Clustering of cancer cell lines using a promoter- Targeted liquid hybridization capture-based bisulfite sequencing approach

Technology in Cancer Research and Treatment

Volumn 14, Issue 4, 2015, Pages 383-394

  Gao, Fei ^a   Wang, Junwen ^a   Ji, Guanyu ^a   Liu, Siyang ^a   Yao, Yu ^a   Wang, Tong ^a   Wu, Honglong ^a   Xia, Yudong ^a   Gong, Desheng ^a   Jiang, Hui ^a   Yang, Huanming ^a,b,c   Zhang, Xiuqing ^a  

^a BGI SHENZHEN   (China)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^c James D Watson Institute of Genome Science   (China)

Author keywords

Cancer classification; CIMP; DNA methylation; Promoter; Targeted bisulfite sequencing

Indexed keywords

DECITABINE; GENOMIC DNA; RNA;

ARTICLE; BIOLOGY; CELL CULTURE; CELL PROLIFERATION ASSAY; CLUSTER ANALYSIS; CONTROLLED STUDY; CPG ISLAND; FLUOROMETRY; GENE LIBRARY; HUMAN; HUMAN CELL; HYBRIDIZATION; KARYOTYPE 46,XY; LIQUID HYBRIDIZATION CAPTURE BASED BISULFITE SEQUENCING; MOLECULAR PROBE; OVARIAN CANCER CELL LINE; PHENOTYPE; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; VALIDATION PROCESS; DNA METHYLATION; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; NEOPLASM; NUCLEIC ACID HYBRIDIZATION; TUMOR CELL LINE;

CELL LINE, TUMOR; CLUSTER ANALYSIS; DNA METHYLATION; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; NEOPLASMS; NUCLEIC ACID HYBRIDIZATION; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84957547530     PISSN: 15330346     EISSN: 15330338     Source Type: Journal    
DOI: 10.7785/tcrt.2012.500416     Document Type: Article

References (45)

