Epigenetic and genetic features of 24 colon cancer cell lines

Oncogenesis

Volumn 2, Issue , 2013, Pages

  Ahmed, D ^a,b   Eide, P W ^a,b   Eilertsen, I A ^a,b   Danielsen, S A ^a,b   Eknaes M ^a,b   Hektoen, M ^a,b   Lind, G E ^a,b   Lothe, R A ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

Cell line; CIMP; Colorectal neoplasms; DNA methylation; Microsatellite instability; Point mutation

Indexed keywords

B RAF KINASE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; K RAS PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN KINASE B; PROTEIN P53;

ARTICLE; COLON CANCER; CPG ISLAND; ENZYME ACTIVATION; EPIGENETICS; GENE MUTATION; GENETICS; HUMAN; HUMAN CELL; IN VITRO STUDY; MICROSATELLITE INSTABILITY; ONCOGENE; PHENOTYPE; PRIORITY JOURNAL;

EID: 84884732676     PISSN: None     EISSN: 21579024     Source Type: Journal    
DOI: 10.1038/oncsis.2013.35     Document Type: Article

References (74)

1. Gazdar AF, Gao B, Minna JD. Lung cancer cell lines: useless artifacts or invaluable tools for medical science? Lung Cancer 2010; 68: 309
2. Shoemaker RH. The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 2006; 6: 813.
3. Ashraf SQ, Nicholls AM, Wilding JL, Ntouroupi TG, Mortensen NJ, Bodmer WF. Direct and immune mediated antibody targeting of ERBB receptors in a colorectal cancer cell-line panel. Proc Natl Acad Sci USA 2012; 109: 21046.
4. Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI et al. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas, Mol. Cancer 2011; 10: 85.
5. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483: 603.
6. Saaf AM, Halbleib JM, Chen X, Yuen ST, Leung SY, Nelson WJ et al. Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer. Mol Biol Cell 2007; 18: 4245.
7. van Staveren WC, Solis DY, Hebrant A, Detours V, Dumont JE, Maenhaut C. Human cancer cell lines: experimental models for cancer cells in situ? For cancer stem cells? Biochim Biophys Acta 2009; 1795: 92.
8. MacLeod RA, Dirks WG, Matsuo Y, Kaufmann M, Milch H, Drexler HG. Widespread intraspecies cross-contamination of human tumor cell lines arising at source, Int. J Cancer 1999; 83: 555.
9. Jones S, Chen WD, Parmigiani G, Diehl F, Beerenwinkel N, Antal T et al. Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci USA 2008; 105: 4283.
10. Gayet J, Zhou XP, Duval A, Rolland S, Hoang JM, Cottu P et al. Extensive characterization of genetic alterations in a series of human colorectal cancer cell lines. Oncogene 2001; 20: 5025.
11. Nowak MA, Komarova NL, Sengupta A, Jallepalli PV, Shih I, Vogelstein B et al. The role of chromosomal instability in tumor initiation. Proc Natl Acad Sci USA 2002; 99: 16226.
12. Hermsen M, Postma C, Baak J, Weiss M, Rapallo A, Sciutto A et al. Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. Gastroenterology 2002; 123: 1109.
13. Lengauer C, Kinzler . , Vogelstein B. Genetic instability in colorectal cancers. Nature 1997; 386: 623.
14. Lothe RA. Microsatellite . in human solid tumors. Mol Med Today 1997; 3: 61.
15. Shibata D, Peinado MA, Ionov Y, Malkhosyan S, Perucho M. Genomic instability in repeated sequences is an early somatic event in colorectal tumorigenesis that persists after transformation. Nat Genet 1994; 6: 273.
16. Issa JP. CpG . methylator phenotype in cancer. Nat Rev Cancer 2004; 4: 988.
17. Masters JR. Cell. line authentication: end the scandal of false cell lines. Nature 2012; 492: 186.
18. Chen TR, Dorotinsky CS, McGuire LJ, Macy ML, Hay RJ. DLD-1 and HCT-15 cell lines derived separately from colorectal carcinomas have totally different chromosome changes but the same genetic origin. Cancer Genet Cytogenet 1995; 81: 103.
19. Chen TR, Drabkowski D, Hay RJ, Macy M, Peterson Jr. W. WiDr is a derivative of another colon adenocarcinoma cell line, HT-29. Cancer Genet Cytogenet 1987; 27: 125.
20. Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006; 38: 787.
21. Liu Y, Bodmer WF. Analysis of P53 mutations and their expression in colorectal cancer cell lines. Proc Natl Acad Sci USA 2006; 103: 976
22. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009; 4: 1073.
23. Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P et al. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat 2007; 28: 622.
