臺灣博碩士論文加值系統

腫瘤發生為一癌症形成過程經由細胞本體、基因體、表觀基因體的改變造成細胞不正常分裂。基因體的不穩定及表觀基因體的修飾作用經由干擾正常程序的調節作用、破壞細胞生長與死亡的平衡、免疫反應的脫逃、能量代謝的重整、活化轉移能力及血管新生造成細胞突破正常分裂過程而失序。近年來，精準醫學採用量身訂做的方式來治療各種疾病包括癌症，也就是針對造成癌症所改變的基因為目標來研究標靶治療，冀以得到高本益比的治療效果。根據過去的研究報告指出發炎物質與癌症發生有高度相關性，且ALPK1的表現與發炎及各種相關疾病有關，而該基因座落於4q25區編碼為一新穎蛋白激?﹛A能特別針對具有富含alpha-螺旋二級結構的標的蛋白質進行磷酸化，因此，本研究乃針對ALPK1表現是否對腫瘤發生的影響，並進一步仔細檢查它的基因多型性，以更明確地了解其臨床意義。另一方面，在過去的研究中，TCH1036為一新合成的Indeno[1,2-c] quinoline衍生物並有抑制DNA拓撲異構??(DNA-topoisomerase)能力類似TCH1030在乳癌上的抑制機轉；gamma-bisabolene在口腔癌中能有效經由活化PP1 (protein phosphatases 1)來抑制HDAC2 (histone deacetylase 2)磷酸化，且進而誘導活化p53相關的口腔癌細胞凋亡。由於這兩種化合物均能有效地影響基因穩定性的特性，因此我們要進一步透過組蛋白修飾?﹞峊h氧核醣核酸甲基?〞漯穛{所造成的影響來了解兩個化合物包括TCH1036在抑制腦癌細胞(GBM)以及gamma-bisabolene抑制口腔癌細胞(Ca9-22)上表觀基因的調節是否扮演著重要角色。

Tumorigenesis is the formation of a cancer by changes at the cellular, genetic, and epigenetic levels leading to the abnormal cell division. According to the hall markers of cancer progression, genome instability and epigenetic modifications lead to cancer disrupt these orderly processes by disturbing the natural programming regulation, upsetting the normal balance between proliferation and cell death. Recently, the precision medicine has been tailored to the genomic changes in each person’s cancer. Most of studies are going on now to test whether treating patients with drugs that target the cancer-causing genetic changes in their tumors, that is, targeted therapies. In these years, several studies have indicated that the expression of ALPK1 located in the 4q25 region is related to inflammation and various diseases; therefore, the first section of this study is to determine whether the expression of ALPK1 has an influence on tumorigenesis and to further scrutinize its gene polymorphism in order to better understand its clinical importance. In addition, TCH1036, a newly synthesized Indeno[1,2-c]quinoline derivative, have previously been found to potentially trap DNA-topoisomerase cleavage complexes. Also, γ-bisabolene would suppress histone deacetylase 2 (HDAC2) by activating protein phosphatases 1 (PP1), and induce p53-mediated apoptosis of human oral squamous cell carcinoma in previous data. Therefore, the second section of this study is to explore whether the epigenetics regulation is involved with the mechanisms of the cancer suppression.

Table of Contents
page
LIST OF ILLUSTRATIONS IV.
LIST OF TABLES VII.
ACKNOWLEDGMENTS VIII.
ABSTRACT IN CHINESE IX.
ABSTRACT OF THE DISSERTATION X.
CHAPTER 1 INTRODUCTION
1.1 Tumorigenesis with genome instability 1.
1.2 The epigenetic regulations in the cancer progression 3.
1.3 Protein methylation as the important post-translational modifications 5.
1.4 The involvement of inflammation in the cancer progression 8.
1.5 The inflammation related to ALPK1 8.
1.6 The application of high resolution melting (HRM) analysis 9.
1.7 The epidemiology of the glioblastoma multiforme (GBM) 11.
1.8 The current treatment on the glioblastoma multiforme (GBM) 12.
1.9 The relation of the epigenetics and the glioblastoma multiforme (GBM) 12.
1.10 The regulation of the DNA methylation 17.
1.11 γ-bisabolene 17.
CHAPTER 2 MATERIAL AND METHODS
2.1 Sample preparation and DNA extraction 20.
2.2 Reverse-transcription for complementary DNA, and real-time quantitative Polymerase chainreaction (RT-qPCR) 20.
2.3 Design of ALPK1 exon primers for HRM assay 21.
2.4 The high resolution melting (HRM) technique and melting curve analysis 21.
2.5 Direct sequencing 22.
2.6 ALPK1 transfection and knockdown in the Lovo colorectal and A549 lung cancer cell lines 23.
2.7 Cell viability and wound healing assays 24.
2.8 Modeling of ALPK1 and evaluation of the functional impact of the mutant type 24.
2.9 Immunofluorescence Staining and microscopy 24.
2.10 Cell culture and DNA profiling 25.
2.11 Chemicals and reagents 26.
2.12 Cell viability analysis 27.
2.13 Cell cycle analysis 28.
2.14 Quantitative Polymerase Chain Reaction Analysis 28.
2.15 Western blot 29.
2.16 Differential analysis sets 30.
2.17 Molecular docking modeling 30.
2.18 Combined bisulfite restriction analysis (COBRA) assay 31.
2.19 Statistical analysis 32.
CHAPTER 3 RESULTS
3.1.1 Detection of ALPK1 mRNA level in clinical lung and colorectal cancer tissues 33.
3.1.2 Screening of ALPK1 mutations in clinical samples of lung and colorectal cancers
by HRM (high resolution melting) analysis 33.