1. Suzuki, R. , Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540-1542 (2006). DOI: 10. 1093/bioinformatics/btl117
2. Cheung, H. H. , Lee, T. L. , Rennert, O. M. , Chan, W. Y. DNA methylation of cancer genome. Birth Defects Res C Embryo Today 87, 335-350 (2009). DOI: 10. 1002/bdrc. 20163
3. Herceg, Z. , Vaissiere, T. Epigenetic mechanisms and cancer: an interface between the environment and the genome. Epigenetics 6, 804-819 (2011). DOI:10. 4161/epi. 6. 7. 16262
4. Robertson, K. D. DNA methylation and human disease. Nat Rev Genet 6, 597-610 (2005). DOI:10. 1038/nrg1655
5. Esteller, M. Cancer epigenomics: DNA methylomes and histonemodification maps. Nat Rev Genet 8, 286-298 (2007). DOI:10. 1038/nrg2005
6. Irizarry, R. A. , Ladd-Acosta, C. , Wen, B. , Wu, Z. , Montano, C. , Onyango, P. , Cui, H. , Gabo, K. , Rongione, M. , Webster, M. , Ji, H. , Potash, J. B. , Sabunciyan, S. , Feinberg, A. P. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41, 178-186 (2009). DOI: 10. 1038/ng. 298
7. Illingworth, R. S. , Bird, A. P. CpG islands-'a rough guide'. FEBS Lett 583, 1713-1720 (2009). DOI: 10. 1016/j.febslet.2009.04. 012
8. Hansen, K. D. , Timp, W. , Bravo, H. C. , Sabunciyan, S. , Langmead, B. , McDonald, O. G. , Wen, B. , Wu, H. , Liu, Y. , Diep, D. , Briem, E. , Zhang, K. , Irizarry, R. A. , Feinberg, A. P. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43, 768-775 (2011). DOI:10. 1038/ng. 865
9. Yeoh, E. J. , Ross, M. E. , Shurtleff, S. A. , Williams, W. K. , Patel, D. , Mahfouz, R. , Behm, F. G. , Raimondi, S. C. , Relling, M. V. , Patel, A. , Cheng, C. , Campana, D. , Wilkins, D. , Zhou, X. , Li, J. , Liu, H. , Pui, C. H. , Evans, W. E. , Naeve, C. , Wong, L. , Downing, J. R. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1, 133-143 (2002). DOI: 10. 1016/S1535-6108(02)00032-6
10. Wang, Y. , Wu, R. , Cho, K. R. , Shedden, K. A. , Barder, T. J. , Lubman, D. M. Classification of cancer cell lines using an automated two-dimensional liquid mapping method with hierarchical clustering techniques. Mol Cell Proteomics 5, 43-52 (2006). DOI: 10. 1074/mcp. T500023-MCP200
11. Schwartz, D. R. , Kardia, S. L. , Shedden, K. A. , Kuick, R. , Michailidis, G. , Taylor, J. M. , Misek, D. E. , Wu, R. , Zhai, Y. , Darrah, D. M. , Reed, H. , Ellenson, L. H. , Giordano, T. J. , Fearon, E. R. , Hanash, S. M. , Cho, K. R. Gene expression in ovarian cancer reflects both morphology and biological behavior, distinguishing clear cell from other poor-prognosis ovarian carcinomas. Cancer Res 62, 4722-4729 (2002).
12. Golub, T. R. , Slonim, D. K. , Tamayo, P. , Huard, C. , Gaasenbeek, M. , Mesirov, J. P. , Coller, H. , Loh, M. L. , Downing, J. R. , Caligiuri, M. A. , Bloomfield, C. D. , Lander, E. S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999). DOI: 10. 1126/science. 286. 5439. 531
13. Toyota, M. , Ahuja, N. , Suzuki, H. , Itoh, F. , Ohe-Toyota, M. , Imai, K. , Baylin, S. B. , Issa, J. P. Aberrant methylation in gastric cancer associated with the CpG island methylator phenotype. Cancer Res 59, 5438-5442 (1999).
14. Toyota, M. , Ahuja, N. , Ohe-Toyota, M. , Herman, J. G. , Baylin, S. B. , Issa, J. P. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 96, 8681-8686 (1999).
15. Issa, J. P. CpG island methylator phenotype in cancer. Nat Rev Cancer 4, 988-993 (2004). DOI: 10. 1038/nrc1507
16. Carvalho, B. , Pinto, M. , Cirnes, L. , Oliveira, C. , Machado, J. C. , Suriano, G. , Hamelin, R. , Carneiro, F. , Seruca, R. Concurrent hypermethylation of gene promoters is associated with a MSI-H phenotype and diploidy in gastric carcinomas. Eur J Cancer 39, 1222-1227 (2003). DOI: 10. 1016/S0959-8049(03)00177-1
17. Zouridis, H. , Deng, N. , Ivanova, T. , Zhu, Y. , Wong, B. , Huang, D. , Wu, Y. H. , Wu, Y. , Tan, I. B. , Liem, N. , Gopalakrishnan, V. , Luo, Q. , Wu, J. , Lee, M. , Yong, W. P. , Goh, L. K. , Teh, B. T. , Rozen, S. , Tan, P. Methylation subtypes and large-scale epigenetic alterations in gastric cancer. Sci Transl Med 4, 156ra40 (2012). DOI: 10. 1126/scitranslmed. 3004504
