Epigenetic and Genetic Features of 24 Colon Cancer Cell Lines

Overview

Journal Oncogenesis

Date 2013 Sep 18

PMID 24042735

Citations 466

Authors

D Ahmed

P W Eide

I A Eilertsen

S A Danielsen

M Eknaes

M Hektoen

G E Lind

R A Lothe

Affiliations

Soon will be listed here.

Abstract

Cell lines are invaluable biomedical research tools, and recent literature has emphasized the importance of genotype authentication and characterization. In the present study, 24 out of 27 cell line identities were confirmed by short tandem repeat profiling. The molecular phenotypes of the 24 colon cancer cell lines were examined, and microsatellite instability (MSI) and CpG island methylator phenotype (CIMP) were determined, using the Bethesda panel mononucleotide repeat loci and two epimarker panels, respectively. Furthermore, the BRAF, KRAS and PIK3CA oncogenes were analyzed for mutations in known hotspots, while the entire coding sequences of the PTEN and TP53 tumor suppressors were investigated. Nine cell lines showed MSI. Thirteen and nine cell lines were found to be CIMP positive, using the Issa panel and the Weisenberger et al. panel, respectively. The latter was found to be superior for CIMP classification of colon cancer cell lines. Seventeen cell lines harbored disrupting TP53 mutations. Altogether, 20/24 cell lines had the mitogen-activated protein kinase pathway activating mutually exclusive KRAS or BRAF mutations. PIK3CA and PTEN mutations leading to hyperactivation of the phosphoinositide 3-kinase/AKT pathway were observed in 13/24 cell lines. Interestingly, in four cell lines there were no mutations in neither BRAF, KRAS, PIK3CA nor in PTEN. In conclusion, this study presents molecular features of a large number of colon cancer cell lines to aid the selection of suitable in vitro models for descriptive and functional research.

Citing Articles

WBP1 regulates mitochondrial function and ferroptosis to modulate chemoresistance in colorectal cancer.

Wang Y, Qi D, Ge G, Cao N, Liu X, Zhu N Mol Med. 2025; 31(1):93.

PMID: 40075333 PMC: 11900258. DOI: 10.1186/s10020-025-01151-3.

Dietary polyunsaturated fatty acids affect PPARγ promoter methylation status and regulate the PPARγ/COX2 pathway in some colorectal cancer cell lines.

Babaeenezhad E, Khosravi P, Moradi Sarabi M Genes Nutr. 2025; 20(1):2.

PMID: 40038577 PMC: 11877738. DOI: 10.1186/s12263-025-00764-x.

Feature Selection and Network-Driven Analyses to Unveil Common RNA Signatures in Colon and Pancreatic KRAS-Mutant Cancers.

Pane K, Zanfardino M, Grimaldi A, Leone I, Nuzzo S, Salvatore M Cancer Med. 2025; 14(5):e70468.

PMID: 40013338 PMC: 11865888. DOI: 10.1002/cam4.70468.

Recombinant Lectin Exerts Differential Proapoptotic Activity on EGFR and EGFR Colon Cancer Cells and Provokes T Cell-Assisted Antitumor Responses in Mice.

Lujan-Mendez F, Garcia-Lopez P, Berumen L, Garcia-Alcocer G, Ferriz-Martinez R, Ramirez-Carrera A Pharmaceuticals (Basel). 2025; 18(2).

PMID: 40006027 PMC: 11858825. DOI: 10.3390/ph18020213.

Model systems to study tumor-microbiome interactions in early-onset colorectal cancer.

Richter K, Wrage M, Krekeler C, De Oliveira T, Conradi L, Menck K EMBO Mol Med. 2025; 17(3):395-413.

PMID: 39948421 PMC: 11903813. DOI: 10.1038/s44321-025-00198-3.

