Clinical significance of DNA methylation mRNA levels of TET family members in colorectal cancer

Journal of Cancer Research and Clinical Oncology

Volumn 141, Issue 8, 2015, Pages 1379-1392

  Rawłuszko Wieczorek, Agnieszka Anna ^a   Siera, Agnieszka ^a   Horbacka, Karolina ^a   Horst, Nikodem ^a   Krokowicz, Piotr ^a   Jagodziński, Paweł Piotr ^a  

^a POZNAN UNIVERSITY OF MEDICAL SCIENCES   (Poland)

Author keywords

Colorectal cancer; DNA methylation; Prognostic factor; TET enzymes

Indexed keywords

ENZYME; MESSENGER RNA; TEN ELEVEN TRANSLOCATION 1 ENZYME; TEN ELEVEN TRANSLOCATION 2 ENZYME; TEN ELEVEN TRANSLOCATION 3 ENZYME; UNCLASSIFIED DRUG; DIOXYGENASE; DNA BINDING PROTEIN; ONCOPROTEIN; TET1 PROTEIN, HUMAN; TET2 PROTEIN, HUMAN; TET3 PROTEIN, HUMAN;

AGED; ARTICLE; CANCER LOCALIZATION; CANCER STAGING; CANCER SURVIVAL; COLORECTAL CANCER; CPG ISLAND; DISEASE FREE SURVIVAL; DNA METHYLATION; DNA SEQUENCE; FEMALE; FOLLOW UP; GENETIC TRANSCRIPTION; HIGH RESOLUTION MELTING ANALYSIS; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MALE; OVERALL SURVIVAL; PRIORITY JOURNAL; PROMOTER REGION; COLORECTAL NEOPLASMS; GENE EXPRESSION REGULATION; GENETICS; MIDDLE AGED; MORTALITY; MULTIGENE FAMILY; PATHOLOGY; PROGNOSIS;

AGED; COLORECTAL NEOPLASMS; DIOXYGENASES; DNA METHYLATION; DNA-BINDING PROTEINS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MALE; MIDDLE AGED; MULTIGENE FAMILY; PROGNOSIS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEINS; RNA, MESSENGER;

EID: 84931571827     PISSN: 01715216     EISSN: 14321335     Source Type: Journal    
DOI: 10.1007/s00432-014-1901-2     Document Type: Article

References (47)