18. Shinjo, K. , Okamoto, Y. , An, B. , Yokoyama, T. , Takeuchi, I. , Fujii, M. , Osada, H. , Usami, N. , Hasegawa, Y. , Ito, H. , Hida, T. , Fujimoto, N. , Kishimoto, T. , Sekido, Y. , Kondo, Y. Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma. Carcinogenesis 33, 1277-1285 (2012). DOI: 10. 1093/carcin/bgs154
19. Xi, Y. , Li, W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009). DOI: 10. 1186/1471-2105-10-232
20. Illingworth, R. S. , Gruenewald-Schneider, U. , Webb, S. , Kerr, A. R. , James, K. D. , Turner, D. J. , Smith, C. , Harrison, D. J. , Andrews, R. , Bird, A. P. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6, e1001134 (2010). DOI: 10. 1371/journal. pgen. 1001134
21. Deaton, A. M. , Bird, A. CpG islands and the regulation of transcription. Genes Dev 25, 1010-1022 (2011). DOI: 10. 1101/gad. 2037511
22. Wang, J. , Jiang, H. , Ji, G. , Gao, F. , Wu, M. , Sun, J. , Luo, H. , Wu, J. , Wu, R. , Zhang, X. High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing. BMC Genomics 12, 597 (2011). DOI: 10. 1186/1471-2164-12-597
23. Weber, M. , Hellmann, I. , Stadler, M. B. , Ramos, L. , Paabo, S. , Rebhan, M. , Schubeler, D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457-466 (2007). DOI: 10. 1038/ng1990
24. Lee, E. J. , Pei, L. , Srivastava, G. , Joshi, T. , Kushwaha, G. , Choi, J. H. , Robertson, K. D. , Wang, X. , Colbourne, J. K. , Zhang, L. , Schroth, G. P. , Xu, D. , Zhang, K. , Shi, H. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res 39, e127 (2011). DOI: 10. 1093/nar/gkr598
25. Gao, F. , Liu, X. , Wu, X. P. , Wang, X. L. , Gong, D. , Lu, H. , Xia, Y. , Song, Y. , Wang, J. , Du, J. , Liu, S. , Han, X. , Tang, Y. , Yang, H. , Jin, Q. , Zhang, X. , Liu, M. Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis. Genome Biol 13, R100 (2012). DOI: 10. 1186/gb-2012-13-10-r100
26. Sun J, W. H. , Ji G, Wu B, Yan S, Gao W, Lam R, Zhang W, Zhang, X. High quality bisulfite sequencing using nanogram amounts of genomic DNA. Int J Biochem Biotechnol 2, 449-456 (2013).
27. Wang, J. , Wang, W. , Li, R. , Li, Y. , Tian, G. , Goodman, L. , Fan, W. , Zhang, J. , Li, J. , Guo, Y. , Feng, B. , Li, H. , Lu, Y. , Fang, X. , Liang, H. , Du, Z. , Li, D. , Zhao, Y. , Hu, Y. , Yang, Z. , Zheng, H. , Hellmann, I. , Inouye, M. , Pool, J. , Yi, X. , Zhao, J. , Duan, J. , Zhou, Y. , Qin, J. , Ma, L. , Li, G. , Zhang, G. , Yang, B. , Yu, C. , Liang, F. , Li, W. , Li, S. , Ni, P. , Ruan, J. , Li, Q. , Zhu, H. , Liu, D. , Lu, Z. , Li, N. , Guo, G. , Ye, J. , Fang, L. , Hao, Q. , Chen, Q. , Liang, Y. , Su, Y. , San, A. , Ping, C. , Yang, S. , Chen, F. , Li, L. , Zhou, K. , Ren, Y. , Yang, L. , Gao, Y. , Yang, G. , Li, Z. , Feng, X. , Kristiansen, K. , Wong, G. K. , Nielsen, R. , Durbin, R. , Bolund, L. , Zhang, X. , Yang, H. The diploid genome sequence of an Asian individual. Nature 456, 60-65 (2008). DOI: 10. 1038/nature07484
28. Li, Y. , Zhu, J. , Tian, G. , Li, N. , Li, Q. , Ye, M. , Zheng, H. , Yu, J. , Wu, H. , Sun, J. , Zhang, H. , Chen, Q. , Luo, R. , Chen, M. , He, Y. , Jin, X. , Zhang, Q. , Yu, C. , Zhou, G. , Huang, Y. , Cao, H. , Zhou, X. , Guo, S. , Hu, X. , Li, X. , Kristiansen, K. , Bolund, L. , Xu, J. , Wang, W. , Yang, H. , Wang, J. , Li, R. , Beck, S. , Zhang, X. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 8, e1000533 (2010). DOI: 10. 1371/journal. pbio. 1000533
29. Tahiliani, M. , Koh, K. P. , Shen, Y. , Pastor, W. A. , Bandukwala, H. , Brudno, Y. , Agarwal, S. , Iyer, L. M. , Liu, D. R. , Aravind, L. , Rao, A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935 (2009). DOI: 10. 1126/science. 1170116
30. Kriaucionis, S. , Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930 (2009). DOI: 10. 1126/science. 1169786