3.1.3 Confirming the novel mutation sites of ALPK1 using the peripheral blood leukocytes
(PBL) of healthy people 34.
3.1.4 Prediction of the structural and functional alterations of the newly found ALPK1 mutants 35.
3.1.5 Exploring the impact of proliferation and migration in the alteration of the encoded
ALPK1 of the Lovo and A549 cancer cells 35.
3.1.6 Determining whether the actin distribution would be altered in the Lovo and A549 cancer cells with knockdown and overexpression of ALPK1 36.
3.2.1 Determining the cell cytotoxicity effects in various cancer cells treated with TCH1036, TCH1030 and TCH1259, respectively 37.
3.2.2 TCH1036 dose-dependently induced GBM cell cycle arrest in the G2/M phase, but not in the S-phase 38.
3.2.3 The mRNA level of histone-modifier related enzymes was determined in the GBM cells after respectively treating them with the TCH compounds 39.
3.2.4 The Determination of the expression of Suv39h1 and the cleaved form of PARP in the GBM cell treated with TCH compounds 40.
3.2.5 The virtual docking model implied that TCH 1036 could effectively hinder the catalytic domain in the PARP1 protein 40.
3.3.1 Growth inhibition of γ-bisabolene in human cancer cell lines 42.
3.3.2 Determination of gene expressions of histone modification-related and DNA methylation-related molecules in Ca9-22 and HepG2 cells after treating with
γ-bisabolene 42.
3.3.3 Regulation of γ-bisabolene on protein expressions of SET7, LSD1, DNMT1, and p53 lysine 372 mono-methylation in Ca9-22 and HepG2 cells 43.
3.3.4 DNMT1 mRNA level in oral cavity carcinoma and hepatoma cancer tissues, and computer simulation of γ-bisabolene docking to the ligand-binding pocket of
DNMT1 44.
3.3.5 Influence of γ-bisabolene on maintenance methylation in Ca9-22 and HepG2 cells 45.
CHAPTER 4 DISCUSSION 46.
CHAPTER 5 CONCLUSION AND IMPROVMENTS 54.
ABBREVIATIONS 58.
REFERNECES 104.

REFERENCES
1Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646-674, doi:10.1016/j.cell.2011.02.013 (2011).
2Burrell, R. A., McGranahan, N., Bartek, J. & Swanton, C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501, 338-345, doi:10.1038/nature12625 (2013).
3Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719-724, doi:10.1038/nature07943 (2009).
4Ashley, E. A. The precision medicine initiative: a new national effort. JAMA 313, 2119-2120, doi:10.1001/jama.2015.3595 (2015).
5Chappell, G., Kutanzi, K., Uehara, T., Tryndyak, V., Hong, H. H., Hoenerhoff, M., Beland, F. A., Rusyn, I. & Pogribny, I. P. Genetic and epigenetic changes in fibrosis-associated hepatocarcinogenesis in mice. International journal of cancer. Journal international du cancer 134, 2778-2788, doi:10.1002/ijc.28610 (2014).
6Guo, Y., Su, Z. Y. & Kong, A. T. Current Perspectives on Epigenetic Modifications by Dietary Chemopreventive and Herbal Phytochemicals. Current pharmacology reports 1, 245-257, doi:10.1007/s40495-015-0023-0 (2015).
7Szyf, M. DNA methylation and demethylation as targets for anticancer therapy. Biochemistry. Biokhimiia 70, 533-549 (2005).
8Wilting, R. H. & Dannenberg, J. H. Epigenetic mechanisms in tumorigenesis, tumor cell heterogeneity and drug resistance. Drug Resist Updat 15, 21-38, doi:10.1016/j.drup.2012.01.008 (2012).
9Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nature reviews. Genetics 8, 286-298, doi:10.1038/nrg2005 (2007).
10Wang, Y. & Shang, Y. Epigenetic control of epithelial-to-mesenchymal transition and cancer metastasis. Exp Cell Res 319, 160-169, doi:10.1016/j.yexcr.2012.07.019 (2013).
11Paschall, A. V. & Liu, K. Epigenetic Regulation of Apoptosis and Cell Cycle Regulatory Genes in Human Colon Carcinoma Cells. Genom Data 5, 189-191, doi:10.1016/j.gdata.2015.05.043 (2015).
12Rao-Bindal, K. & Kleinerman, E. S. Epigenetic regulation of apoptosis and cell cycle in osteosarcoma. Sarcoma 2011, 679457, doi:10.1155/2011/679457 (2011).
13Esteller, M., Garcia-Foncillas, J., Andion, E., Goodman, S. N., Hidalgo, O. F., Vanaclocha, V., Baylin, S. B. & Herman, J. G. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. The New England journal of medicine 343, 1350-1354, doi:10.1056/NEJM200011093431901 (2000).