1. Abdel-Wahab O et al (2009) Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 114:144–147
2. Asmar F et al (2013) Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma. Haematologica 98:1912–1920. doi:10.3324/haematol.2013.088740
3. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (Oxford, England) 21:4067–4068
4. Calabrese R et al (2014) TET2 gene expression and 5-hydroxymethylcytosine level in multiple sclerosis peripheral blood cells. Biochim Biophys Acta 1842:1130–1136. doi:10.1016/j.bbadis.2014.04.010
5. Chim CS, Wan TS, Fung TK, Wong KF (2010) Methylation of TET2, CBL and CEBPA in Ph-negative myeloproliferative neoplasms. J Clin Pathol 63:942–946. doi:10.1136/jcp.2010.080218
6. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction. Anal Biochem 162:156–159
7. Ciccarone F et al (2014) Poly(ADP-ribosyl)ation is involved in the epigenetic control of TET1 gene transcription. Oncotarget 5:10356–10367
8. Couronne L, Bastard C, Bernard OA (2012) TET2 and DNMT3A mutations in human T-cell lymphoma. N Engl J Med 366:95–96. doi:10.1056/NEJMc1111708
9. CpGPlot/CpGReport/Isochore E. http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/
10. Dawson MA, Kouzarides T (2012) Cancer epigenetics: from mechanism to therapy. Cell 150:12–27
11. Delatte B, Deplus R, Fuks F (2014) Playing TETris with DNA modifications. EMBO J 33:1198–1211
12. Delhommeau F et al (2009) Mutation in TET2 in myeloid cancers. N Engl J Med 360:2289–2301
13. Distler P, Holt PR (1997) Are right- and left-sided colon neoplasms distinct tumors? Dig Dis 15:302–311
14. Frycz BA et al (2014) Decreased expression of ten-eleven translocation 1 protein is associated with some clinicopathological features in gastric cancer. Biomed Pharmacother 68:209–212. doi:10.1016/j.biopha.2013.12.011
15. Glebov OK et al (2003) Distinguishing right from left colon by the pattern of gene expression. Cancer Epidemiol Biomarkers Prev 12:755–762
16. Guo JU, Su Y, Zhong C, Ming GL, Song H (2011) Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145:423–434
17. Hashimoto H et al (2012) Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res 40:4841–4849. doi:10.1093/nar/gks155
18. He YF et al (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science (New York, NY) 333:1303–1307
19. Hsu CH et al (2012) TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. Cell Reports 2:568–579
20. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466:1129–1133
21. Ito S et al (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333:1300–1303
22. Jankowska AM et al (2009) Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 113:6403–6410. doi:10.1182/blood-2009-02-205690
23. Jass JR (2007) Classification of colorectal cancer based on correlation of clinical, morphological and molecular features. Histopathology 50:113–130. doi:10.1111/j.1365-2559.2006.02549.x
24. Ko M et al (2011) Ten-eleven-translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice. Proc Natl Acad Sci USA 108:14566–14571
25. Kudo Y et al (2012) Loss of 5-hydroxymethylcytosine is accompanied with malignant cellular transformation. Cancer Sci 103:670–676. doi:10.1111/j.1349-7006.2012.02213.x
26. Langemeijer SM et al (2009) Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 41:838–842
27. Lian CG et al (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150:1135–1146
28. Linhart HG et al (2007) Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev 21:3110–3122
29. Liu C et al (2013) Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One 8:e62828. doi:10.1371/journal.pone.0062828
30. Migliore L, Migheli F, Spisni R, Coppede F (2011) Genetics, cytogenetics, and epigenetics of colorectal cancer. J Biomed Biotechnol 2011:792362
31. Moran-Crusio K et al (2011) Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 20:11–24
32. Muller T et al (2012) Nuclear exclusion of TET1 is associated with loss of 5-hydroxymethylcytosine in IDH1 wild-type gliomas. Am J Pathol 181:675–683. doi:10.1016/j.ajpath.2012.04.017
33. Musialik E, Bujko M, Wypych A, Matysiak M, Siedlecki JA (2014) TET2 promoter DNA methylation and expression analysis in pediatric B-cell acute lymphoblastic leukemia. Hematol Rep 6:5333. doi:10.4081/hr.2014.5333
34. Orr BA, Haffner MC, Nelson WG, Yegnasubramanian S, Eberhart CG (2012) Decreased 5-hydroxymethylcytosine is associated with neural progenitor phenotype in normal brain and shorter survival in malignant glioma. PLoS One 7:e41036. doi:10.1371/journal.pone.0041036
35. Papaxoinis K, Triantafyllou K, Sasco AJ, Nicolopoulou-Stamati P, Ladas SD (2010) Subsite-specific differences of estrogen receptor beta expression in the normal colonic epithelium: implications for carcinogenesis and colorectal cancer epidemiology. Eur J Gastroenterol Hepatol 22:614–619. doi:10.1097/MEG.0b013e328335ef50
36. Putiri EL, Tiedemann RL, Thompson JJ, Liu C, Ho T, Choi JH, Robertson KD (2014) Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol 15:R81
37. Rawluszko AA, Horbacka K, Krokowicz P, Jagodzinski PP (2011) Decreased expression of 17-beta-hydroxysteroid dehydrogenase type 1 is associated with DNA hypermethylation in colorectal cancer located in the proximal colon. BMC Cancer 11:522
38. Rawluszko-Wieczorek AA, Horbacka K, Krokowicz P, Misztal M, Jagodzinski PP (2014) Prognostic potential of DNA methylation and transcript levels of HIF1A and EPAS1 in colorectal cancer. Mol Cancer Res. doi:10.1158/1541-7786.MCR-14-0054
39. Rohde C, Zhang Y, Jurkowski TP, Stamerjohanns H, Reinhardt R, Jeltsch A (2008) Bisulfite sequencing data presentation and compilation (BDPC) web server—a useful tool for DNA methylation analysis. Nucleic Acids Res 36:e34
40. Schiesser S, Hackner B, Pfaffeneder T, Muller M, Hagemeier C, Truss M, Carell T (2012) Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing. Angewandte Chemie (International ed) 51:6516–6520
41. Searcher CI CpG Island Searcher. http://cpgislands.usc.edu/
42. Site UGB UCSC Genome Bioinformatics Site. http://genome.ucsc.edu/
43. Stivers JT, Jiang YL (2003) A mechanistic perspective on the chemistry of DNA repair glycosylases. Chem Rev 103:2729–2759. doi:10.1021/cr010219b
44. Sun M et al (2013) HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis. Proc Natl Acad Sci USA 110:9920–9925. doi:10.1073/pnas.1305172110
45. Tahiliani M et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935
46. Wojdacz TK, Dobrovic A (2007) Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 35:e41
47. Yang H et al (2013) Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 32:663–669