31. Ito, S. , Shen, L. , Dai, Q. , Wu, S. C. , Collins, L. B. , Swenberg, J. A. , He, C. , Zhang, Y. Tet proteins can convert 5-methylcytosine to 5- formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303 (2011). DOI: 10. 1126/science. 1210597
32. Shearer, A. E. , Hildebrand, M. S. , Ravi, H. , Joshi, S. , Guiffre, A. C. , Novak, B. , Happe, S. , Leproust, E. M. , Smith, R. J. Precapture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment. BMC Genomics 13, 618 (2012). DOI: 10. 1186/1471-2164-13-618
33. Saxonov, S. , Berg, P. , Brutlag, D. L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103, 1412-1417 (2006). DOI: 10. 1073/pnas. 0510310103
34. Liu, J. , Yang, G. , Thompson-Lanza, J. A. , Glassman, A. , Hayes, K. , Patterson, A. , Marquez, R. T. , Auersperg, N. , Yu, Y. , Hahn, W. C. , Mills, G. B. , Bast, R. C. Jr. A genetically defined model for human ovarian cancer. Cancer Res 64, 1655-1663 (2004).
35. Mei, F. C. , Young, T. W. , Liu, J. , Cheng, X. RAS-mediated epigenetic inactivation of OPCML in oncogenic transformation of human ovarian surface epithelial cells. FASEB J 20, 497-499 (2006). DOI: 10. 1096/fj. 05-4586fje
36. Zhang, Y. , Wang, R. , Song, H. , Huang, G. , Yi, J. , Zheng, Y. , Wang, J. , Chen, L. Methylation of multiple genes as a candidate biomarker in non-small cell lung cancer. Cancer Lett 303, 21-28 (2011). DOI: 10. 1016/j.canlet.2010.12. 011
37. van Hoesel, A. Q. , van de Velde, C. J. , Kuppen, P. J. , Putter, H. , de Kruijf, E. M. , van Nes, J. G. , Giuliano, A. E. , Hoon, D. S. Primary tumor classification according to methylation pattern is prognostic in patients with early stage ER-negative breast cancer. Breast Cancer Res Treat 131, 859-869 (2012). DOI: 10. 1007/s10549-011-1485-3
38. Hinoue, T. , Weisenberger, D. J. , Lange, C. P. , Shen, H. , Byun, H. M. , Van Den Berg, D. , Malik, S. , Pan, F. , Noushmehr, H. , van Dijk, C. M. , Tollenaar, R. A. , Laird, P. W. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 22, 271-282 (2012). DOI: 10. 1101/gr. 117523. 110
39. Figueroa, M. E. , Reimers, M. , Thompson, R. F. , Ye, K. , Li, Y. , Selzer, R. R. , Fridriksson, J. , Paietta, E. , Wiernik, P. , Green, R. D. , Greally, J. M. , Melnick, A. An integrative genomic and epigenomic approach for the study of transcriptional regulation. PLoS One 3, e1882 (2008). DOI: 10. 1371/journal. pone. 0001882
40. Figueroa, M. E. , Lugthart, S. , Li, Y. , Erpelinck-Verschueren, C. , Deng, X. , Christos, P. J. , Schifano, E. , Booth, J. , van Putten, W. , Skrabanek, L. , Campagne, F. , Mazumdar, M. , Greally, J. M. , Valk, P. J. , Lowenberg, B. , Delwel, R. , Melnick, A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 17, 13-27 (2010). DOI: 10. 1016/j.ccr.2009.11. 020
41. Wu, X. M. , Shao, X. Q. , Meng, X. X. , Zhang, X. N. , Zhu, L. , Liu, S. X. , Lin, J. , Xiao, H. S. Genome-wide analysis of microRNA and mRNA expression signatures in hydroxycamptothecinresistant gastric cancer cells. Acta Pharmacol Sin 32, 259-269 (2011). DOI: 10. 1038/aps.2010.204
42. An, C. , Choi, I. S. , Yao, J. C. , Worah, S. , Xie, K. , Mansfield, P. F. , Ajani, J. A. , Rashid, A. , Hamilton, S. R. , Wu, T. T. Prognostic significance of CpG island methylator phenotype and microsatellite instability in gastric carcinoma. Clin Cancer Res 11, 656-663 (2005).
43. Oue, N. , Oshimo, Y. , Nakayama, H. , Ito, R. , Yoshida, K. , Matsusaki, K. , Yasui, W. DNA methylation of multiple genes in gastric carcinoma: association with histological type and CpG island methylator phenotype. Cancer Sci 94, 901-905 (2003).
44. Gal-Yam, E. N. , Egger, G. , Iniguez, L. , Holster, H. , Einarsson, S. , Zhang, X. , Lin, J. C. , Liang, G. , Jones, P. A. , Tanay, A. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A 105, 12979-12984 (2008). DOI: 10. 1073/pnas. 0806437105
45. Toyota, M. , Issa, J. P. CpG island methylator phenotypes in aging and cancer. Semin Cancer Biol 9, 349-357 (1999). DOI: 10. 1006/scbi.1999.0135