitive Endogenous Rnas Network Associated With Hepatocellular Carcinoma

10.21203/rs.3.rs-58143/v1 ◽

2020 ◽

Author(s):

jiahui Wan ◽

Xiuli Wang ◽

Fusheng Zhao ◽

Ying Jiang ◽

Wei Ma ◽

...

Keyword(s):

Gene Ontology ◽

Prognostic Value ◽

Enrichment Analysis ◽

Curve Analysis ◽

Differentially Expressed ◽

Migration And Invasion ◽

Roc Curve Analysis ◽

Cerna Network ◽

Competitive Endogenous Rnas ◽

Hcc Cells

Abstract Background: Increasing evidences show that long non-coding RNA (lncRNA) plays the role of competitive endogenous RNAs (ceRNAs) in the development and progression of cancers. The purpose of our study was to identify potential lncRNA biomarkers that serve as a therapeutic target and prognostic biomarker in HCC.Methods: The differential expression of RNAs was examined using the edgeR package. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to predict potential functions. Survival analysis and ROC curve analysis were performed to predict ceRNA network had significant prognostic value. The biological functions of MYLK-AS1 on HCC cells were studied by RNA interference approaches in vitro. Cell proliferation, migration and invasion were detected by Cell Counting Kit-8(CCK-8) assay, wound healing and transwell assay relatively. The mechanism of competitive endogenous RNAs (ceRNAs) were predicted and verified by bioinformatic analysis, western blot analysis and luciferase assays.Results: The newly constructed ceRNA network comprised 76 HCC specific lncRNAs, 15 miRNAs, and 35 mRNAs from the database (Targetscan, miRTarBase, and miRDB). 10 differentially expressed lncRNAs and 10 differentially expressed mRNAs were significantly associated with overall survival in HCC (P value < 0.05). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathways enrichment analysis results showed the differentially expressed mRNAs were involved primarily in the most significant cancer-related signaling pathways. ROC curve analysis demonstrated that MYLK-AS1—has-mir-424—CCNE1 ceRNA network had significant prognostic value. The expression of MYLK-AS1 was up-regulated in HCC cells and tissues. Biological function analyses indicated that down-regulation of MYLK-AS1 suppressed cell proliferation, migration and invasion . MYLK-AS1 and miR-424-5p bound directly and reversibly to each other. MYLK-AS1 could positively regulate CCNE1 expression by competitively binding to miR-424-5p. Conclusion: The current study provides novel insights into the lncRNA-related ceRNA network in HCC and the MYLK-AS1 may be a candidate biomarker for molecular diagnosis and prognosis monitoring of HCC.

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Analysis of mRNA-lncRNA and mRNA-lncRNA-Pathway co-expression networks based on WGCNA in developing pediatric sepsis

10.21203/rs.3.rs-54798/v1 ◽

2020 ◽

Author(s):

Xiaojuan Zhang ◽

Yuqing Cui ◽

Xianfei Ding ◽

Shaohua Liu ◽

Bing Han ◽

...

Keyword(s):

Gene Expression ◽

Gene Ontology ◽

Network Analysis ◽

Pathway Analysis ◽

Kegg Pathway ◽

Gene Expression Omnibus ◽

Kegg Pathway Analysis ◽

Differentially Expressed Mrna ◽

Pediatric Sepsis ◽

Geo Database

Abstract Background: Pediatric sepsis is a great threat in death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis.Methods: This study identified differentially expressed mRNA (DEMs) and lncRNAs (DELs) based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, DEMs‑DELs and DEMs‑DELs-Pathway co-expression network analysis was conducted in selected significant module. Results: A total of 1941 DEMs and 225 DELs were used to conduct WGCNA. And the turquoise module was selected as the significant module that was associated with particular traits. The DEMs functions associated with many vital processes were also shown by GO and KEGG pathway analysis in the turquoise module. Finally, 15 DEMs and 4 DELs (GSEC, NONHSAT160878.1, XR_926068.1 and RARA-AS1) were selected as candidate biomarkers in DEMs-DELs-Pathway co-expression network. Conclusions: Our study identified 15 DEMs and 4 DELs as diagnostic markers, which could also provide more directions to study molecular mechanism of pediatric sepsis.