References

Hinoue T, Weisenberger D, Pan F, Campan M, Kim M, Young J . Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling. PLoS One. 2009; 4(12):e8357. PMC: 2791229. DOI: 10.1371/journal.pone.0008357. View

GAYET J, Zhou X, Duval A, Rolland S, Hoang J, Cottu P . Extensive characterization of genetic alterations in a series of human colorectal cancer cell lines. Oncogene. 2001; 20(36):5025-32. DOI: 10.1038/sj.onc.1204611. View

Forbes S, Bindal N, Bamford S, Cole C, Kok C, Beare D . COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2010; 39(Database issue):D945-50. PMC: 3013785. DOI: 10.1093/nar/gkq929. View

Dexter D, Spremulli E, Fligiel Z, Barbosa J, Vogel R, VanVoorhees A . Heterogeneity of cancer cells from a single human colon carcinoma. Am J Med. 1981; 71(6):949-56. DOI: 10.1016/0002-9343(81)90312-0. View

Meyer L, Zweig A, Hinrichs A, Karolchik D, Kuhn R, Wong M . The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2012; 41(Database issue):D64-9. PMC: 3531082. DOI: 10.1093/nar/gks1048. View

Lind G, Danielsen S, Ahlquist T, Merok M, Andresen K, Skotheim R . Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer. 2011; 10:85. PMC: 3166273. DOI: 10.1186/1476-4598-10-85. View

McBain J, Weese J, Meisner L, WOLBERG W, WILLSON J . Establishment and characterization of human colorectal cancer cell lines. Cancer Res. 1984; 44(12 Pt 1):5813-21. View

Kumar P, Henikoff S, Ng P . Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009; 4(7):1073-81. DOI: 10.1038/nprot.2009.86. View

Rosty C, Laurent-Puig P, Soulie P, Dutrillaux B, Poupon M . Sensitivity to CPT-11 of xenografted human colorectal cancers as a function of microsatellite instability and p53 status. Br J Cancer. 2000; 82(4):913-23. PMC: 2374412. DOI: 10.1054/bjoc.1999.1019. View

10.

Masters J . Cell-line authentication: End the scandal of false cell lines. Nature. 2012; 492(7428):186. DOI: 10.1038/492186a. View

11.

Park J, Oie H, Sugarbaker P, Henslee J, Chen T, Johnson B . Characteristics of cell lines established from human colorectal carcinoma. Cancer Res. 1987; 47(24 Pt 1):6710-8. View

12.

Boland C, Thibodeau S, Hamilton S, Sidransky D, Eshleman J, Burt R . 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(22):5248-57. View

13.

Drewinko B, Romsdahl M, Yang L, Ahearn M, Trujillo J . Establishment of a human carcinoembryonic antigen-producing colon adenocarcinoma cell line. Cancer Res. 1976; 36(2 Pt 1):467-75. View

14.

Issa J . CpG island methylator phenotype in cancer. Nat Rev Cancer. 2004; 4(12):988-93. DOI: 10.1038/nrc1507. View

15.

Shibata D, Peinado M, 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(3):273-81. DOI: 10.1038/ng0394-273. View

16.

Brattain M, Fine W, Khaled F, Thompson J, Brattain D . Heterogeneity of malignant cells from a human colonic carcinoma. Cancer Res. 1981; 41(5):1751-6. View

17.

Saaf A, Halbleib J, Chen X, Yuen S, Leung S, Nelson W . 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(11):4245-60. PMC: 2043540. DOI: 10.1091/mbc.e07-04-0309. View

18.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin A, Kim S . The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012; 483(7391):603-7. PMC: 3320027. DOI: 10.1038/nature11003. View

19.

Fan R, Wu M, Miller D, Wain J, Kelsey K, Wiencke J . The p53 codon 72 polymorphism and lung cancer risk. Cancer Epidemiol Biomarkers Prev. 2000; 9(10):1037-42. View

20.

Kleivi K, Teixeira M, Eknaes M, Diep C, Jakobsen K, Hamelin R . Genome signatures of colon carcinoma cell lines. Cancer Genet Cytogenet. 2004; 155(2):119-31. DOI: 10.1016/j.cancergencyto.2004.03.014. View