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:BACKGROUND: Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs. However, knowledge of ceRNA regulatory networks in macrophages infected with Talaromyces marneffei (T. marneffei, TM) is still limited. This study aims to explore the expression profiles of lncRNA, miRNA and mRNA, and the changes of ceRNA network related to immunity, inflammation, metabolism in TM-infected macrophage. METHODS: Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages and normal macrophages. Cuffdiff and DESeq2 software packages are used to identify differentially expressed lncRNA, miRNA and mRNA. The function enrichment analysis was performed by GOseq package in R platform, and the lncRNA–miRNA–mRNA interaction ceRNA network was established in Cytoscape. Functional enrichment analysis was performed on genes contained in the ceRNA network, and genes significantly enriched in functional pathways were selected for qRT-PCR verification. RESULTS: A total of 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. Among them, 38 lncRNAs, 10 miRNAs and 109 mRNAs are contained in the ceRNA regulatory network. GO analysis and KEGG pathway of mRNA in the ceRNA network showed that macrophages infected with TM activated pathways and functions related to immune response, metabolic response and inflammatory response. Select genes that are significantly abundant in GO analysis and KEGG pathway. The core genes were selected for quantitative real-time PCR (qRT-PCR) to verify consistency with the sequencing results. Eight groups of ceRNAs consisting of 3 mRNAs, 5 lncRNAs, and 2 miRNAs were verified. They are mRNA CSF3, IL24, LIF. lncRNA IL6R-AS1, LINC02009, AC068831.1, AC006252.1, LINC02466. These genes may be involved in immune response and inflammatory response-related pathways and functions in TM-infected macrophages. CONCLUSIONS: The CeRNA network plays an important role in understanding the mechanism of TM infection in macrophages. This study may provide effective and novel insights for further understanding the underlying mechanism of Talaromyces marneffei.

			Action	DRS
	SRR12903336_1.fastq.gz	Fastqsanger.gz
	SRR12903336_2.fastq.gz	Fastqsanger.gz
	SRR12903337_1.fastq.gz	Fastqsanger.gz
	SRR12903337_2.fastq.gz	Fastqsanger.gz
	SRR12903338_1.fastq.gz	Fastqsanger.gz

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Integrated analysis of lncRNA-miRNA-mRNA ceRNA Network elucidates the molecular interactome

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