14Dobrovic, A. & Simpfendorfer, D. Methylation of the BRCA1 gene in sporadic breast cancer. Cancer research 57, 3347-3350 (1997).
15Jaju, R. J., Fidler, C., Haas, O. A., Strickson, A. J., Watkins, F., Clark, K., Cross, N. C., Cheng, J. F., Aplan, P. D., Kearney, L., Boultwood, J. & Wainscoat, J. S. A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia. Blood 98, 1264-1267 (2001).
16Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J. R., Cole, P. A., Casero, R. A. & Shi, Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941-953, doi:10.1016/j.cell.2004.12.012 (2004).
17Hamamoto, R., Saloura, V. & Nakamura, Y. Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat Rev Cancer 15, 110-124, doi:10.1038/nrc3884 (2015).
18Yang, Y. & Bedford, M. T. Protein arginine methyltransferases and cancer. Nat Rev Cancer 13, 37-50, doi:10.1038/nrc3409 (2013).
19Hamamoto, R. & Nakamura, Y. Dysregulation of protein methyltransferases in human cancer: An emerging target class for anticancer therapy. Cancer Sci 107, 377-384, doi:10.1111/cas.12884 (2016).
20Lu, H., Ouyang, W. & Huang, C. Inflammation, a key event in cancer development. Molecular cancer research : MCR 4, 221-233, doi:10.1158/1541-7786.MCR-05-0261 (2006).
21Fernandes, J. V., Cobucci, R. N., Jatoba, C. A., de Medeiros Fernandes, T. A., de Azevedo, J. W. & de Araujo, J. M. The Role of the Mediators of Inflammation in Cancer Development. Pathol Oncol Res, doi:10.1007/s12253-015-9913-z (2015).
22Itzkowitz, S. H. & Yio, X. Inflammation and cancer IV. Colorectal cancer in inflammatory bowel disease: the role of inflammation. Am J Physiol Gastrointest Liver Physiol 287, G7-17, doi:10.1152/ajpgi.00079.2004 (2004).
23Borm, P. J. & Driscoll, K. Particles, inflammation and respiratory tract carcinogenesis. Toxicol Lett 88, 109-113 (1996).
24Ryazanov, A. G., Pavur, K. S. & Dorovkov, M. V. Alpha-kinases: a new class of protein kinases with a novel catalytic domain. Curr Biol 9, R43-45 (1999).
25Heine, M., Cramm-Behrens, C. I., Ansari, A., Chu, H. P., Ryazanov, A. G., Naim, H. Y. & Jacob, R. Alpha-kinase 1, a new component in apical protein transport. The Journal of biological chemistry 280, 25637-25643, doi:10.1074/jbc.M502265200 (2005).
26Wang, S. J., Tu, H. P., Ko, A. M., Chiang, S. L., Chiou, S. J., Lee, S. S., Tsai, Y. S., Lee, C. P. & Ko, Y. C. Lymphocyte alpha-kinase is a gout-susceptible gene involved in monosodium urate monohydrate-induced inflammatory responses. J Mol Med (Berl) 89, 1241-1251, doi:10.1007/s00109-011-0796-5 (2011).
27Ko, A. M., Tu, H. P., Liu, T. T., Chang, J. G., Yuo, C. Y., Chiang, S. L., Chang, S. J., Liu, Y. F., Ko, A. M., Lee, C. H., Lee, C. P., Chang, C. M., Tsai, S. F. & Ko, Y. C. ALPK1 genetic regulation and risk in relation to gout. Int J Epidemiol 42, 466-474, doi:10.1093/ije/dyt028 (2013).
28Yamada, Y., Nishida, T., Ichihara, S., Kato, K., Fujimaki, T., Oguri, M., Horibe, H., Yoshida, T., Watanabe, S., Satoh, K., Aoyagi, Y., Fukuda, M. & Sawabe, M. Identification of chromosome 3q28 and ALPK1 as susceptibility loci for chronic kidney disease in Japanese individuals by a genome-wide association study. J Med Genet 50, 410-418, doi:10.1136/jmedgenet-2013-101518 (2013).
29Fujimaki, T., Horibe, H., Oguri, M., Kato, K. & Yamada, Y. Association of genetic variants of the alpha-kinase 1 gene with myocardial infarction in community-dwelling individuals. Biomed Rep 2, 127-131, doi:10.3892/br.2013.190 (2014).
30Reed, G. H. & Wittwer, C. T. Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clinical chemistry 50, 1748-1754, doi:10.1373/clinchem.2003.029751 (2004).
31Chen, J. H., Cheng, V. C., Chan, J. F., She, K. K., Yan, M. K., Yau, M. C., Kwan, G. S., Yam, W. C. & Yuen, K. Y. The use of high-resolution melting analysis for rapid spa typing on methicillin-resistant Staphylococcus aureus clinical isolates. Journal of microbiological methods 92, 99-102, doi:10.1016/j.mimet.2012.11.006 (2013).
32White, H. E., Hall, V. J. & Cross, N. C. Methylation-sensitive high-resolution melting-curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes. Clinical chemistry 53, 1960-1962, doi:10.1373/clinchem.2007.093351 (2007).
