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Anti-Cancer Agents in Medicinal Chemistry

Author(s): Shuang Zhao, Ye Zhang, Xujun Liang, Maoyu Li, Fang Peng, Zhuchu Chen and Yongheng Chen*

DOI: 10.2174/1871520619666190204094815

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Detection and Analysis of RNAs Expression Profile for Methylated Candidate Tumor Suppressor Genes in Nasopharyngeal Carcinoma

Page: [772 - 782] Pages: 11

  • * (Excluding Mailing and Handling)

Abstract

Background: DNA methylation, which acts as an expression regulator for multiple Tumor Suppressor Genes (TSGs), is believed to play an important role in Nasopharyngeal Carcinoma (NPC) development.

Methods: We compared the effects of 5-aza-2-deoxycytidine (decitabine, DAC) on gene expression using RNA sequencing in NPC cells.

Results: We analyzed Differentially Expressed Genes (DEGs) in NPC cells using DAC demethylation treatment and found that 2182 genes were significantly upregulated (≥ 2-fold change), suggesting that they may play a key role in cell growth, proliferation, development, and death. For data analysis, we used the Gene Ontology database and pathway enrichment analysis of the DEGs to discover differential patterns of DNA methylation associated with changes in gene expression. Furthermore, we evaluated 74 methylated candidate TSGs from the DEGs in NPC cells and summarized these genes in several important signaling pathways frequently disrupted by promoter methylation in NPC tumorigenesis.

Conclusion: Our study analyzes the DEGs and identifies a set of genes whose promoter methylation in NPC cells is reversed by DAC. These genes are potential substrates of DNMT inhibitors and may serve as tumor suppressors in NPC cells.

Keywords: Nasopharyngeal carcinoma, DNA methylation, tumor suppressor genes, RNA-sequencing, expression profile, NPC tumorigenesis.

