KDmarkers: A biomarker database for investigating epigenetic methylation and gene expression levels in Kawasaki disease

Wei-Sheng Wu; Tzu-Hsien Yang; Kuang-Den Chen; Po-Heng Lin; Guan-Ru Chen; Ho-Chang Kuo

doi:10.1016/j.csbj.2022.02.032

KDmarkers: A biomarker database for investigating epigenetic methylation and gene expression levels in Kawasaki disease

Comput Struct Biotechnol J. 2022 Mar 10:20:1295-1305. doi: 10.1016/j.csbj.2022.02.032. eCollection 2022.

Authors

Wei-Sheng Wu¹, Tzu-Hsien Yang², Kuang-Den Chen³, Po-Heng Lin¹, Guan-Ru Chen¹, Ho-Chang Kuo^{3

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Affiliations

¹ Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan.
² Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan.
³ Institute for Translational Research in Biomedicine, Liver Transplantation Center and Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan.
⁴ Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan.
⁵ Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan.
⁶ Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan.
⁷ College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.

Abstract

Kawasaki disease (KD) is a form of acute systemic vasculitis that primarily affects children and has become the most common cause of acquired heart disease. While the etiopathogenesis of KD remains unknown, the diagnostic criteria of KD have been well established. Nevertheless, the diagnosis of KD is currently based on subjective clinical symptoms, and no molecular biomarker is yet available. We have previously performed and combined methylation array (Illumina HumanMethylation450 BeadChip) and transcriptome array (Affymetrix GeneChip Human Transcriptome Array 2.0) to identify genes that are differentially methylated/expressed in KD patients compared with control subjects. We have found that decreased methylation levels combined with elevated gene expression can indicate genes (e.g., toll-like receptors and CD177) involved in the disease mechanisms of KD. In this study, we constructed a database called KDmarkers to allow researchers to access these valuable potential KD biomarkers identified via methylation array and transcriptome array. KDmarkers provides three search modes. First, users can search genes differentially methylated and/or differentially expressed in KD patients compared with control subjects. Second, users can check the KD patient groups in which a given gene is differentially methylated and/or differentially expressed. Third, users can explore the DNA methylation levels and gene expression levels in all samples (KD patients and controls) for a particular gene of interest. We further demonstrated that the results in KDmarkers are strongly associated with KD immune responses. All analysis results can be downloaded for downstream experimental designs. KDmarkers is available online at https://cosbi.ee.ncku.edu.tw/KDmarkers/.

Keywords: DNA methylation; Gene expression; Kawasaki disease.