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Peripheral whole blood lncRNA expression analysis in patients with eosinophilic asthma.

ABSTRACT: Long noncoding RNA (lncRNA) plays roles in many diseases including asthma. Several lncRNAs function in the early differentiation of T-helper cells. lncRNA controls gene transcription, protein expression, and epigenetic regulation. Of the 4 asthma phenotypes, eosinophilic asthma (EA) is the most common. However, the lncRNAs associated with eosinophilic asthma have yet to be identified.We designed a study to identify the circulating lncRNA signature in EA samples. We tested whether significant differences in lncRNA expression were observed between blood samples from patients with EA and healthy individuals (control). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for the lncRNA-mRNA (messenger RNA) co-expression network. lncRNA expression was measured using quantitative real-time PCR (polymerase chain reaction).A total of 41 dysregulated lncRNAs and 762 dysregulated mRNAs (difference ? 2-fold) were found in EA compared to control samples. GO terms and KEGG pathway annotation data revealed that several lncRNAs are significantly associated with EA. KEGG pathway annotation indicated that the pathways most enriched in EA were measles, T cell receptor signaling pathway, peroxisome proliferator activated-receptors (PPAR) signaling pathway, Fc gamma R-mediated phagocytosis, NF (nuclear factor) kappa B signaling pathway, chemokine signaling pathway, and primary immunodeficiency. Using qRT-PCR, lncRNA was confirmed to differ significantly between EA and control samples.The results presented here show that several lncRNAs may take part in the immune regulation of EA. Whether these lncRNAs can be used as biomarkers needs further study.

SUBMITTER: Zhu YJ

PROVIDER: S-EPMC5842023 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Peripheral whole blood lncRNA expression analysis in patients with eosinophilic asthma.

Zhu Yu-Jin YJ Mao Dan D Gao Wei W Hu Hong H

Medicine 20180201 8

Long noncoding RNA (lncRNA) plays roles in many diseases including asthma. Several lncRNAs function in the early differentiation of T-helper cells. lncRNA controls gene transcription, protein expression, and epigenetic regulation. Of the 4 asthma phenotypes, eosinophilic asthma (EA) is the most common. However, the lncRNAs associated with eosinophilic asthma have yet to be identified.We designed a study to identify the circulating lncRNA signature in EA samples. We tested whether significant dif ...[more]

PMID: 29465565

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Project description:BackgroundAsthma is a chronic disorder of both adults and children affecting more than 300 million people heath worldwide. Diagnose and treatment for asthma, particularly in childhood asthma have always remained a great challenge because of its complex pathogenesis and multiple triggers, such as allergen, viral infection, tobacco smoke, dust, etc. It is thereby great significant to deeply investigate the transcriptome changes in asthmatic children before and after desensitization treatment, in order that we could identify potential and key mRNAs and lncRNAs which might be considered as useful RNA molecules for observing and supervising desensitization therapy for asthma, which might guide the diagnose and therapy in childhood asthma.MethodsIn the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment, including identification of lncRNAs using a stringent filtering pipeline, differential expression analysis and network analysis, etc. RESULTS: First, a large number of lncRNAs were identified and characterized. Then differential expression analysis revealed 39 mRNAs and 15 lncRNAs significantly differentially expressed which involved in two biological processes and pathways. A co-expressed network analysis figured out a desensitization-treatment-related module which contains 27 mRNAs and 21 lncRNAs using WGCNA R package. Module analysis disclosed 17 genes associated to asthma at distinct level. Subsequent network analysis based on PCC figured out several key lncRNAs probably interacted to those key asthma-related genes, i.e., LINC02145, GUSBP2. Our functional investigation indicated that their functions might involve in immune, inflammatory response and apoptosis process.ConclusionsOur study successfully discovered many key noncoding RNA molecules related to pathogenesis of asthma and relevant treatment, which may provide some clues for asthmatic diagnose and therapy in future.

Dataset Information

Peripheral whole blood lncRNA expression analysis in patients with eosinophilic asthma.

Publications

Peripheral whole blood lncRNA expression analysis in patients with eosinophilic asthma.

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