33Hjelmso, M. H., Hansen, L. H., Baelum, J., Feld, L., Holben, W. E. & Jacobsen, C. S. High-resolution melt analysis for rapid comparison of bacterial community compositions. Applied and environmental microbiology 80, 3568-3575, doi:10.1128/AEM.03923-13 (2014).
34Druml, B. & Cichna-Markl, M. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis. Food Chem 158, 245-254, doi:10.1016/j.foodchem.2014.02.111 (2014).
35Reed, G. H., Kent, J. O. & Wittwer, C. T. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8, 597-608, doi:10.2217/14622416.8.6.597 (2007).
36Chang, Y. C., Chang, Y. S., Chang, C. C., Liu, T. C., Ko, Y. C., Lee, C. C., Chang, S. J. & Chang, J. G. Development of a high-resolution melting method for the screening of TNFAIP3 gene mutations. Oncology reports 35, 2936-2942, doi:10.3892/or.2016.4662 (2016).
37Chang, Y. S., Lin, C. Y., Yang, S. F., Ho, C. M. & Chang, J. G. High-resolution Melting Analysis for Gene Scanning of Adenomatous Polyposis Coli (APC) Gene With Oral Squamous Cell Carcinoma Samples. Appl Immunohistochem Mol Morphol 24, 97-104, doi:10.1097/PAI.0000000000000158 (2016).
38Montgomery, J. L., Sanford, L. N. & Wittwer, C. T. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 10, 219-240, doi:10.1586/erm.09.84 (2010).
39Louis, D. N., Ohgaki, H., Wiestler, O. D., Cavenee, W. K., Burger, P. C., Jouvet, A., Scheithauer, B. W. & Kleihues, P. The 2007 WHO classification of tumours of the central nervous system. Acta neuropathologica 114, 97-109, doi:10.1007/s00401-007-0243-4 (2007).
40Thakkar, J. P., Dolecek, T. A., Horbinski, C., Ostrom, Q. T., Lightner, D. D., Barnholtz-Sloan, J. S. & Villano, J. L. Epidemiologic and molecular prognostic review of glioblastoma. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 23, 1985-1996, doi:10.1158/1055-9965.EPI-14-0275 (2014).
41Chen, R., Cohen, A. L. & Colman, H. Targeted Therapeutics in Patients With High-Grade Gliomas: Past, Present, and Future. Curr Treat Options Oncol 17, 42, doi:10.1007/s11864-016-0418-0 (2016).
42Stevens, G. H. Antiepileptic therapy in patients with central nervous system malignancies. Current neurology and neuroscience reports 6, 311-318 (2006).
43Niyazi, M., Siefert, A., Schwarz, S. B., Ganswindt, U., Kreth, F. W., Tonn, J. C. & Belka, C. Therapeutic options for recurrent malignant glioma. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 98, 1-14, doi:10.1016/j.radonc.2010.11.006 (2011).
44Stupp, R., Mason, W. P., van den Bent, M. J., Weller, M., Fisher, B., Taphoorn, M. J., Belanger, K., Brandes, A. A., Marosi, C., Bogdahn, U., Curschmann, J., Janzer, R. C., Ludwin, S. K., Gorlia, T., Allgeier, A., Lacombe, D., Cairncross, J. G., Eisenhauer, E., Mirimanoff, R. O., European Organisation for, Research, Treatment of Cancer Brain, Tumor, Radiotherapy, Groups & National Cancer Institute of Canada Clinical Trials, Group. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. The New England journal of medicine 352, 987-996, doi:10.1056/NEJMoa043330 (2005).
45Ohgaki, H., Dessen, P., Jourde, B., Horstmann, S., Nishikawa, T., Di Patre, P. L., Burkhard, C., Schuler, D., Probst-Hensch, N. M., Maiorka, P. C., Baeza, N., Pisani, P., Yonekawa, Y., Yasargil, M. G., Lutolf, U. M. & Kleihues, P. Genetic pathways to glioblastoma: a population-based study. Cancer research 64, 6892-6899, doi:10.1158/0008-5472.CAN-04-1337 (2004).
46Zhao, H., Rybak, P., Dobrucki, J., Traganos, F. & Darzynkiewicz, Z. Relationship of DNA damage signaling to DNA replication following treatment with DNA topoisomerase inhibitors camptothecin/topotecan, mitoxantrone, or etoposide. Cytometry. Part A : the journal of the International Society for Analytical Cytology 81, 45-51, doi:10.1002/cyto.a.21172 (2012).
47Lesimple, T., Riffaud, L., Frappaz, D., Ben Hassel, M., Gedouin, D., Bay, J. O., Linassier, C., Hamlat, A., Piot, G., Fabbro, M., Saikali, S., Carsin, B. & Guegan, Y. Topotecan in combination with radiotherapy in unresectable glioblastoma: a phase 2 study. Journal of neuro-oncology 93, 253-260, doi:10.1007/s11060-008-9774-3 (2009).
48Spyropoulou, A., Piperi, C., Adamopoulos, C. & Papavassiliou, A. G. Deregulated chromatin remodeling in the pathobiology of brain tumors. Neuromolecular medicine 15, 1-24, doi:10.1007/s12017-012-8205-y (2013).