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Microarray analysis reveals an inflammatory transcriptomic signature in peripheral blood for sciatica

BMC Neurology ◽

10.1186/s12883-021-02078-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yi Wang ◽

Guogang Dai ◽

Ling Jiang ◽

Shichuan Liao ◽

Jiao Xia

Keyword(s):

Functional Analysis ◽

Network Analysis ◽

Peripheral Blood ◽

Differentially Expressed ◽

Healthy Controls ◽

Toll Like Receptor ◽

Qrt Pcr ◽

Transcriptomic Signature ◽

Transcriptional Changes ◽

Key Genes

Abstract Background Although the pathology of sciatica has been studied extensively, the transcriptional changes in the peripheral blood caused by sciatica have not been characterized. This study aimed to characterize the peripheral blood transcriptomic signature for sciatica. Methods We used a microarray to identify differentially expressed genes in the peripheral blood of patients with sciatica compared with that of healthy controls, performed a functional analysis to reveal the peripheral blood transcriptomic signature for sciatica, and conducted a network analysis to identify key genes that contribute to the observed transcriptional changes. The expression levels of these key genes were assessed by qRT-PCR. Results We found that 153 genes were differentially expressed in the peripheral blood of patients with sciatica compared with that of healthy controls, and 131 and 22 of these were upregulated and downregulated, respectively. A functional analysis revealed that these differentially expressed genes (DEGs) were strongly enriched for the inflammatory response or immunity. The network analysis revealed that a group of genes, most of which are related to the inflammatory response, played a key role in the dysregulation of these DEGs. These key genes are Toll-like receptor 4, matrix metallopeptidase 9, myeloperoxidase, cathelicidin antimicrobial peptide, resistin and Toll-like receptor 5, and a qRT-PCR analysis validated the higher transcript levels of these key genes in the peripheral blood of patients with sciatica than in that of healthy controls. Conclusion We revealed inflammatory characteristics that serve as a peripheral blood transcriptomic signature for sciatica and identified genes that are essential for mRNA dysregulation in the peripheral blood of patients with sciatica.

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Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network

BMC Cancer ◽

10.1186/s12885-021-07845-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yang Xi ◽

Zhuang Jing ◽

Wu Wei ◽

Zhang Chun ◽

Qi Quan ◽

...

Keyword(s):

Cell Proliferation ◽

Sodium Butyrate ◽

Molecular Network ◽

Differentially Expressed ◽

Cell Counting ◽

Molecular Networks ◽

Ppi Network ◽

Invasion And Metastasis ◽

Cerna Network ◽

Proliferation Ability

Abstract Background Sodium butyrate (NaB) is produced through the fermentation of dietary fiber that is not absorbed and digested by the small intestine. Purpose Here, we aimed to investigate the effects of NaB on the proliferation, invasion, and metastasis of CRC cells and their potential underlying molecular mechanism(s). Methods The cell counting kit-8 (CCK-8) assay and EdU assay were used to detect cell proliferation ability, flow cytometry was used to investigate the induction of apoptosis and cell cycle progression, and the scratch-wound healing and transwell assays were used to evaluate cell migration and invasion, respectively. The human CRC genome information for tissues and CRC cells treated with NaB obtained from the NCBI GEO database was reannotated and used for differential RNA analysis. Functional and pathway enrichment analyses were performed for differentially expressed lncRNAs and mRNAs. A protein-protein interaction (PPI) network for the hub genes was constructed using the Cytoscape software. Targeted miRNAs were predicted based on the lnCeDB database, and a ceRNA network was constructed using the Cytoscape software. The Kaplan-Meier method was used to analyze patient prognosis using the clinical information and exon-seq data for CRC obtained from the Broad Institute’s GDAC Firehose platform. Results NaB decreased the proliferation ability of CRC cells in a dose- and time-dependent manner. The number of apoptotic CRC cells increased with the increase in NaB concentrations, and NaB induced a G1 phase block in CRC cells. Moreover, NaB suppressed the migratory and invasive capabilities of CRC cells. There were 666 differentially expressed mRNAs and 30 differentially expressed lncRNAs involved in the CRC inhibition by NaB. The PPI network and ceRNA network were constructed based on the differentially expressed mRNAs and lncRNAs. Three differentially expressed mRNAs, including HMGA2, LOXL2, and ST7, were significantly correlated with the prognosis of CRC. Conclusion NaB induces the apoptosis and inhibition of CRC cell proliferation, invasion, and metastasis by modulating complex molecular networks. RNA prediction and molecular network construction need to be the focus of further research in this direction.

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Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

Bulletin of Entomological Research ◽

10.1017/s0007485321000171 ◽

2021 ◽

pp. 1-14

Author(s):

Peirong Li ◽

Xinru Li ◽

Wei Wang ◽

Xiaoling Tan ◽

Xiaoqi Wang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Developmental Stages ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Mythimna Separata ◽

Kegg Pathway Analysis ◽

Oriental Armyworm ◽

Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

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