Graphical Abstract

[1]
Tao, Q.; Chan, A.T. Nasopharyngeal carcinoma: Molecular pathogenesis and therapeutic developments. Expert Rev. Mol. Med., 2007, 9(12), 1-24.
[2]
Bhattacharyya, N. The impact of race on survival in nasopharyngeal carcinoma: A matched analysis. Am. J. Otolaryngol., 2004, 25(2), 94-97.
[3]
Lo, K.W.; Huang, D.P. Genetic and epigenetic changes in nasopharyngeal carcinoma. Semin. Cancer Biol., 2002, 12(6), 451-462.
[4]
Jones, P.A.; Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 2002, 3(6), 415-428.
[5]
Jin, P.; Chen, X. Current status of epigenetics and anticancer drug discovery. Anticancer. Agents Med. Chem., 2016, 16(6), 699-712.
[6]
Balakin, K.V.; Ivanenkov, Y.A.; Kiselyov, A.S.; Tkachenko, S.E. Histone deacetylase inhibitors in cancer therapy: Latest developments, trends and medicinal chemistry perspective. Anti- Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry - Anti-Cancer Agents), 2007, 7(5), 576-592.
[7]
Jones, P.A.; Baylin, S.B. The epigenomics of cancer. Cell, 2007, 128(4), 683-692.
[8]
Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet., 2007, 8(4), 286-298.
[9]
Li, K.K.; Li, F.; Li, Q.S.; Yang, K.; Jin, B. DNA methylation as a target of epigenetic therapeutics in cancer. Anticancer. Agents Med. Chem., 2013, 13(2), 242-247.
[10]
Mund, C.; Hackanson, B.; Stresemann, C.; Lübbert, M.; Lyko, F. Characterization of DNA demethylation effects induced by 5-Aza-2′-deoxycytidine in patients with myelodysplastic syndrome. Cancer Res., 2005, 65(16), 7086-7090.
[11]
Gore, S.D.; Baylin, S.; Sugar, E.; Carraway, H.; Miller, C.B.; Carducci, M.; Grever, M.; Galm, O.; Dauses, T.; Karp, J.E. Combined DNA methyltransferase and histone deacetylase inhibition in the treatment of myeloid neoplasms. Cancer Res., 2006, 66(12), 6361-6369.
[12]
Soriano, A.O.; Yang, H.; Faderl, S.; Estrov, Z.; Giles, F.; Ravandi, F.; Cortes, J.; Wierda, W.G.; Ouzounian, S.; Quezada, A. Safety and clinical activity of the combination of 5-azacytidine, valproic acid, and all-trans retinoic acid in acute myeloid leukemia and myelodysplastic syndrome. Blood, 2007, 110(7), 2302.
[13]
Kihslinger, J.E.; Godley, L.A. The use of hypomethylating agents in the treatment of hematologic malignancies. Leuk. Lymphoma, 2007, 48(9), 1676-1695.
[14]
Taylor, S.M.; Jones, P.A. Mechanism of action of eukaryotic DNA methyltransferase: Use of 5-azacytosine-containing DNA. J. Mol. Biol., 1982, 162(3), 679-692.
[15]
Santi, D.V.; Norment, A.; Garrett, C.E. Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine. Proc. Natl. Acad. Sci. USA, 1984, 81(22), 6993-6997.
[16]
Schermelleh, L.; Spada, F.; Easwaran, H.P.; Zolghadr, K.; Margot, J.B.; Cardoso, M.C.; Leonhardt, H. Trapped in action: Direct visualization of DNA methyltransferase activity in living cells. Nat. Methods, 2005, 2(10), 751-756.
[17]
Yan, L.; Gu, H.; Li, J.; Xu, M.; Liu, T.; Shen, Y.; Chen, B.; Zhang, G. RKIP and 14-3-3ε exert an opposite effect on human gastric cancer cells SGC7901 by regulating the ERK/MAPK pathway differently. Dig. Dis. Sci., 2013, 58(2), 389-396.
[18]
Yan, L.; Wang, Y.; Wang, Z.Z.; Rong, Y.T.; Chen, L.L.; Li, Q.; Liu, T.; Chen, Y.H.; Li, Y.D.; Huang, Z.H. Cell motility and spreading promoted by CEACAM6 through cyclin D1/CDK4 in human pancreatic carcinoma. Oncol. Rep., 2016, 35(1), 418.
[19]
Hu, Q.; Chu, Y.; Hu, W.; Peng, M.; Song, Q. The cytotoxic effect of GW843682X on nasopharyngeal carcinoma. Anticancer. Agents Med. Chem., 2016, 16(12), 1640-1645.
[20]
Li, D.J.; Deng, G.; Xiao, Z.Q.; Yao, H.X.; Li, C.; Peng, F.; Li, M.Y.; Zhang, P.F.; Chen, Y.H.; Chen, Z.C. Identificating 14-3-3 sigma as a lymph node metastasis-related protein in human lung squamous carcinoma. Cancer Lett., 2009, 279(1), 65.
