Epigenetic activation of POTE genes in ovarian cancer

References

• Cancer Facts and Figures 2013. American Cancer Society 2013.
   Google Scholar
• Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474:609–615.
   PubMed Web of Science ®Google Scholar
• Ciriello G, Miller ML, Aksoy BA, et al. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013;45:1127–1133.
   PubMed Web of Science ®Google Scholar
• Huang RL, Gu F, Kirma NB, et al. Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers. Epigenetics. 2013;8:624–634.
   PubMed Web of Science ®Google Scholar
• Widschwendter M, Jiang G, Woods C, et al. DNA hypomethylation and ovarian cancer biology. Cancer Res. 2004;64:4472–4480.
   PubMed Web of Science ®Google Scholar
• Nephew KP, Balch C, Zhang S, et al. Epigenetics and ovarian cancer. Cancer Treat Res. 2009;149:131–146.
   PubMedGoogle Scholar
• Woloszynska-Read A, Mhawech-Fauceglia P, Yu J, et al. Intertumor and intratumor NY-ESO-1 expression heterogeneity is associated with promoter-specific and global DNA methylation status in ovarian cancer. Clin Cancer Res off J Am Assoc Cancer Res. 2008;14:3283–3290.
   PubMed Web of Science ®Google Scholar
• Woloszynska-Read A, Zhang W, Yu J, et al. Coordinated cancer germline antigen promoter and global DNA hypomethylation in ovarian cancer: association with the BORIS/CTCF expression ratio and advanced stage. Clin Cancer Res off J Am Assoc Cancer Res. 2011;17:2170–2180.
   PubMed Web of Science ®Google Scholar
• Bera TK, Saint Fleur A, Lee Y, et al. POTE paralogs are induced and differentially expressed in many cancers. Cancer Res. 2006;66:52–56.
   PubMed Web of Science ®Google Scholar
• Bera TK, Zimonjic DB, Popescu NC, et al. POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer. Proc Natl Acad Sci U S A. 2002;99:16975–16980.
   PubMed Web of Science ®Google Scholar
• Hahn Y, Bera TK, Pastan IH, et al. Duplication and extensive remodeling shaped POTE family genes encoding proteins containing ankyrin repeat and coiled coil domains. Gene. 2006;366:238–245.
   PubMed Web of Science ®Google Scholar
• Bera TK, Saint Fleur A, Ha D, et al. Selective POTE paralogs on chromosome 2 are expressed in human embryonic stem cells. Stem Cells Dev. 2008;17:325–332.
   PubMed Web of Science ®Google Scholar
• Noris P, Perrotta S, Seri M, et al. Mutations in ANKRD26 are responsible for a frequent form of inherited thrombocytopenia: analysis of 78 patients from 21 families. Blood. 2011;117:6673–6680.
   PubMed Web of Science ®Google Scholar
• Pippucci T, Savoia A, Perrotta S, et al. Mutations in the 5’ UTR of ANKRD26, the ankirin repeat domain 26 gene, cause an autosomal-dominant form of inherited thrombocytopenia, THC2. Am J Hum Genet. 2011;88:115–120.
   PubMed Web of Science ®Google Scholar
• Lee Y, Ise T, Ha D, et al. Evolution and expression of chimeric POTE-actin genes in the human genome. Proc Natl Acad Sci U S A. 2006;103:17885–17890.
   PubMed Web of Science ®Google Scholar
• Bera TK, Huynh N, Maeda H, et al. Five POTE paralogs and their splice variants are expressed in human prostate and encode proteins of different lengths. Gene. 2004;337:45–53.
   PubMed Web of Science ®Google Scholar
• Das S, Ise T, Nagata S, et al. Palmitoylation of POTE family proteins for plasma membrane targeting. Biochem Biophys Res Commun. 2007;363:751–756.
   PubMed Web of Science ®Google Scholar
• Akers SN, Odunsi K, Karpf AR. Regulation of cancer germline antigen gene expression: implications for cancer immunotherapy. Future Oncol. 2010;6:717–732.
