Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma
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RESEARCH ARTICLE
Open Access
Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma Peiyan Zheng1†, Chen Huang2†, Dongliang Leng2, Baoqing Sun1* and Xiaohua Douglas Zhang2,3*
Abstract Background: Asthma 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. Methods: In 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. Conclusions: Our 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. Keywords: Childhood asthma, Deep RNA-sequencing, Transcriptome, Long non-coding RNAs
* Correspondence: [email protected]; [email protected] † Peiyan Zheng and Chen Huang contributed equally to this work. 1 Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China 2 CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau, China Full list of author information is available at the end of the article
Background Asthma is a chronic disease of the airways of the lungs, characterized by various symptoms, such as wheezing, coughing, chest tightness, short
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