49Turner, B. M. Reading signals on the nucleosome with a new nomenclature for modified histones. Nature structural & molecular biology 12, 110-112, doi:10.1038/nsmb0205-110 (2005).
50Wang, G. G., Allis, C. D. & Chi, P. Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling. Trends in molecular medicine 13, 373-380, doi:10.1016/j.molmed.2007.07.004 (2007).
51Nagarajan, R. P. & Costello, J. F. Epigenetic mechanisms in glioblastoma multiforme. Seminars in cancer biology 19, 188-197, doi:10.1016/j.semcancer.2009.02.005 (2009).
52Northcott, P. A., Nakahara, Y., Wu, X., Feuk, L., Ellison, D. W., Croul, S., Mack, S., Kongkham, P. N., Peacock, J., Dubuc, A., Ra, Y. S., Zilberberg, K., McLeod, J., Scherer, S. W., Sunil Rao, J., Eberhart, C. G., Grajkowska, W., Gillespie, Y., Lach, B., Grundy, R., Pollack, I. F., Hamilton, R. L., Van Meter, T., Carlotti, C. G., Boop, F., Bigner, D., Gilbertson, R. J., Rutka, J. T. & Taylor, M. D. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nature genetics 41, 465-472, doi:10.1038/ng.336 (2009).
53Lu, C., Ward, P. S., Kapoor, G. S., Rohle, D., Turcan, S., Abdel-Wahab, O., Edwards, C. R., Khanin, R., Figueroa, M. E., Melnick, A., Wellen, K. E., O''Rourke, D. M., Berger, S. L., Chan, T. A., Levine, R. L., Mellinghoff, I. K. & Thompson, C. B. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483, 474-478, doi:10.1038/nature10860 (2012).
54Tseng, C. H., Tzeng, C. C., Yang, C. L., Lu, P. J., Chen, H. L., Li, H. Y., Chuang, Y. C., Yang, C. N. & Chen, Y. L. Synthesis and antiproliferative evaluation of certain indeno[1,2-c]quinoline derivatives. Part 2. Journal of medicinal chemistry 53, 6164-6179, doi:10.1021/jm1005447 (2010).
55Tseng, C. H., Chen, Y. L., Lu, P. J., Yang, C. N. & Tzeng, C. C. Synthesis and antiproliferative evaluation of certain indeno[1,2-c]quinoline derivatives. Bioorganic & medicinal chemistry 16, 3153-3162, doi:10.1016/j.bmc.2007.12.028 (2008).
56Liu, Y. P., Chen, H. L., Tzeng, C. C., Lu, P. J., Lo, C. W., Lee, Y. C., Tseng, C. H., Chen, Y. L. & Yang, C. N. TCH-1030 targeting on topoisomerase I induces S-phase arrest, DNA fragmentation, and cell death of breast cancer cells. Breast cancer research and treatment 138, 383-393, doi:10.1007/s10549-013-2441-1 (2013).
57Miremadi, A., Oestergaard, M. Z., Pharoah, P. D. & Caldas, C. Cancer genetics of epigenetic genes. Human molecular genetics 16 Spec No 1, R28-49, doi:10.1093/hmg/ddm021 (2007).
58Wang, J., Hevi, S., Kurash, J. K., Lei, H., Gay, F., Bajko, J., Su, H., Sun, W., Chang, H., Xu, G., Gaudet, F., Li, E. & Chen, T. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nature genetics 41, 125-129, doi:10.1038/ng.268 (2009).
59Subramaniam, D., Thombre, R., Dhar, A. & Anant, S. DNA methyltransferases: a novel target for prevention and therapy. Frontiers in oncology 4, 80, doi:10.3389/fonc.2014.00080 (2014).
60Shukla, S., Meeran, S. M. & Katiyar, S. K. Epigenetic regulation by selected dietary phytochemicals in cancer chemoprevention. Cancer letters 355, 9-17, doi:10.1016/j.canlet.2014.09.017 (2014).
61McEnroe, Frank J. & Fenical, William. Structures and synthesis of some new antibacterial sesquiterpenoids from the gorgonian coral Pseudopterogorgia rigida. Tetrahedron 34, 1661-1664, doi:http://dx.doi.org/10.1016/0040-4020(78)80198-7 (1978).
62Yeo, S. K., Ali, A. Y., Hayward, O. A., Turnham, D., Jackson, T., Bowen, I. D. & Clarkson, R. beta-Bisabolene, a Sesquiterpene from the Essential Oil Extract of Opoponax (Commiphora guidottii), Exhibits Cytotoxicity in Breast Cancer Cell Lines. Phytother Res 30, 418-425, doi:10.1002/ptr.5543 (2016).
63Jou, Y. J., Chen, C. J., Liu, Y. C., Way, T. D., Lai, C. H., Hua, C. H., Wang, C. Y., Huang, S. H., Kao, J. Y. & Lin, C. W. Quantitative phosphoproteomic analysis reveals gamma-bisabolene inducing p53-mediated apoptosis of human oral squamous cell carcinoma via HDAC2 inhibition and ERK1/2 activation. Proteomics 15, 3296-3309, doi:10.1002/pmic.201400568 (2015).
