ABSTRACT
Background
Hypermethylation of DNA silences gene expression and is an important event in colorectal cancer (CRC). This study aimed to identify aberrantly methylated genes that contribute to a poor prognosis for patients with CRC.
Methods
The study comprehensively explored DNA methylation microarray profiles from 396 CRC samples and 45 normal control samples in a database and selected aberrantly methylated transcription factors associated with prognosis and metastasis. Using quantitative reverse transcription polymerase chain reaction, the identified genes in 140 patients with CRC were validated to assess the relationship between expression of methylated genes and prognosis.
Results
In the study, FOXE1 was newly identified as a gene associated with prognosis and metastasis in CRC. Expression of FOXE1 in CRC tissues was significantly lower than in normal colorectal tissues (p = 0.01). The survival rate for the patients with low expression of FOXE1 was significantly lower than that for patients with high expression of FOXE1 in uni- and multivariate analyses. Inhibition of DNA methylation recovered FOXE1 expression in CRC cells.
Conclusions
Methylation-mediated silencing of FOXE1 expression was shown to be a potential prognostic factor in CRC.
Similar content being viewed by others
References
Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61:69–90.
Markowitz SD, Bertagnolli MM. Molecular origins of cancer: molecular basis of colorectal cancer. N Engl J Med. 2009;361:2449–60.
Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 2007;128:669–81.
Weber M, Hellmann I, Stadler MB, et al. Distribution, silencing potential, and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007;39:457–66.
Yuan BZ, Durkin ME, Popescu NC. Promoter hypermethylation of DLC-1, a candidate tumor suppressor gene, in several common human cancers. Cancer Genet Cytogenet. 2003;140:113–7.
Fang JY, Lu R, Mikovits JA, Cheng ZH, Zhu HY, Chen YX. Regulation of hMSH2 and hMLH1 expression in the human colon cancer cell line SW1116 by DNA methyltransferase 1. Cancer Lett. 2006;233:124–30.
Chen QW, Zhu XY, Li YY, Meng ZQ. Epigenetic regulation and cancer (review). Oncol Rep. 2014;31:523–32.
van Engeland M, Derks S, Smits KM, Meijer GA, Herman JG. Colorectal cancer epigenetics: complex simplicity. J Clin Oncol. 2011;29:1382–91.
Simmer F, Brinkman AB, Assenov Y, et al. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics. 2012;7:1355–67.
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215–6
Seki M, Nishimura R, Yoshida K, et al. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun. 2015;6:7557.
Bernstein BE, Mikkelsen TS, Xie X, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315–26.
Voigt P, Tee WW, Reinberg D. A double take on bivalent promoters. Genes Dev. 2013;27:1318–38.
Ohm JE, McGarvey KM, Yu X, et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet. 2007;39:237–42.
Schlesinger Y, Straussman R, Keshet I, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet. 2007;39:232–6.
Katoh M, Katoh M. Human FOX gene family (review). Int J Oncol. 2004;25:1495–500.
Katoh M, Igarashi M, Fukuda H, Nakagama H, Katoh M. Cancer genetics and genomics of human FOX family genes. Cancer Lett. 2013;328:198–206.
Kimura S. Thyroid-specific transcription factors and their roles in thyroid cancer. J Thyroid Res. 2011;2011:710213.
Venza I, Visalli M, Tripodo B, et al. FOXE1 is a target for aberrant methylation in cutaneous squamous cell carcinoma. Br J Dermatol. 2010;162:1093–7.
Sato N, Fukushima N, Maitra A, et al. Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays. Cancer Res. 2003;63:3735–42.
Nonaka D, Tang Y, Chiriboga L, Rivera M, Ghossein R. Diagnostic utility of thyroid transcription factors Pax8 and TTF-2 (FoxE1) in thyroid epithelial neoplasms. Mod Pathol. 2008;21:192–200.
Fernandez LP, Lopez-Marquez A, Martinez AM, Gomez-Lopez G, Santisteban P. New insights into FoxE1 functions: identification of direct FoxE1 targets in thyroid cells. PLoS One. 2013;8:e62849.
Weisenberger DJ, Trinh BN, Campan M, et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008;36:4689–98.
Baylin SB, Jones PA. A decade of exploring the cancer epigenome: biological and translational implications. Nat Rev Cancer. 2011;11:726–34.
Landa I, Ruiz-Llorente S, Montero-Conde C, et al. The variant rs1867277 in FOXE1 gene confers thyroid cancer susceptibility through the recruitment of USF1/USF2 transcription factors. PLoS Genet. 2009;5:e1000637.
Mond M, Bullock M, Yao Y, Clifton-Bligh RJ, Gilfillan C, Fuller PJ. Somatic mutations of FOXE1 in papillary thyroid cancer. Thyroid. 2015;25:904–10.
Kohler A, Chen B, Gemignani F, et al. Genome-wide association study on differentiated thyroid cancer. J Clin Endocrinol Metab. 2013;98:E1674–81.
Cancer Genome Atlas N. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.
Noreen F, Roosli M, Gaj P, et al. Modulation of age- and cancer-associated DNA methylation change in the healthy colon by aspirin and lifestyle. J Natl Cancer Inst. 2014;106:123.
Acknowledgments
We thank K. Oda, M. Kasagi, and T. Kawano for their technical assistance. This work was supported in part by the following grants and foundations: Japan Science and Technology Agency (JST), Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research (Grant Nos. 24592005, 25461953, 25861199, 25861200, and 26861085), Japan Science and Technology Agency (JSTA) (A-step grant no. AS242Z03987P), the Founding Program for Next Generation World-Leading Researchers (LS094), and the Daiwa Securities Health Foundation.
Conflict of interest
There are no conflicts of interest.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Sugimachi, K., Matsumura, T., Shimamura, T. et al. Aberrant Methylation of FOXE1 Contributes to a Poor Prognosis for Patients with Colorectal Cancer. Ann Surg Oncol 23, 3948–3955 (2016). https://doi.org/10.1245/s10434-016-5289-x
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1245/s10434-016-5289-x