   PubMed Web of Science ®Google Scholar
• Simpson AJ, Caballero OL, Jungbluth A, et al. Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer. 2005;5:615–625.
   PubMed Web of Science ®Google Scholar
• Coulie PG, Van Den Eynde BJ, van der Bruggen P, et al. Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy. Nat Rev Cancer. 2014;14:135–146.
   PubMed Web of Science ®Google Scholar
• Saghafinia S, Mina M, Riggi N, et al. Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Rep. 2018;25:1066–80 e8.
   PubMed Web of Science ®Google Scholar
• Caballero OL, Cohen T, Gurung S, et al. Effects of CT-Xp gene knock down in melanoma cell lines. Oncotarget. 2013;4:531–541.
   PubMedGoogle Scholar
• Monte M, Simonatto M, Peche LY, et al. MAGE-A tumor antigens target p53 transactivation function through histone deacetylase recruitment and confer resistance to chemotherapeutic agents. Proc Natl Acad Sci U S A. 2006;103:11160–11165.
   PubMed Web of Science ®Google Scholar
• Doyle JM, Gao J, Wang J, et al. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. Mol Cell. 2010;39:963–974.
   PubMed Web of Science ®Google Scholar
• Bai S, He B, Wilson EM. Melanoma antigen gene protein MAGE-11 regulates androgen receptor function by modulating the interdomain interaction. Mol Cell Biol. 2005;25:1238–1257.
   PubMed Web of Science ®Google Scholar
• Shaw RJ. Tumor metabolism: MAGE-A proteins help TRIM turn over AMPK. Curr Biol. 2015;25:R418–R420.
   PubMed Web of Science ®Google Scholar
• Pineda CT, Ramanathan S, Fon Tacer K, et al. Degradation of AMPK by a cancer-specific ubiquitin ligase. Cell. 2015;160:715–728.
   PubMed Web of Science ®Google Scholar
• Whitehurst AW. Cause and consequence of cancer/testis antigen activation in cancer. Annu Rev Pharmacol Toxicol. 2014;54:251–272.
   PubMed Web of Science ®Google Scholar
• Lee AK, Potts PR. A comprehensive guide to the MAGE family of ubiquitin ligases. J Mol Biol. 2017;429:1114–1142.
   Web of Science ®Google Scholar
• Maine EA, Westcott JM, Prechtl AM, et al. The cancer-testis antigens SPANX-A/C/D and CTAG2 promote breast cancer invasion. Oncotarget. 2016;7:14708–14726.
   PubMedGoogle Scholar
• Maxfield KE, Taus PJ, Corcoran K, et al. Comprehensive functional characterization of cancer-testis antigens defines obligate participation in multiple hallmarks of cancer. Nat Commun. 2015;6:8840.
   PubMed Web of Science ®Google Scholar
• Cappell KM, Sinnott R, Taus P, et al. Multiple cancer testis antigens function to support tumor cell mitotic fidelity. Mol Cell Biol. 2012;32:4131–4140.
   PubMed Web of Science ®Google Scholar
• Whitehurst AW, Xie Y, Purinton SC, et al. Tumor antigen acrosin binding protein normalizes mitotic spindle function to promote cancer cell proliferation. Cancer Res. 2010;70:7652–7661.
   PubMed Web of Science ®Google Scholar
• Gibbs ZA, Whitehurst AW. Emerging contributions of cancer/testis antigens to neoplastic behaviors. Trends Cancer. 2018;4:701–712.
   PubMed Web of Science ®Google Scholar
• Van Tongelen A, Loriot A, De Smet C. Oncogenic roles of DNA hypomethylation through the activation of cancer-germline genes. Cancer Lett. 2017;396:130–137.
   PubMed Web of Science ®Google Scholar
• Barger CJ, Zhang W, Sharma A, et al. Expression of the POTE gene family in human ovarian cancer. Sci Rep. 2018;8:17136.
   PubMed Web of Science ®Google Scholar
• De Smet C, Loriot A. DNA hypomethylation and activation of germline-specific genes in cancer. Adv Exp Med Biol. 2013;754:149–166.
