414 ISSN 0026-8933, Molecular Biology, 2018, Vol. 52, No. 3, pp. 414–418. © Pleiades Publishing, Inc., 2018. Original Russian Text © A.V. Kudryavtseva, K.M. Nyushko, A.R. Zaretsky, D.A. Shagin, A.F. Sadritdinova, M.S. Fedorova, M.V. Savvateeva, Z.G. Guvatova, E.A. Pudova, B.Y. Alekseev, A.A. Dmitriev, A.V. Snezhkina, 2018, published in Molekulyarnaya Biologiya, 2018, Vol. 52, No. 3, pp. 482–488. Suppression of NR0B2 gene in Clear Cell Renal Cell Carcinoma Is Associated with Hypermethylation of Its Promoter A. V. Kudryavtseva a, b, *, K. M. Nyushko b , A. R. Zaretsky c, d , D. A. Shagin c , A. F. Sadritdinova a, b , M. S. Fedorova a , M. V. Savvateeva a , Z. G. Guvatova a , E. A. Pudova a , B. Y. Alekseev b , A. A. Dmitriev a , and A. V. Snezhkina a a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia b National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia c Pirogov Russian National Research Medical University, Moscow, 117997 Russia d Evrogen Lab LCC, Moscow, 117437 Russia *e-mail: rhizamoeba@mail.ru Received May 11, 2017; in final form, July 12, 2017 Abstract—Clear cell renal cell carcinoma (ccRCC) is a common urologic malignancy. Understanding of the transcriptional regulation of oncogenes and tumor suppressor genes involved is critical for the development of the treatments for renal tumors. Using ccRCC subdivision of the TCGA dataset, we identified NR0B2 encoding orphan nuclear receptor as a tumor suppressor candidate in renal tissue. In independent cohort of primary renal tumors, quantitative PCR experiments confirmed significant suppression of NR0B2 mRNA in 86% of ccRCC samples studied. In 80% of these cases, we detected the hypermethylation of the NR0B2 pro- moter region. These results suggest that NR0B2 is a tumor suppressor gene in ccRCC, and that the hyper- methylation of promoter region is the main mechanism of its downregulation. Keywords: clear cell renal cell carcinoma, NR0B2, quantitative PCR, bisulfite sequencing, tumor suppressor gene, DNA methylation DOI: 10.1134/S0026893318030081 INTRODUCTION The constantly growing incidence of kidney cancer makes it a topical issue of modern oncourology. Over 1983–2002, the incidence of kidney cancer in the United States increased from 7.1 to 10.8 cases per 100000 in the population, and the tumor-specific mortality rate increased from 1.2 to 3.2 [1]. The principal histological type of kidney cancer is clear cell renal cell carcinoma (ccRCC), which amounts to 70‒75% of all cases of kidney cancer. As a rule, kidney cancer occurs sporadically with equal fre- quencies in either kidney; the incidence is 1.5 times higher in men than in women. Early stages of kidney cancer are most commonly asymptomatic. However, in patients diagnosed at stage I, the survival rates can be as high as 70%. Kidney cancer is frequently resis- tant to chemo-, radio-, and hormonal therapy; there- fore, the investigation of molecular genetic aberrations associated with kidney cancer is important for the search of diagnostic and prognostic markers, as well as for the development of targeted therapy of the disease. In order to evaluate the role of particular genes in carcinogenesis, the expression of the corresponding mRNA and protein products is compared in tumor and normal tissues. The mechanisms that regulate gene activity, such as DNA methylation, microRNA expression profiles, or histone modifications, are also studied [2‒8]. Using bioinformatic analysis of the data presented in The Cancer Genome Atlas (TCGA), we identified NR0B2 as a candidate tumor suppressor gene in ccRCC. The orphan nuclear receptor encoded by NR0B2 (SHP, SHP-1) plays an important role in the regulation of gene transcription and participates in different metabolic and signaling pathways [9]. Genetic and epigenetic changes involving NR0B2, such as dele- tions, insertions, single-nucleotide polymorphisms, chromosomal rearrangements, or promoter hyper- methylation have been implicated in a number of dis- eases, including obesity, diabetes mellitus, and malignant tumors [10‒13]. Using quantitative PCR (qPCR), we determined NR0B2 expression levels in a representa- tive set of ccRCC specimens. To identify the potential cause of aberrant NR0B2 expression in ccRCC, the methylation of the gene promoter region was investi- gated using bisulfite sequencing. Abbreviations: qPCR, quantitative PCR; ccRCC, clear cell renal cell carcinoma; RNA-Seq, RNA sequencing. MOLECULAR CELL BIOLOGY UDC 577.2:616-006