Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [lncRNA-mRNA]
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ABSTRACT: We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.
Project description:We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.
Project description:We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.
Project description:To determine ceRNA transcribed during the PBMCs, we have employed whole genome microarray expression profiling as a discovery platform to identify ceRNA expression in PBMCs donated by T1DM (type 1 diabetes mellitus) patients and healthy volunteers.
Project description:Adiponectin (APN) is an endogenous adipokine secreted from adipocytes that exerts an anti-inflammation property. AdipoAI is an orally active adiponectin receptor agonist identified by our group, which can emulate APN's anti-inflammatory properties through mechanisms not fully understood. To explore AdipoAI function, we used lncRNA microarray and got differential lncRNA/mRNA expression medicated by AdipoAI. Identified as one kind of non-coding RNA with more than 200bp length, lncRNA has been demonstrated to have abundance biological functions, including anti-inflammatory response. In the current study, we performed an lncRNA microarray in LPS-induced Raw264.7 cells which pre-stimulated with AdipoAI, and screened 110 DElncRNAs and 190 DEmRNAs. Enrichment analyses were conducted to total mRNAs and DEmRNAs, including GSVA, ssGSEA, GO/KEGG, GSEA and PPI analysis. Among all these processes, endocytosis was significantly enriched. A co-expression analysis was built based on DElncRNAs and DEmRNAs. Then, using Targetscan and miRwalk to predict related microRNAs of DElncRNAs and DEmRNAs respectively, we established competing endogenous RNA (ceRNA) networks including 54 mRNAs from 8 GO items. Furthermore, 33 m6A methylation related marker genes were obtained from previous study and used for the construction of m6A related-lncRNA network using the co-expression analysis. We identified FTO as the hub gene of the network, and 14 lncRNAs that interacted with it. The expression levels of 10 lncRNAs selected from ceRNA and FTO- related lncRNAs networks were validated with qRT-PCR. Finally, Macrophage phenotype scores showed that AdipoAI could attenuate the M2b and M2c polarization of macrophage and correlate with the above lncRNAs. Our work reveals that lncRNA might involve in the anti-inflammation process of AdipoAI in LPS-induced macrophages through ceRNA network and epigenetic regulation of m6A. Mechanistically, these lncRNAs associated with AdipoAI might be related to endocytosis and polarization in macrophage, and provide new candidates for the anti-inflammatory application of APN and its receptor agonist.
Project description:Purpose: We aimed to detected the circRNA expression profile and constructed a circRNA-based competing endogenous RNA (ceRNA) network in autism. Methods:Valproate acid was used to establish an in vivo model of autism in mice. circRNAs in autism group was identified by RNA sequencing. The expression of circRNAs were detected by real-time PCR. Module analysis was conducted followed by GO and KEGG pathway enrichment analysis. Results: A total of 1059 differentially expressed circRNAs (477 upregulated and 582 downregulated) in autism group. The expression of novel_circ_015779 and novel_circ_035247 were detected by real-time PCR. A ceRNA network based on altered circRNAs was established, with 9715 nodes and 150408 edges. The top three modules were all correlated with autism-related pathways involving ‘TGF-beta signaling pathway’, ‘Notch signaling pathway’, ‘MAPK signaling pathway’, ‘long term depression’, ‘thyroid hormone signaling pathway’, etc. Conclusions: The present study reveals a novel circRNA involved mechanisms in the pathogenesis of autism.
Project description:In order to develop novel biomarkers in prostate cancer, we applied a competing endogenous RNA (ceRNA) microarray to identify differentially expressed mRNAs, circRNAs and lncRNAs in PCa tissue.
Project description:Based on the microarray detection results and bioinformatics analysis, we screened ferroptosis related gene Becn1 and constructed the lncRNA/miRNA/mRNA ceRNA network of regulated ferroptosis in DIMI.
Project description:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, and the molecular mechanisms of AD remain unclear. Accumulating evidence indicates the involvement of non-coding RNAs in AD pathogenesis. Here, we applied RNA-seq to explore the expression changes of circRNA, miRNA, and mRNA simultaneously, and investigate competing endogenous RNA (ceRNA) networks in hippocampus of 4-month APP/PS1 and wild-type mice.
Project description:In order to develop novel biomarkers in breast cancer, we applied a competing endogenous RNA (ceRNA) microarray to identify differentially expressed lncRNAs in BC tissue.