   PubMed Web of Science ®Google Scholar
• De Smet C, Lurquin C, Lethe B, et al. DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter. Mol Cell Biol. 1999;19:7327–7335.
   PubMed Web of Science ®Google Scholar
• De Smet C, De Backer O, Faraoni I, et al. The activation of human gene MAGE-1 in tumor cells is correlated with genome-wide demethylation. Proc Natl Acad Sci U S A. 1996;93:7149–7153.
   PubMed Web of Science ®Google Scholar
• Zhang W, Barger CJ, Eng KH, et al. PRAME expression and promoter hypomethylation in epithelial ovarian cancer. Oncotarget. 2016;7:45352–45369.
   PubMedGoogle Scholar
• Zhang W, Barger CJ, Link PA, et al. DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer. Epigenetics. 2015;10:736–748.
   PubMed Web of Science ®Google Scholar
• James SR, Cedeno CD, Sharma A, et al. DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11. Epigenetics. 2013;8:849–863.
   PubMed Web of Science ®Google Scholar
• Link PA, Zhang W, Odunsi K, et al. BORIS/CTCFL mRNA isoform expression and epigenetic regulation in epithelial ovarian cancer. Cancer Immun. 2013;13:6.
   PubMedGoogle Scholar
• Ademuyiwa FO, Bshara W, Attwood K, et al. NY-ESO-1 cancer testis antigen demonstrates high immunogenicity in triple negative breast cancer. PLoS One. 2012;7:e38783.
   PubMed Web of Science ®Google Scholar
• Karpf AR, Bai S, James SR, et al. Increased expression of androgen receptor coregulator MAGE-11 in prostate cancer by DNA hypomethylation and cyclic AMP. Mol Cancer Res. 2009;7:523–535.
   PubMed Web of Science ®Google Scholar
• Woloszynska-Read A, James SR, Link PA, et al. DNA methylation-dependent regulation of BORIS/CTCFL expression in ovarian cancer. Cancer Immun. 2007;7:21.
   PubMedGoogle Scholar
• Link PA, Gangisetty O, James SR, et al. Distinct roles for histone methyltransferases G9a and GLP in cancer germ-line antigen gene regulation in human cancer cells and murine embryonic stem cells. Mol Cancer Res. 2009;7:851–862.
   PubMed Web of Science ®Google Scholar
• Karpf AR. A potential role for epigenetic modulatory drugs in the enhancement of cancer/germ-line antigen vaccine efficacy. Epigenetics. 2006;1:116–120.
   PubMed Web of Science ®Google Scholar
• James SR, Link PA, Karpf AR. Epigenetic regulation of X-linked cancer/germline antigen genes by DNMT1 and DNMT3b. Oncogene. 2006;25:6975–6985.
   PubMed Web of Science ®Google Scholar
• Rao M, Chinnasamy N, Hong JA, et al. Inhibition of histone lysine methylation enhances cancer-testis antigen expression in lung cancer cells: implications for adoptive immunotherapy of cancer. Cancer Res. 2011;71:4192–4204.
   PubMed Web of Science ®Google Scholar
• Wischnewski F, Pantel K, Schwarzenbach H. Promoter demethylation and histone acetylation mediate gene expression of MAGE-A1, -A2, -A3, and -A12 in human cancer cells. Mol Cancer Res. 2006;4:339–349.
   PubMed Web of Science ®Google Scholar
• Dejardin J. Switching between Epigenetic States at Pericentromeric Heterochromatin. Trends Genet. 2015;31:661–672.
   PubMed Web of Science ®Google Scholar
• Nishiyama R, Qi L, Tsumagari K, et al. A DNA repeat, NBL2, is hypermethylated in some cancers but hypomethylated in others. Cancer Biol Ther. 2005;4:440–448.
   PubMed Web of Science ®Google Scholar
• Choi SH, Worswick S, Byun HM, et al. Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer. Int J Cancer J Inter Du Cancer. 2009;125:723–729.
   PubMed Web of Science ®Google Scholar
• Gadalla SM, Katki HA, Shebl FM, et al. The relationship between DNA methylation and telomere length in dyskeratosis congenita. Aging Cell. 2012;11:24–28.
