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Analysis of differential expression of long non?coding RNAs in exosomes derived from mature and immature dendritic cells.

ABSTRACT: Dendritic cells release bioactive exosomes involved in immune regulation. Long non?coding RNAs (lncRNAs) are implicated in a number of immunoregulatory mechanisms. However, the roles of lncRNAs in dendritic cell?derived exosomes remain to be elucidated. The present study aimed to investigate the roles of lncRNAs in exosomes derived from mature and immature dendritic cells and to find specific lncRNAs with immunoregulatory function. The expression profiles of lncRNAs in exosomes derived from bone marrow dendritic cells of C57 mice were illustrated. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses and Gene Set Enrichment Analysis were performed to identify potential targets correlated with immune regulation. In addition, lncRNA?miRNA?mRNA networks were predicted using bioinformatics methods. Representative lncRNAs were further validated via reverse transcription?quantitative PCR. A total of 437 lncRNAs were analyzed using RNA?seq. Among these, the expression of ~87 lncRNAs was upregulated and 21 lncRNAs was downregulated in mature dendritic cell?derived exosomes (Dex) compared with immature Dex. GO analyses indicated the involvement of upregulated lncRNAs in multiple biological functions, such as the immune system process, while downregulated lncRNAs were involved in poly(A) RNA binding. Analysis of the KEGG pathway identified the relationship of TNF signaling and ribosome pathway with upregulated lncRNAs and downregulated lncRNAs, respectively. The results of gene set enrichment analysis identified that three lncRNA?associated transcripts (Procr?203, Clec4e?202 and Traf1?203) were highly associated with immunoregulatory functions including T helper cell differentiation and Janus kinase?STAT signaling pathway. The results indicated the involvement of candidate lncRNAs in immunoregulation and suggested a new perspective on the modulation of lncRNAs in Dex.

SUBMITTER: Wu J

PROVIDER: S-EPMC7751491 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Analysis of differential expression of long non‑coding RNAs in exosomes derived from mature and immature dendritic cells.

Wu Jiachang J Zhao Renli R Dai Jingxing J Lai Guohua G Khan Asmat Ullah AU Yu Xiao X Wu Sha S Ouyang Jun J Sang Hongxun H

Molecular medicine reports 20201214 2

Dendritic cells release bioactive exosomes involved in immune regulation. Long non‑coding RNAs (lncRNAs) are implicated in a number of immunoregulatory mechanisms. However, the roles of lncRNAs in dendritic cell‑derived exosomes remain to be elucidated. The present study aimed to investigate the roles of lncRNAs in exosomes derived from mature and immature dendritic cells and to find specific lncRNAs with immunoregulatory function. The expression profiles of lncRNAs in exosomes derived from bone ...[more]

PMID: 33313954

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Project description:RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.

Project description:Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs. Compared to round spermatids, 1,794 upregulated and 165 downregulated lncRNAs and 4,435 upregulated and 3,920 downregulated mRNAs were identified in sperm. Based on the "Cis and Trans" RNA-RNA interaction principle, we found 14,259 targeted coding genes of differently expressed lncRNAs. In terms of Gene ontology (GO) analysis, differentially expressed lncRNAs targeted genes mainly related to nucleic acid metabolic, protein modification, chromatin and histone modification, heterocycle compound metabolic, sperm function, spermatogenesis and other processes. In contrast, differentially expressed transcripts of mRNAs were highly enriched for protein metabolic process and RNA metabolic, spermatogenesis, sperm motility, cell cycle, chromatin organization, heterocycle and aromatic compound metabolic processes. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the differentially expressed lncRNAs were involved in RNA transport, mRNA surveillance pathway, PI3K-Akt signaling pathway, AMPK signaling pathway, protein processing in endoplasmic reticulum. Metabolic pathways, mRNA surveillance pathway, AMPK signaling pathway, cell cycle, RNA transport splicesome and endocytosis incorporated with the differentially expressed mRNA. Furthermore, many lncRNAs were specifically expressed in testis/sperm, and 880 lncRNAs were conserved between human and mouse. In summary, this study provides a preliminary database valuable for identifying lncRNAs critical in the late stage of spermatogenesis or important for sperm function regulation, fertilization and early embryo development.

Project description:ObjectiveThe objective of this study is to explore the long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) expression profiles of monocyte-derived dendritic cells (DCs) obtained from peripheral blood mononuclear cells (PBMCs). DCs are known to play a major role in the regulating function of allergic rhinitis (AR).MethodsPBMCs were separately isolated from the human peripheral blood of patients with AR and normal person (NP). The mixed lymphocyte reaction (MLR) assay was used to evaluate the function of DCs. Flow cytometry was used to determine the immune regulatory function of immature DCs (imDCs) and mature DCs (mDCs). lncRNAs and mRNAs in the NP group (DCs isolated from NP) and the test group (DCs isolated from patients with AR) were identified via chip technology and bioinformatic analyses. Moreover, bioinformatic analyses were employed to identify the related biological functions of monocyte-derived DCs and construct the functional networks of lncRNAs and mRNAs that are differentially expressed (DE) in imDCs and mDCs.ResultsMLR was significantly higher in the mDCs group than that in the imDCs group. CD14 was highly expressed in imDCs, whereas HLA-DR, CD80, and CD86 were highly expressed in mDCs (p < 0.001). We identified 962 DE lncRNAs and 308 DE mRNAs in the imDCs of NP and patients with AR. Additionally, there were 601 DE lncRNAs and 168 DE mRNAs in the mDCs in the NP and test groups. Quantitative RT-qPCR was used to study the significant fold changes of lncRNAs and mRNAs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found 16 significant regulated pathways in imDCs and 10 significant regulated pathways in mDCs, including the phagosome, cell adhesion signaling pathway, and inflammatory mediator regulation of TRP channels pathway.ConclusionOur research studied the lncRNA and mRNA expression profiles of monocyte-derived DCs and demonstrated the functional networks that are involved in monocyte-derived DCs-mediated regulation in AR. These results provided possible molecular mechanisms of monocyte-derived DCs in the immunoregulating function and laid the foundation for the molecular therapeutic targets of AR.

Dataset Information

Analysis of differential expression of long non?coding RNAs in exosomes derived from mature and immature dendritic cells.

Publications

Analysis of differential expression of long non‑coding RNAs in exosomes derived from mature and immature dendritic cells.

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