Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

// Chau-Chyun Sheu 1, 2, 3, * , Ming-Ju Tsai 1, 2, 3, 5, * , Feng-Wei Chen 1 , Kuo-Feng Chang 4 , Wei-An Chang 1, 2 , Inn-Wen Chong 2, 5 , Po-Lin Kuo 1, 6, 7 and Ya-Ling Hsu 1, 7 1 Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan 3 Department of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 4 Welgene Biotech Inc, Taipei, Taiwan 5 Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 6 Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan 7 Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan * These authors have contributed equally to this work Correspondence to: Po-Lin Kuo, email: kuopolin@seed.net.tw Ya-Ling Hsu, email: hsuyl326@gmail.com Keywords: next-generation sequencing, bioinformatics, microRNA, airway remodeling, asthma Received: April 23, 2017      Accepted: June 19, 2017      Published: July 31, 2017 ABSTRACT Airway epithelial cells play important roles in airway remodeling. Understanding gene regulations in airway epithelial homeostasis may provide new insights into pathogenesis and treatment of asthma. This study aimed to combine gene expression (GE) microarray, next generation sequencing (NGS), and bioinformatics to explore genetic regulations associated with airway epithelial homeostasis. We analyzed expression profiles of mRNAs (GE microarray) and microRNAs (NGS) in normal and asthmatic bronchial epithelial cells, and identified 9 genes with potential microRNA-mRNA interactions. Of these 9 dysregulated genes, downregulation of MEF2C and MDGA1 were validated in a representative microarray (GSE43696) from the gene expression omnibus (GEO) database. Our findings suggested that upregulated mir-203a may repress MEF2C , a transcription factor, leading to decreased cellular proliferation. In addition, upregulated mir-3065-3p may repress MDGA1 , a cell membrane anchor protein, resulting in suppression of cell-cell adhesion. We also found that KCNJ2 , a potassium channel, was downregulated in severe asthma and may promote epithelial cell apoptosis. We proposed that aberrant regulations of mir-203a- MEF2C and mir-3065-3p- MDGA1 , as well as downregulation of KCNJ2 , play important roles in airway epithelial homeostasis in asthma. These findings provide new perspectives on diagnostic or therapeutic strategies targeting bronchial epithelium for asthma. The approach in this study also provides a new aspect of studying asthma.