24. Weng Y, Lu L, Yuan G, Guo J, Zhang Z, Xie X et al. p53 codon 72 polymorphism and hematological cancer risk: an update meta-analysis. PLoS One 2012; 7: e45820.
25. Fan R, Wu MT, Miller D, Wain JC, Kelsey KT, Wiencke JK et al. The p53 codon 72 polymorphism and lung cancer risk. Cancer Epidemiol Biomarkers Prev 2000; 9: 1037.
26. Langerod A, Bukholm IR, Bregard A, Lonning PE, Andersen TI, Rognum TO et al. The TP53 codon 72 polymorphism may affect the function of TP53 mutations in breast carcinomas but not in colorectal carcinomas. Cancer Epidemiol Biomarkers Prev 2002; 11: 1684.
27. Cantley LC, Neel BG. New insights into tumor suppression: PTEN suppresses tumor formation by restraining the phosphoinositide 3-kinase/AKT pathway. Proc Natl Acad Sci USA 1999; 96: 4240.
28. Hughes LA, Khalid-de Bakker CA, Smits KM, van den Brandt PA, Jonkers D, Ahuja N et al. The CpG island methylator phenotype in colorectal cancer: progress and problems. Biochim Biophys Acta 2012; 1825: 77.
29. Shen L, Toyota M, Kondo Y, Lin E, Zhang L, Guo Y et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci USA 2007; 104: 18654.
30. Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den BD et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012; 22: 271.
31. Ogino S, Cantor M, Kawasaki T, Brahmandam M, Kirkner GJ, Weisenberger DJ et al. CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies. Gut 2006; 55: 1000.
32. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011; 39(suppl 1): D945-D950.
33. Papadopoulos N, Nicolaides . , Liu B, Parsons R, Lengauer C, Palombo F et al. Mutations of GTBP in genetically unstable cells. Science 1995; 268: 1915.
34. Bras-Goncalves RA, Rosty C, Laurent-Puig P, Soulie P, Dutrillaux B, Poupon MF. Sensitivity to CPT-11 of xenografted human colorectal cancers as a function of microsatellite instability and p53 status, Br. J Cancer 2000; 82: 913.
35. Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype- low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J Mol Diagn 2006; 8: 582.
36. Toledo F, Wahl GM. Regulating the p53 pathway: in vitro hypotheses, in vivo veritas. Nat Rev Cancer 2006; 6: 909.
37. Cheng Q, Chen L, Li Z, Lane WS, Chen J. ATM activates p53 by regulating MDM2 oligomerization and E3 processivity. EMBO J 2009; 28: 3857.
38. Mayo LD, Donner DB. The PTEN, Mdm2, p53 tumor suppressor-oncoprotein network. Trends Biochem Sci 2002; 27: 462.
39. Hinoue T, Weisenberger DJ, Pan F, Campan M, Kim M, Young J et al. Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling. PLoS One 2009; 4: e8357.
40. TCGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330.
41. Caro I, Boulenc X, Rousset M, Meunier V. Characterization of a newly isolated Caco-2 clone (TC7) as a model of transport processes and biotransformation of drugs. Int J Pharm 1995; 116: 147.
42. Wu Q, Lothe RA, Ahlquist T, Silins I, Trope CG, Micci F et al. DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets. Mol Cancer 2007; 6: 45.
43. Cicek MS, Lindor NM, Gallinger S, Bapat B, Hopper JL, Jenkins MA et al. Quality assessment and correlation of microsatellite instability and immunohistochemical markers among population- and clinic-based colorectal tumors results from the Colon Cancer Family Registry. J Mol Diagn 2011; 13: 271.
44. Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW et al. A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 1998; 58: 5248.
45. Kleivi K, Teixeira . , Eknaes M, Diep CB, Jakobsen KS, Hamelin R et al. Genome signatures of colon carcinoma cell lines. Cancer Genet Cytogenet 2004; 155: 119.
46. Knutsen T, Padilla-Nash HM, Wangsa D, Barenboim-Stapleton L, Camps J, McNeil N et al. Definitive molecular cytogenetic characterization of 15 colorectal cancer cell lines. Genes Chromosomes Cancer 2010; 49: 204.
47. Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA et al. Chromosomal instability confers intrinsic multidrug resistance. Cancer Res 2011; 71: 1858.
48. Thompson SL, Compton DA. Examining the link between chromosomal instability and aneuploidy in human cells. J Cell Biol 2008; 180: 665.
49. Frazier ML, Xi L, Zong J, Viscofsky N, Rashid A, Wu EF et al. Association of the CpG island methylator phenotype with family history of cancer in patients with colorectal cancer. Cancer Res 2003; 63: 4805.
50. Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E et al. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 2005; 33: 6823.
51. Berg M, Danielsen SA, Ahlquist T, Merok MA, Ågesen TH, Vatn MH et al. DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CAPTEN- TP53 related to age at disease onset. PLoS One 2010; 5: e13978.
52. Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009; 19: 1316.
53. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 2013; 41(Database issue): D64-D69.
54. den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 2000; 15: 7.
55. Janakiraman M, Vakiani E, Zeng Z, Pratilas CA, Taylor BS, Chitale D et al. Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res 2010; 70: 5901.
56. Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S et al. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther 2006; 5: 2606.
57. Carrel S, Sordat B, Merenda C. Establishment of a cell line (Co-115) from a human colon carcinoma transplanted into nude mice. Cancer Res 1976; 36(Pt 1): 3978.
58. Quinn LA, Moore GE, Morgan RT, Woods LK. Cell lines from human colon carcinoma with unusual cell products, double minutes, and homogeneously staining regions. Cancer Res 1979; 39: 4914.
59. Dexter DL, Spremulli EN, Fligiel Z, Barbosa JA, Vogel R, VanVoorhees A et al. Heterogeneity of cancer cells from a single human colon carcinoma. Am J Med 1981; 71: 949.
60. Brattain MG, Levine . , Chakrabarty S, Yeoman LC, Willson JK, Long B. Heterogeneity of human colon carcinoma. Cancer Metastasis Rev 1984; 3: 177.
61. Brattain MG, Brattain DE, Fine WD, Khaled FM, Marks ME, Kimball PM et al. Initiation and characterization of cultures of human colonic carcinoma with different biological characteristics utilizing feeder layers of confluent fibroblasts. Oncodev Biol Med 1981; 2: 355.
62. Chantret I, Barbat A, Dussaulx E, Brattain MG, Zweibaum A. Epithelial polarity, villin expression, and enterocytic differentiation of cultured human colon carcinoma cells: a survey of twenty cell lines. Cancer Res 1988; 48: 1936.
63. Tibbetts LM, Chu MY, Hager JC, Dexter DL, Calabresi P. Chemotherapy of cell-linederived human colon carcinomas in mice immunosuppressed with antithymocyte serum. Cancer 1977; 40(Suppl 5): 2651.
64. Dexter DL, Barbosa JA, Calabresi P. N,N-dimethylformamide-induced alteration of cell culture characteristics and loss of tumorigenicity in cultured human colon carcinoma cells. Cancer Res 1979; 39: 1020.
65. Brattain MG, Fine WD, Khaled FM, Thompson J, Brattain DE. Heterogeneity of malignant cells from a human colonic carcinoma. Cancer Res 1981; 41: 1751.
66. Eshleman JR, Lang EZ, Bowerfind GK, Parsons R, Vogelstein B, Willson JK et al. Increased mutation rate at the hprt locus accompanies microsatellite instability in colon cancer. Oncogene 1995; 10: 33.
67. Fogh J. Human Tumor Cell In Vitro. Plenum Press: New York, USA, 1975.
68. Cajot JF, Sordat I, Silvestre T, Sordat B. Differential display cloning identifies motility-related protein (MRP1/CD9) as highly expressed in primary compared to metastatic human colon carcinoma cells. Cancer Res 1997; 57: 2593.
69. Drewinko B, Romsdahl MM, Yang LY, Ahearn MJ, Trujillo JM. Establishment of a human carcinoembryonic antigen-producing colon adenocarcinoma cell line. Cancer Res 1976; 36(Pt 1): 467.
70. Suardet L, Gaide AC, Calmes JM, Sordat B, Givel JC, Eliason JF et al. Responsiveness of three newly established human colorectal cancer cell lines to transforming growth factors beta 1 and beta 2. Cancer Res 1992; 52: 3705.
71. Tom BH, Rutzky LP, Jakstys MM, Oyasu R, Kaye CI, Kahan BD. Human colonic adenocarcinoma cells. I. Establishment and description of a new line. In Vitro 1976; 12: 180.
72. Park JG, Oie HK, Sugarbaker PH, Henslee JG, Chen TR, Johnson BE et al. Characteristics of cell lines established from human colorectal carcinoma. Cancer Res 1987; 47(Pt 1): 6710.
73. Leibovitz A, Stinson JC, McCombs III WB, McCoy CE, Mazur KC, Mabry ND. Classification of human colorectal adenocarcinoma cell lines. Cancer Res 1976; 36: 4562.
74. McBain JA, Weese JL, Meisner LF, Wolberg WH, Willson JK. Establishment and characterization of human colorectal cancer cell lines. Cancer Res 1984; 44(Pt 1): 5813.