[21]
Li, M.X.; Xiao, Z.Q.; Chen, Y.H.; Peng, F.; Li, C.; Zhang, P.F.; Li, M.Y.; Li, F.; Duan, C.J.; Li, D.J. Proteomic analysis of the stroma-related proteins in nasopharyngeal carcinoma and normal nasopharyngeal epithelial tissues. Med. Oncol., 2010, 27(1), 134-144.
[22]
Liu, T.; Wu, H.J.; Liang, Y.; Liang, X.J.; Huang, H.C.; Zhao, Y.Z.; Liao, Q.C.; Chen, Y.Q.; Leng, A.M.; Yuan, W.J. Tumor-specific expression of sh VEGF and suicide gene as a novel strategy for esophageal cancer therapy. World J. Gastroenterol., 2016, 22(23), 5342.
[23]
Mi, H.; Lazarevaulitsky, B.; Loo, R.; Kejariwal, A.; Vandergriff, J.; Rabkin, S.; Guo, N.; Muruganujan, A.; Doremieux, O.; Campbell, M.J. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 2005, 33(Database issue), D284.
[24]
Minoru, K.; Michihiro, A.; Susumu, G.; Masahiro, H.; Mika, H.; Masumi, I.; Toshiaki, K.; Shuichi, K.; Shujiro, O.; Toshiaki, T. KEGG for linking genomes to life and the environment. Nucleic Acids Res., 2008, 36(Database issue), 480-484.
[25]
Li, B.; Dewey, C.N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 2011, 12(1), 323-323.
[26]
Eisen, M.B.; Botstein, D.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 1998, 14863-14868.
[27]
De Hoon, M.J.L.; Imoto, S.; Nolan, J.; Miyano, S. Open source clustering software. Bioinformatics, 2004, 20(9), 1453.
[28]
Saldanha, A.J. Java Treeview--Extensible visualization of microarray data. Bioinformatics, 2004, 20(17), 3246-3248.
[29]
Ye, J.; Fang, L.; Zheng, H.; Zhang, Y.; Chen, J.; Zhang, Z.; Wang, J.; Li, S.; Li, R.; Bolund, L. WEGO: A web tool for plotting GO annotations. Nucleic Acids Res, 2006. 34(Web Server issue), W293-W297.
[30]
Wang, S.; Xue, X.; Zhou, X.; Huang, T.; Du, C.; Yu, N.; Mo, Y.; Lin, L.; Zhang, J.; Ning, M. TFPI-2 is a putative tumor suppressor gene frequently inactivated by promoter hypermethylation in nasopharyngeal carcinoma. BMC Cancer, 2010, 10(1), 617.
[31]
Li, L.; Tao, Q.; Jin, H.; Van, H.A.; Poon, F.F.; Wang, X.; Zeng, M.S.; Jia, W.H.; Zeng, Y.X.; Chan, A.T. The tumor suppressor UCHL1 forms a complex with p53/MDM2/ARF to promote p53 signaling and is frequently silenced in nasopharyngeal carcinoma. Clin. Cancer Res., 2010, 16(11), 2949-2958.
[32]
Hong, L.L.; Cheng, Y.; Kumaran, M.K.; Liu, T.B.; Murakami, Y.; Chan, C.Y.; Yau, W.L.; Ko, J.M.Y.; Stanbridge, E.J.; Lung, M.L. Fine mapping of the 11q22–23 tumor suppressive region and involvement of TSLC1 in nasopharyngeal carcinoma. Int. J. Cancer, 2004, 112(4), 628-635.
[33]
Chang, H.W.; Chan, A.; Kwong, D.L.; Wei, W.I.; Sham, J.S.; Yuen, A.P. Evaluation of hypermethylated tumor suppressor genes as tumor markers in mouth and throat rinsing fluid, nasopharyngeal swab and peripheral blood of nasopharygeal carcinoma patient. Int. J. Cancer, 2003, 105(6), 851.
[34]
Wong, T.S.; Kwong, L.W.; Sham, S.T.; Wei, W.I.; Kwong, Y.L.; Yuen, P.W. Quantitative plasma hypermethylated DNA markers of undifferentiated nasopharyngeal carcinoma. Clin. Cancer Res., 2004, 10(7), 2401.
[35]
Kwong, J.; Lo, K.W.; To, K.F.; Teo, P.M.L.; Johnson, P.J.; Huang, D.P. Promoter hypermethylation of multiple genes in nasopharyngeal carcinoma. Clin. Cancer Res., 2002, 8(1), 131-137.
[36]
Ying, J.; Srivastava, G.; Hsieh, W.S.; Gao, Z.; Murray, P.; Liao, S.K.; Ambinder, R.; Tao, Q. The stress-responsive gene GADD45G is a functional tumor suppressor, with its response to environmental stresses frequently disrupted epigenetically in multiple tumors. Clin. Cancer Res., 2005, 11(18), 6442.
[37]
Law, E.W.L.; Cheung, A.K.L.; Kashuba, V.I.; Pavlova, T.V.; Zabarovsky, E.R.; Lung, H.L.; Cheng, Y.; Chua, D.; Kwong, D.L.; Tsao, S.W. Anti-angiogenic and tumor-suppressive roles of candidate tumor-suppressor gene, Fibulin-2, in nasopharyngeal carcinoma. Oncogene, 2012, 31(6), 728-738.
