Integration of transcriptome and methylome analysis of aldosterone-producing adenomas Masanori Murakami 1 , Takanobu Yoshimoto 1 , Kazuhiko Nakabayashi 2 , Kyoichiro Tsuchiya 1 , Isao Minami 1 , Ryotaro Bouchi 1 , Hajime Izumiyama 1,3 , Yasuhisa Fujii 4 , Kosei Abe 2 , Chiharu Tayama 2 , Koshi Hashimoto 1,5 , Takayoshi Suganami 6,7 , Ken-ichiro Hata 2 , Kazunori Kihara 4 and Yoshihiro Ogawa 1,8 1 Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan, 2 Department of Maternal–Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan, 3 Center for Medical Welfare and Liaison Services, Departments of 4 Urology, 5 Preemptive Medicine and Metabolism and 6 Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, 7 Japan Science and Technology Agency, PRESTO, Tokyo 102-0076, Japan and 8 Japan Science and TechnologyAgency, CREST, Tokyo 102-0076, Japan Correspondence should be addressed to T Yoshimoto Email tyoshimoto.mem@tmd.ac.jp Abstract Objective: The pathophysiology of aldosterone-producing adenomas (APA) has been investigated intensively through genetic and genomic approaches. However, the role of epigenetics in APA is not fully understood. In the present study, we explored the relationship between gene expression and DNA methylation status in APA. Methods: We conducted an integrated analysis of transcriptome and methylome data of paired APA-adjacent adrenal gland (AAG) samples from the same patient. The adrenal specimens were obtained from seven Japanese patients with APA who underwent adrenalectomy. Gene expression and genome-wide CpG methylation profiles were obtained from RNA and DNA samples that were extracted from those seven paired tissues. Results: Methylome analysis showed global CpG hypomethylation in APA relative to AAG. The integration of gene expression and methylation status showed that 34 genes were up-regulated with CpG hypomethylation in APA. Of these, three genes (CYP11B2, MC2R, and HPX) may be related to aldosterone production, and five genes (PRRX1, RAB38, FAP , GCNT2, and ASB4) are potentially involved in tumorigenesis. Conclusion: The present study is the first methylome analysis to compare APA with AAG in the same patients. Our integrated analysis of transcriptome and methylome revealed DNA hypomethylation in APA and identified several up-regulated genes with DNA hypomethylation that may be involved in aldosterone production and tumorigenesis. European Journal of Endocrinology (2015) 173, 185–195 Introduction Acquired epigenetic changes, such as DNA methylation at CpG dinucleotides, play a role in a variety of physiologic and pathophysiologic conditions (1). It has been shown that global DNA hypomethylation is associated with chromosomal instability in oncogenic processes (2). In addition, aberrant DNA methylation patterns have been shown to alter transcriptional regulation in specific genes, such as tumor suppressor genes, and to thereby lead to tumor development (2). Recent studies have also revealed aberrant DNA methylation status in adrenocortical ade- noma and carcinoma (3, 4, 5). However, the pathophy- siologic significance of differentially methylated genes in aldosterone-producing adenoma (APA) is unknown. APA is a subtype of primary aldosteronism (PA), which is the most common form of endocrine hypertension (6, 7) and is closely associated with severe cardiovascular European Journal of Endocrinology Clinical Study M Murakami and others Transcriptome and methylome analysis of APAs 173 :2 185–195 www.eje-online.org Ñ 2015 European Society of Endocrinology DOI: 10.1530/EJE-15-0148 Printed in Great Britain Published by Bioscientifica Ltd. Downloaded from Bioscientifica.com at 05/29/2020 07:14:53PM via Massachusetts Inst of Technology