64Lin, Y. C., Er, T. K., Yeh, K. T., Hung, C. H. & Chang, J. G. Rapid Identification of FGFR2 Gene Mutations in Taiwanese Patients With Endometrial Cancer Using High-resolution Melting Analysis. Appl Immunohistochem Mol Morphol, doi:10.1097/PAI.0000000000000114 (2014).
65Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J. & Zhang, Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods 12, 7-8, doi:10.1038/nmeth.3213 (2015).
66Choi, Y. & Chan, A. P. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics, doi:10.1093/bioinformatics/btv195 (2015).
67Capriotti, E., Fariselli, P. & Casadio, R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33, W306-310, doi:10.1093/nar/gki375 (2005).
68Lin, W. D., Wu, J. Y., Tsai, F. J., Gau, M. T. & Lee, C. C. Type identification of autosomal dominant polycystic kidney disease by analysis of fluorescent short tandem repeat markers. Journal of the Formosan Medical Association = Taiwan yi zhi 101, 567-571 (2002).
69Tseng, C. H., Tzeng, C. C., Yang, C. L., Lu, P. J., Liu, Y. P., Chen, H. L., Chen, C. Y., Yang, C. N. & Chen, Y. L. Discovery of indeno[1, 2 - c] quinoline derivatives as dual topoisomerases I/II inhibitors: part 3. Molecular diversity 17, 781-799, doi:10.1007/s11030-013-9475-5 (2013).
70Papeo, G., Posteri, H., Borghi, D., Busel, A. A., Caprera, F., Casale, E., Ciomei, M., Cirla, A., Corti, E., D''Anello, M., Fasolini, M., Forte, B., Galvani, A., Isacchi, A., Khvat, A., Krasavin, M. Y., Lupi, R., Orsini, P., Perego, R., Pesenti, E., Pezzetta, D., Rainoldi, S., Riccardi-Sirtori, F., Scolaro, A., Sola, F., Zuccotto, F., Felder, E. R., Donati, D. & Montagnoli, A. Discovery of 2-[1-(4,4-Difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoind ole-4-carboxamide (NMS-P118): A Potent, Orally Available, and Highly Selective PARP-1 Inhibitor for Cancer Therapy. Journal of medicinal chemistry 58, 6875-6898, doi:10.1021/acs.jmedchem.5b00680 (2015).
71Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry 31, 455-461, doi:10.1002/jcc.21334 (2010).
72Yang, A. S., Estecio, M. R., Doshi, K., Kondo, Y., Tajara, E. H. & Issa, J. P. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32, e38, doi:10.1093/nar/gnh032 (2004).
73Mazzolini, R., Dopeso, H., Mateo-Lozano, S., Chang, W., Rodrigues, P., Bazzocco, S., Alazzouzi, H., Landolfi, S., Hernandez-Losa, J., Andretta, E., Alhopuro, P., Espin, E., Armengol, M., Tabernero, J., Ramon y Cajal, S., Kloor, M., Gebert, J., Mariadason, J. M., Schwartz, S., Jr., Aaltonen, L. A., Mooseker, M. S. & Arango, D. Brush border myosin Ia has tumor suppressor activity in the intestine. Proceedings of the National Academy of Sciences of the United States of America 109, 1530-1535, doi:10.1073/pnas.1108411109 (2012).
74Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074-1080, doi:10.1126/science.1063127 (2001).
75Murata-Hori, M., Tatsuka, M. & Wang, Y. L. Probing the dynamics and functions of aurora B kinase in living cells during mitosis and cytokinesis. Molecular biology of the cell 13, 1099-1108, doi:10.1091/mbc.01-09-0467 (2002).
76Morey, L. & Helin, K. Polycomb group protein-mediated repression of transcription. Trends in biochemical sciences 35, 323-332, doi:10.1016/j.tibs.2010.02.009 (2010).
77Spyropoulou, A., Gargalionis, A., Dalagiorgou, G., Adamopoulos, C., Papavassiliou, K. A., Lea, R. W., Piperi, C. & Papavassiliou, A. G. Role of histone lysine methyltransferases SUV39H1 and SETDB1 in gliomagenesis: modulation of cell proliferation, migration, and colony formation. Neuromolecular medicine 16, 70-82, doi:10.1007/s12017-013-8254-x (2014).
78Chassot, A., Canale, S., Varlet, P., Puget, S., Roujeau, T., Negretti, L., Dhermain, F., Rialland, X., Raquin, M. A., Grill, J. & Dufour, C. Radiotherapy with concurrent and adjuvant temozolomide in children with newly diagnosed diffuse intrinsic pontine glioma. Journal of neuro-oncology 106, 399-407, doi:10.1007/s11060-011-0681-7 (2012).
79Murai, J., Zhang, Y., Morris, J., Ji, J., Takeda, S., Doroshow, J. H. & Pommier, Y. Rationale for poly(ADP-ribose) polymerase (PARP) inhibitors in combination therapy with camptothecins or temozolomide based on PARP trapping versus catalytic inhibition. The Journal of pharmacology and experimental therapeutics 349, 408-416, doi:10.1124/jpet.113.210146 (2014).
