Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE139876 | GEO | 2020/02/26
REPOSITORIES: GEO
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Project description:BACKGROUND Codonopsis pilosula is a traditional Chinese medicine that has an anti-aging effect. However, the anti-aging effect of Codonopsis pilosula on the lungs remains largely unknown, and the molecular mechanism also needs to be further studied. Thus, we investigated the protective effect of Codonopsis pilosula on the lungs of aging mice, and explored the underlying molecular mechanism. MATERIAL AND METHODS We established an aging mouse model and then treated the mice with Codonopsis pilosula. Microarray analysis and bioinformatics methods were used to comprehensively analyze the lncRNA-miRNA-mRNA (ceRNA) network. RESULTS Our results showed that we successfully established the aging mouse model. The microarray analysis showed that 138 lncRNAs, 128 mRNAs, and 7 miRNAs were significantly changed after aging, and 282 lncRNAs, 283 mRNAs, and 19 miRNAs were dysregulated after treatment with Codonopsis pilosula. To explore the signaling pathways involved, KEGG pathway analysis was performed. Compared with the ceRNA network in aging mice and after treatment with Codonopsis pilosula, we found that 3 mRNAs (Hif3a, Zbtb16, Plxna2) and 1 lncRNA (NONMMUT063872) were associated with the anti-aging effect of Codonopsis pilosula and they were validated by quantitative real-time polymerase chain reaction (qRT-PCR) analysis. CONCLUSIONS Our results showed that Codonopsis pilosula has a protective effect on the aging lung, and the ceRNA network plays an important role in the anti-aging effect of Codonopsis pilosula.
| S-EPMC7034407 | biostudies-literature
Project description:Codonopsis pilosula, a kind of traditional Chinese medicine, possesses anti-aging effect. However, the anti-aging effect of Codonopsis pilosula on lung remains largely unknow and the exact molecular mechanism of Codonopsis pilosula anti-aging also needs to be further studied. Thus, we investigated the protective effect of Codonopsis pilosula on aging lung and the exact molecular mechanism of Codonopsis pilosula anti-aging. To test this hypothesis, we established the aging mice model, and then used Codonopsis pilosula to intervene. Microarray analysis and bioinformatics methods were used to comprehensively analyze lncRNA-miRNA-mRNA (ceRNA) network. Our results showed that the aging mice model was established. From the microarray analysis, 138 lncRNAs, 128 mRNAs and seven miRNAs significantly changed after aging, whereas, 282 lncRNAs, 283 mRNAs and 19 miRNAs were dysregulated after intervention of Codonopsis pilosula. KEGG pathway analysis was performed to explore the signaling pathways involved. Compared with the ceRNA network in aging mice and after intervention of Codonopsis pilosula, we found three mRNAs (Hif3a, Zbtb16, Plxna2) and one lncRNA (NONMMUT063872) associated with Codonopsis pilosula anti-aging and they were validated by qRT-PCR. Altogether, our results showed that Codonopsis pilosula has the protective effect on aging lung and the ceRNA network plays an important role in Codonopsis pilosula anti-aging.
2020-02-26 | GSE139874 | GEO
Project description:Codonopsis pilosula, a kind of traditional Chinese medicine, possesses anti-aging effect. However, the anti-aging effect of Codonopsis pilosula on lung remains largely unknow and the exact molecular mechanism of Codonopsis pilosula anti-aging also needs to be further studied. Thus, we investigated the protective effect of Codonopsis pilosula on aging lung and the exact molecular mechanism of Codonopsis pilosula anti-aging. To test this hypothesis, we established the aging mice model, and then used Codonopsis pilosula to intervene. Microarray analysis and bioinformatics methods were used to comprehensively analyze lncRNA-miRNA-mRNA (ceRNA) network. Our results showed that the aging mice model was established. From the microarray analysis, 138 lncRNAs, 128 mRNAs and seven miRNAs significantly changed after aging, whereas, 282 lncRNAs, 283 mRNAs and 19 miRNAs were dysregulated after intervention of Codonopsis pilosula. KEGG pathway analysis was performed to explore the signaling pathways involved. Compared with the ceRNA network in aging mice and after intervention of Codonopsis pilosula, we found three mRNAs (Hif3a, Zbtb16, Plxna2) and one lncRNA (NONMMUT063872) associated with Codonopsis pilosula anti-aging and they were validated by qRT-PCR. Altogether, our results showed that Codonopsis pilosula has the protective effect on aging lung and the ceRNA network plays an important role in Codonopsis pilosula anti-aging.
2020-02-26 | GSE139875 | GEO
Project description:Atopic dermatitis (AD) is a prevalent inflammatory skin disease characterized by its chronic nature and relapse. Ample evidence suggests that non-coding RNAs play a major role in AD pathogenesis. However, the mechanism remains unknown, particularly in AD recurrence. Dynamic morphological and cytokine changes were measured throughout the whole course of an FITC-induced AD recurrence murine model. Microarray assay and integrative analysis were performed to comprehensively explore long non-coding RNA (lncRNA), messenger RNA (mRNA), and microRNA (miRNA) networks. Our results showed that an AD recurrence model was established. Overall, 5766 lncRNAs, 4025 mRNAs, and 202 miRNAs changed after elicitation, whereas, 419 lncRNAs, 349 mRNAs, and more notably, only 23 miRNAs, were dysregulated in the remission phase. Gene ontology (GO) and KEGG pathway enrichment analyses were used to investigate the potential functions of the dysregulated genes. The altered regulation of seven miRNAs and seven lncRNAs were validated in different stages of the model. The competing endogenous RNA (ceRNA) network inferred that lncRNA humanlincRNA0490+ could compete for miR-155-5p binding, through which it might affect Pki? expression. Altogether, our findings have provided a novel perspective on the potential roles of non-coding RNAs in AD, and suggest that specific non-coding RNAs could be new therapeutic targets against AD recurrence.