[38]
Jin, H.; Wang, X.; Ying, J.; Wong, A.H.Y.; Cui, Y.; Srivastava, G.; Shen, Z.Y.; Li, E.M.; Zhang, Q.; Jin, J. Epigenetic silencing of a Ca(2+)-regulated Ras GTPase-activating protein RASAL defines a new mechanism of Ras activation in human cancers. Proc. Natl. Acad. Sci. USA, 2007, 104(30), 12353-12358.
[39]
Yang, X.; Dai, W.; Kwong, D.L.W.; Szeto, C.Y.Y.; Wong, E.H.W.; Ng, W.T.; Lee, A.W.M.; Ngan, R.K.C.; Yau, C.C.; Tung, S.Y. Epigenetic markers for noninvasive early detection of nasopharyngeal carcinoma by methylation‐sensitive high resolution melting. Int. J. Cancer, 2015, 136(4), E127-E135.
[40]
Wong, V.C.L.; Chen, H.; Ko, J.M.Y.; Chan, K.W.; Chan, Y.P.; Law, S.; Chua, D.; Kwong, L.W.; Hong, L.L.; Srivastava, G.; Wong, V.C.; Chen, H.; Ko, J.M.; Chan, K.W.; Chan, Y.P.; Law, S. Tumor suppressor Dual-specificity Phosphatase 6 (DUSP6) impairs cell invasion and Epithelial-Mesenchymal Transition (EMT)-associated phenotype. Int. J. Cancer, 2012, 130(1), 83-95.
[41]
Wong, T.S.; Tang, K.C.; Kwong, D.L.; Sham, J.S.; Wei, W.I.; Kwong, Y.L.; Yuen, A.P. Differential gene methylation in undifferentiated nasopharyngeal carcinoma. Int. J. Oncol., 2003, 22(4), 869.
[42]
Cheung, A.K.; Lung, H.L.; Hung, S.C.; Law, E.W.; Cheng, Y.; Yau, W.L.; Bangarusamy, D.K.; Miller, L.D.; Liu, E.T.; Shao, J.Y. Functional analysis of a cell cycle-associated, tumor-suppressive gene, protein tyrosine phosphatase receptor type G, in nasopharyngeal carcinoma. Cancer Res., 2008, 68(19), 8137-8145.
[43]
Zhou, X.; Xue, X.; Huang, T.; Du, C.; Wang, S.; Mo, Y.; Ning, M.; Murata, M.; Bo, L.; Wen, W. Epigenetic inactivation of follistatin-like 1 mediates tumor immune evasion in nasopharyngeal carcinoma. Oncotarget, 2016, 7(13), 16433-16444.
[44]
Seng, T.J.; Low, J.S.W.; Li, H.; Cui, Y.; Goh, H.K.; Wong, M.L.Y.; Srivastava, G.; Sidransky, D.; Califano, J.; Steenbergen, R.D.M. The major 8p22 tumor suppressor DLC1 is frequently silenced by methylation in both endemic and sporadic nasopharyngeal, esophageal, and cervical carcinomas, and inhibits tumor cell colony formation. Oncogene, 2007, 26(6), 934.
[45]
Dai, W.; Cheung, A.K.; Ko, J.M.; Cheng, Y.; Zheng, H.; Ngan, R.K.; Ng, W.T.; Lee, A.W.; Yau, C.C.; Lee, V.H. Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma. Cancer Med., 2015, 4(7), 1079-1090.
[46]
Lo, K.W.; Tsang, Y.S.; Kwong, J.; To, K.F.; Teo, P.M.; Huang, D.P. Promoter hypermethylation of the EDNRB gene in nasopharyngeal carcinoma. Int. J. Cancer, 2002, 98(5), 651-655.
[47]
Lung, H.L.; Lo, C.C.; Wong, C.C.; Cheung, A.K.; Cheong, K.F.; Wong, N.; Kwong, F.M.; Chan, K.C.; Law, E.W.; Tsao, S.W. Identification of tumor suppressive activity by irradiation microcell-mediated chromosome transfer and involvement of alpha B-crystallin in nasopharyngeal carcinoma. Int. J. Cancer, 2008, 122(6), 1288-1296.
[48]
Muller, P.A.J.; Vousden, K.H. p53 mutations in cancer. Nat. Cell Biol., 2013, 15(1), 2-8.
[49]
Sun, Y.; Hegamyer, G.; Cheng, Y.J.; Hildesheim, A.; Chen, J.Y.; Chen, I.H.; Cao, Y.; Yao, K.T.; Colburn, N.H. An infrequent point mutation of the p53 gene in human nasopharyngeal carcinoma. Proc. Natl. Acad. Sci. USA, 1992, 89(14), 6516-6520.
[50]
De, S.H.; Nuyts, S. Radiosensitizing potential of epigenetic anticancer drugs. Anticancer. Agents Med. Chem., 2009, 9(1), 99-108.
[51]
Jiang, W.; Li, Y.Q.; Liu, N.; Sun, Y.; He, Q.M.; Jiang, N.; Xu, Y.F.; Chen, L.; Ma, J. 5-Azacytidine enhances the radiosensitivity of CNE2 and SUNE1 cells in vitro and in vivo possibly by altering DNA methylation. PLoS One, 2014, 9(4), e93273.