80Leonetti, C., Biroccio, A., Graziani, G. & Tentori, L. Targeted therapy for brain tumours: role of PARP inhibitors. Current cancer drug targets 12, 218-236 (2012).
81Pradhan, S., Chin, H. G., Esteve, P. O. & Jacobsen, S. E. SET7/9 mediated methylation of non-histone proteins in mammalian cells. Epigenetics : official journal of the DNA Methylation Society 4, 383-387 (2009).
82Peng, C. H., Liao, C. T., Peng, S. C., Chen, Y. J., Cheng, A. J., Juang, J. L., Tsai, C. Y., Chen, T. C., Chuang, Y. J., Tang, C. Y., Hsieh, W. P. & Yen, T. C. A novel molecular signature identified by systems genetics approach predicts prognosis in oral squamous cell carcinoma. PloS one 6, e23452, doi:10.1371/journal.pone.0023452 (2011).
83Toruner, G. A., Ulger, C., Alkan, M., Galante, A. T., Rinaggio, J., Wilk, R., Tian, B., Soteropoulos, P., Hameed, M. R., Schwalb, M. N. & Dermody, J. J. Association between gene expression profile and tumor invasion in oral squamous cell carcinoma. Cancer genetics and cytogenetics 154, 27-35, doi:10.1016/j.cancergencyto.2004.01.026 (2004).
84Roessler, S., Jia, H. L., Budhu, A., Forgues, M., Ye, Q. H., Lee, J. S., Thorgeirsson, S. S., Sun, Z., Tang, Z. Y., Qin, L. X. & Wang, X. W. A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer research 70, 10202-10212, doi:10.1158/0008-5472.CAN-10-2607 (2010).
85Laird, P. W., Jackson-Grusby, L., Fazeli, A., Dickinson, S. L., Jung, W. E., Li, E., Weinberg, R. A. & Jaenisch, R. Suppression of intestinal neoplasia by DNA hypomethylation. Cell 81, 197-205 (1995).
86Ramchandani, S., MacLeod, A. R., Pinard, M., von Hofe, E. & Szyf, M. Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide. Proceedings of the National Academy of Sciences of the United States of America 94, 684-689 (1997).
87Wodarz, A. & Nathke, I. Cell polarity in development and cancer. Nat Cell Biol 9, 1016-1024, doi:10.1038/ncb433 (2007).
88Mazzolini, R., Rodrigues, P., Bazzocco, S., Dopeso, H., Ferreira, A. M., Mateo-Lozano, S., Andretta, E., Woerner, S. M., Alazzouzi, H., Landolfi, S., Hernandez-Losa, J., Macaya, I., Suzuki, H., Ramon y Cajal, S., Mooseker, M. S., Mariadason, J. M., Gebert, J., Hofstra, R. M., Reventos, J., Yamamoto, H., Schwartz, S., Jr. & Arango, D. Brush border myosin Ia inactivation in gastric but not endometrial tumors. International journal of cancer. Journal international du cancer 132, 1790-1799, doi:10.1002/ijc.27856 (2013).
89Rea, S., Eisenhaber, F., O''Carroll, D., Strahl, B. D., Sun, Z. W., Schmid, M., Opravil, S., Mechtler, K., Ponting, C. P., Allis, C. D. & Jenuwein, T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593-599, doi:10.1038/35020506 (2000).
90Czvitkovich, S., Sauer, S., Peters, A. H., Deiner, E., Wolf, A., Laible, G., Opravil, S., Beug, H. & Jenuwein, T. Over-expression of the SUV39H1 histone methyltransferase induces altered proliferation and differentiation in transgenic mice. Mechanisms of development 107, 141-153 (2001).
91Chu, L., Zhu, T., Liu, X., Yu, R., Bacanamwo, M., Dou, Z., Chu, Y., Zou, H., Gibbons, G. H., Wang, D., Ding, X. & Yao, X. SUV39H1 orchestrates temporal dynamics of centromeric methylation essential for faithful chromosome segregation in mitosis. Journal of molecular cell biology 4, 331-340, doi:10.1093/jmcb/mjs023 (2012).
92de Murcia, G., Menissier-de Murcia, J. & Schreiber, V. Poly(ADP-ribose) polymerase: molecular biological aspects. BioEssays : news and reviews in molecular, cellular and developmental biology 13, 455-462, doi:10.1002/bies.950130905 (1991).
93Tangutoori, S., Baldwin, P. & Sridhar, S. PARP inhibitors: A new era of targeted therapy. Maturitas 81, 5-9, doi:10.1016/j.maturitas.2015.01.015 (2015).
94Ratnam, K. & Low, J. A. Current development of clinical inhibitors of poly(ADP-ribose) polymerase in oncology. Clinical cancer research : an official journal of the American Association for Cancer Research 13, 1383-1388, doi:10.1158/1078-0432.CCR-06-2260 (2007).
95Cimmino, G., Pepe, S., Laus, G., Chianese, M., Prece, D., Penitente, R. & Quesada, P. Poly(ADPR)polymerase-1 signalling of the DNA damage induced by DNA topoisomerase I poison in D54(p53wt) and U251(p53mut) glioblastoma cell lines. Pharmacological research 55, 49-56, doi:10.1016/j.phrs.2006.10.005 (2007).