   PubMed Web of Science ®Google Scholar
• Yang AS, Estecio MR, Doshi K, et al. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res. 2004;32:e38.
   PubMed Web of Science ®Google Scholar
• Patch AM, Christie EL, Etemadmoghadam D, et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature. 2015;521:489–494.
   PubMed Web of Science ®Google Scholar
• Bowtell DD, Bohm S, Ahmed AA, et al. Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer. Nat Rev Cancer. 2015;15:668–679.
   PubMed Web of Science ®Google Scholar
• Cameron EE, Bachman KE, Myohanen S, et al. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet. 1999;21:103–107.
   PubMed Web of Science ®Google Scholar
• Rhee I, Bachman KE, Park BH, et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature. 2002;416:552–556.
   PubMed Web of Science ®Google Scholar
• Song L, James SR, Kazim L, et al. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem. 2005;77:504–510.
   PubMed Web of Science ®Google Scholar
• Domcke S, Sinha R, Levine DA, et al. Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun. 2013;4:2126.
   PubMed Web of Science ®Google Scholar
• Verma SK, Tian X, LaFrance LV, et al. Identification of potent, selective, cell-active inhibitors of the histone lysine methyltransferase EZH2. ACS Med Chem Lett. 2012;3:1091–1096.
   PubMed Web of Science ®Google Scholar
• Kubicek S, O’Sullivan RJ, August EM, et al. Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase. Mol Cell. 2007;25:473–481.
   PubMed Web of Science ®Google Scholar
• Greiner D, Bonaldi T, Eskeland R, et al. Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9. Nat Chem Biol. 2005;1:143–145.
   PubMed Web of Science ®Google Scholar
• Wong NC, Wong LH, Quach JM, et al. Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation. PLoS Genet. 2006;2:e17.
   PubMed Web of Science ®Google Scholar
• Kondo T, Bobek MP, Kuick R, et al. Whole-genome methylation scan in ICF syndrome: hypomethylation of non-satellite DNA repeats D4Z4 and NBL2. Hum Mol Genet. 2000;9:597–604.
   PubMed Web of Science ®Google Scholar
• Han H, Cortez CC, Yang X, et al. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet. 2011;20:4299–4310.
   PubMed Web of Science ®Google Scholar
• Vo MC, Nguyen-Pham TN, Lee HJ, et al. Chaetocin enhances dendritic cell function via the induction of heat shock protein and cancer testis antigens in myeloma cells. Oncotarget. 2017;8:46047–46056.
   PubMedGoogle Scholar
• Redfield SM, Mao J, Zhu H, et al. The C-terminal common to group 3 POTES (CtG3P): a newly discovered nucleolar marker associated with malignant progression and metastasis. Am J Cancer Res. 2013;3:278–289.
   PubMed Web of Science ®Google Scholar
• Liu XF, Bera TK, Liu LJ, et al. A primate-specific POTE-actin fusion protein plays a role in apoptosis. Apoptosis. 2009;14:1237–1244.
   PubMed Web of Science ®Google Scholar
• Vekariya U, Rawat K, Saxena R, et al. Identification of MPhi specific POTEE expression: its role in mTORC2 activation via protein-protein interaction in TAMs. Cell Immunol. 2019;335:30–40.
   PubMed Web of Science ®Google Scholar
• Akers SN, Moysich K, Zhang W, et al. LINE1 and Alu repetitive element DNA methylation in tumors and white blood cells from epithelial ovarian cancer patients. Gynecol Oncol. 2014;132:462–467.
   PubMed Web of Science ®Google Scholar
• Barger CJ, Zhang W, Hillman J, et al. Genetic determinants of FOXM1 overexpression in epithelial ovarian cancer and functional contribution to cell cycle progression. Oncotarget. 2015;6:27613–27627.
   PubMedGoogle Scholar
• Dale RK, Pedersen BS, Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics. 2011;27:3423–3424.
   PubMed Web of Science ®Google Scholar
• Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842.
   PubMed Web of Science ®Google Scholar