| S-EPMC6214145 | biostudies-literature
Project description:Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula
| PRJNA587421 | ENA
Project description:Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula (lncRNA, mRNA datasets)
| PRJNA587427 | ENA
Project description:Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula (miRNA dataset)
| PRJNA587426 | ENA
Project description:Intrahepatic cholangiocarcinoma (ICC) is the second most common lethal liver cancer worldwide. Currently, despite the latest developments in genomics and transcriptomics for ICC in recent years, the molecular pathogenesis promoting ICC remains elusive, especially in regulatory mechanisms of long noncoding RNAs (lncRNAs), which acts as competing endogenous RNA (ceRNA). In order to elucidate the molecular mechanism of functional lncRNA, expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were obtained from The Cancer Genome Atlas (TCGA) database and an integrative analysis of the ICC-associated ceRNA network was performed. Moreover, gene oncology enrichment analyses for the genes in the ceRNA network were implemented and novel prognostic biomarker lncRNA molecules were identified. In total, 6,738 differentially expressed mRNAs (DEmRNAs), 2,768 lncRNAs (DElncRNAs), and 173 miRNAs (DEmiRNAs) were identified in tumor tissues and adjacent nontumor ICC tissues with the thresholds of adjusted P < 0.01 and |logFC| > 2. An ICC-specific ceRNA network was successfully constructed with 30 miRNAs, 16 lncRNAs, and 80 mRNAs. Gene oncology enrichment analyses revealed that they were associated with the adaptive immune response, T cell selection and positive regulation of GTPase activity categories. Among the ceRNA networks, DElncRNAs ARHGEF26-AS1 and MIAT were found to be hub genes in underexpressed and overexpressed networks, respectively. Notably, univariate Cox regression analysis indicated that DElncRNAs HULC significantly correlated with overall survival (OS) in ICC patients (P value?<?0.05), and an additional survival analysis for HULC was reconfirmed in an independent ICC cohort from the Gene Expression Omnibus (GEO) database. These findings contribute to a more comprehensive understanding of the ICC-specific ceRNA network and provide novel strategies for subsequent functional studies of lncRNAs in ICC.
| S-EPMC6899321 | biostudies-literature
Project description:Objective: To explore the molecular mechanism of Codonopsis pilosula in enhancing the immune function of aging mice, the expression profile of long-chain non-coding RNA (lncRNA), mRNA in spleen of mice was detected. Methods: An aging mouse model was established, the aging mice were treated with low, middle and high doses of Codonopsis pilosula, and the aging related indexes, spleen pathology and cellular ultrastructure were detected and analyzed. Then microarray analysis and bioinformatics methods were used to analyze the lncRNA and mRNA expression profile. GO enrichment analysis and KEGG pathway analysis were performed to analyze the differential genes between groups using KOBAS. Finally, the common lncRNAs and mRNAs in high-dose Codonopsis pilosula treatment group compared with the model group and the model group compared with the control group were selected for lncRNA-mRNA co-expression network construction, and real-time quantitative polymerase chain reaction (qRT-PCR) was used to verify the genes in the network. Results: The aging mouse model was successfully established. Codonopsis pilosula can improve the pathology and cellular ultrastructure of spleen in aging mice. Microarray analysis showed that 96 lncRNAs and 65 mRNAs changed significantly after aging, 623 lncRNAs and 435 mRNAs expressed abnormally after high-dose Codonopsis pilosula treatment. KEGG pathways involved in aging and high-dose Codonopsis pilosula treatment are mainly related to immunity, including allograft rejection, graft-versus-host disease, autoimmune thyroid disease, antigen processing and presentation and so on. The three mRNAs (Enpp6, Cped1, and Galnt15) in lncRNA-mRNA co-expression network may be related to Codonopsis pilosula improving the immunity of aging mice, which were verified by qRT-PCR. Conclusion: Codonopsis pilosula has a certain protective effect on the spleen of aging mice and the lncRNA-mRNA network may play an important role in enhancing the immunity of aging mice.
2022-05-17 | GSE150773 | GEO
Project description:BACKGROUND:Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. However, an understanding of the ceRNA regulatory network in Wilms tumour (WT) remains limited. METHODS:The expression profiles of mRNAs, miRNAs and lncRNAs in Wilms tumour samples and normal samples were obtained from the Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database. The EdgeR package was employed to identify differentially expressed lncRNAs, miRNAs and mRNAs. Functional enrichment analyses via the ClusterProfile R package were performed, and the lncRNA-miRNA-mRNA interaction ceRNA network was established in Cytoscape. Subsequently, the correlation between the ceRNA network and overall survival was analysed. RESULTS:A total of 2037 lncRNAs, 154 miRNAs and 3609 mRNAs were identified as differentially expressed RNAs in Wilms tumour. Of those, 205 lncRNAs, 26 miRNAs and 143 mRNAs were included in the ceRNA regulatory network. The results of Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in terms related to response to mechanical stimuli, transcription factor complexes, and transcription factor activity (related to RNA polymerase II proximal promoter sequence-specific DNA binding). The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were mainly enriched in pathways related to the cell cycle. The survival analysis results showed that 16 out of the 205 lncRNAs, 1 out of 26 miRNAs and 5 out of 143 mRNAs were associated with overall survival in Wilms tumour patients (P?<?0.05). CONCLUSIONS:CeRNA networks play an important role in Wilms tumour. This finding might provide effective, novel insights for further understanding the mechanisms underlying Wilms tumour.
| S-EPMC6915924 | biostudies-literature