96Tentori, L., Leonetti, C., Scarsella, M., Muzi, A., Mazzon, E., Vergati, M., Forini, O., Lapidus, R., Xu, W., Dorio, A. S., Zhang, J., Cuzzocrea, S. & Graziani, G. Inhibition of poly(ADP-ribose) polymerase prevents irinotecan-induced intestinal damage and enhances irinotecan/temozolomide efficacy against colon carcinoma. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20, 1709-1711, doi:10.1096/fj.06-5916fje (2006).
97Sabbatino, F., Fusciello, C., Somma, D., Pacelli, R., Poudel, R., Pepin, D., Leonardi, A., Carlomagno, C., Della Vittoria Scarpati, G., Ferrone, S. & Pepe, S. Effect of p53 activity on the sensitivity of human glioblastoma cells to PARP-1 inhibitor in combination with topoisomerase I inhibitor or radiation. Cytometry. Part A : the journal of the International Society for Analytical Cytology 85, 953-961, doi:10.1002/cyto.a.22563 (2014).
98Link, A., Balaguer, F. & Goel, A. Cancer chemoprevention by dietary polyphenols: promising role for epigenetics. Biochemical pharmacology 80, 1771-1792, doi:10.1016/j.bcp.2010.06.036 (2010).
99Tollefsbol, T. O. Dietary epigenetics in cancer and aging. Cancer treatment and research 159, 257-267, doi:10.1007/978-3-642-38007-5_15 (2014).
100Anderson, O. S., Sant, K. E. & Dolinoy, D. C. Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation. The Journal of nutritional biochemistry 23, 853-859, doi:10.1016/j.jnutbio.2012.03.003 (2012).
101Urvalek, A., Laursen, K. B. & Gudas, L. J. The roles of retinoic acid and retinoic acid receptors in inducing epigenetic changes. Sub-cellular biochemistry 70, 129-149, doi:10.1007/978-94-017-9050-5_7 (2014).
102Henning, S. M., Wang, P., Carpenter, C. L. & Heber, D. Epigenetic effects of green tea polyphenols in cancer. Epigenomics 5, 729-741, doi:10.2217/epi.13.57 (2013).
103Lv, T., Yuan, D., Miao, X., Lv, Y., Zhan, P., Shen, X. & Song, Y. Over-expression of LSD1 promotes proliferation, migration and invasion in non-small cell lung cancer. PloS one 7, e35065, doi:10.1371/journal.pone.0035065 (2012).
104Schulte, J. H., Lim, S., Schramm, A., Friedrichs, N., Koster, J., Versteeg, R., Ora, I., Pajtler, K., Klein-Hitpass, L., Kuhfittig-Kulle, S., Metzger, E., Schule, R., Eggert, A., Buettner, R. & Kirfel, J. Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer research 69, 2065-2071, doi:10.1158/0008-5472.CAN-08-1735 (2009).
105Zhao, Z. K., Dong, P., Gu, J., Chen, L., Zhuang, M., Lu, W. J., Wang, D. R. & Liu, Y. B. Overexpression of LSD1 in hepatocellular carcinoma: a latent target for the diagnosis and therapy of hepatoma. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 34, 173-180, doi:10.1007/s13277-012-0525-x (2013).
106Kurash, J. K., Lei, H., Shen, Q., Marston, W. L., Granda, B. W., Fan, H., Wall, D., Li, E. & Gaudet, F. Methylation of p53 by Set7/9 mediates p53 acetylation and activity in vivo. Molecular cell 29, 392-400, doi:10.1016/j.molcel.2007.12.025 (2008).
107Binda, O. On your histone mark, SET, methylate! Epigenetics 8, 457-463, doi:10.4161/epi.24451 (2013).
108Jin, L., Hanigan, C. L., Wu, Y., Wang, W., Park, B. H., Woster, P. M. & Casero, R. A. Loss of LSD1 (lysine-specific demethylase 1) suppresses growth and alters gene expression of human colon cancer cells in a p53- and DNMT1(DNA methyltransferase 1)-independent manner. The Biochemical journal 449, 459-468, doi:10.1042/BJ20121360 (2013).
109Jones, P. A. & Gonzalgo, M. L. Altered DNA methylation and genome instability: a new pathway to cancer? Proceedings of the National Academy of Sciences of the United States of America 94, 2103-2105 (1997).
110Chmelarova, M., Krepinska, E., Spacek, J., Laco, J., Beranek, M. & Palicka, V. Methylation in the p53 promoter in epithelial ovarian cancer. Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 15, 160-163, doi:10.1007/s12094-012-0894-z (2013).
111Chik, F. & Szyf, M. Effects of specific DNMT gene depletion on cancer cell transformation and breast cancer cell invasion; toward selective DNMT inhibitors. Carcinogenesis 32, 224-232, doi:10.1093/carcin/bgq221 (2011).
112Cheishvili, D., Boureau, L. & Szyf, M. DNA demethylation and invasive cancer: implications for therapeutics. Br J Pharmacol 172, 2705-2715, doi:10.1111/bph.12885 (2015).