Tumor Biology

, Volume 33, Issue 2, pp 363–372 | Cite as

DNA methylation biomarker candidates for early detection of colon cancer

  • Joo Mi Yi
  • Mashaal Dhir
  • Angela A. Guzzetta
  • Christine A. Iacobuzio-Donahue
  • Kyu Heo
  • Kwang Mo Yang
  • Hiromu Suzuki
  • Minoru Toyota
  • Hwan-Mook Kim
  • Nita Ahuja
Research Article


Promoter CpG island hypermethylation of tumor suppressor genes is a common hallmark of all human cancers. Many researchers have been looking for potential epigenetic therapeutic targets in cancer using gene expression profiling with DNA microarray approaches. Our recent genome-wide platform of CpG island hypermethylation and gene expression in colorectal cancer (CRC) cell lines revealed that FBN2 and TCERG1L gene silencing is associated with DNA hypermethylation of a CpG island in the promoter region. In this study, promoter DNA hypermethylation of FBN2 and TCERG1L in CRC occurs as an early and cancer-specific event in colorectal cancer. Both genes showed high frequency of methylation in colon cancer cell lines (>80% for both of genes), adenomas (77% for FBN2, 90% for TCERG1L, n = 39), and carcinomas (86% for FBN2, 99% for TCERG1L, n = 124). Bisulfite sequencing confirmed cancer-specific methylation of FBN2 and TCERG1L of promoters in colon cancer cell line and cancers but not in normal colon. Methylation of FBN2 and TCERG1L is accompanied by downregulation in cell lines and in primary tumors as described in the Oncomine™ website. Together, our results suggest that gene silencing of FBN2 and TCERG1L is associated with promoter DNA hypermethylation in CRC tumors and may be excellent biomarkers for the early detection of CRC.


DNA hypermethylation Biomarker Early detection Colorectal Cancer (CRC) FBN2 TCERGIL 



The study is supported by the National R&D program (50595 and 50596) through the Dongnam Institute of Radiological & Medical Sciences (DIRAMS) funded by the Korean Ministry of Education, Science and Technology. This study is also supported by NIH/NCI K23CA127141, American College of Surgeons/Society of University Surgeons Career Development Award and the Jeannik M. Littlefield-AACR grant in metastatic colon cancer research. We thank the Johns Hopkins Cancer Registry for the assistance with the primary cancer databases.

Conflicts of interest



  1. 1.
    Jemal ASR, Ward E, Hao Y, Xu J, Thun MJ. Cancer statistics. CA Cancer J Clin. 2009;59:225–49.PubMedCrossRefGoogle Scholar
  2. 2.
    Heresbach DMS, D'halluin PN, Bretagne JF, Branger B. Review in depth and meta-analysis of controlled trials on colorectal cancer screening by faecal occult blood test. Eur J Gastroenterol Hepatol. 2006;18:427–33.PubMedCrossRefGoogle Scholar
  3. 3.
    Meissner HI, Breen N, Klabunde CN, Vernon SW. Patterns of colorectal cancer screening uptake among men and women in the United States. Cancer Epidemiol Biomarkers & Prevention. 2006;15:389–94.CrossRefGoogle Scholar
  4. 4.
    Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003;349:2042–54.PubMedCrossRefGoogle Scholar
  5. 5.
    Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128:683–92.PubMedCrossRefGoogle Scholar
  6. 6.
    Suzuki H, Watkins DN, Jair KW, Schuebel KE, Markowitz SD, Dong Chen W, et al. Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer. Nat Genet. 2004;36:417–22.PubMedCrossRefGoogle Scholar
  7. 7.
    Akiyama Y, Watkins N, Suzuki H, Jair KW, van Engeland M, Esteller M, et al. Gata-4 and gata-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer. Mol Cell Biol. 2003;23:8429–39.PubMedCrossRefGoogle Scholar
  8. 8.
    Glockner SC, Dhir M, Yi JM, McGarvey KE, Van Neste L, Louwagie J, et al. Methylation of tfpi2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer. Cancer Res. 2009;69:4691–9.PubMedCrossRefGoogle Scholar
  9. 9.
    Schuebel KE, Chen W, Cope L, Glöckner SC, Suzuki H, Yi JM, et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genetics. 2007;3:1709–23.PubMedCrossRefGoogle Scholar
  10. 10.
    Karpf AR JD. Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer. Oncogene. 2002;21:5496–503.PubMedCrossRefGoogle Scholar
  11. 11.
    Yang Q, Ota K, Tian Y, Kumar A, Wada J, Kashihara N, et al. Cloning of rat fibrillin-2 cDNA and its role in branching morphogenesis of embryonic lung. Dev Biol. 1999;212:229–42.PubMedCrossRefGoogle Scholar
  12. 12.
    Hagihara A, Miyamoto K, Furuta J, Hiraoka N, Wakazono K, Seki S, et al. Identification of 27 5′ CpG islands aberrantly methylated and 13 genes silenced in human pancreatic cancers. Oncogene. 2004;23:8705–10.PubMedCrossRefGoogle Scholar
  13. 13.
    Sune C, Hayashi T, Liu Y, Lane WS, Young RA, Garcia-Blanco MA. Ca150, a nuclear protein associated with the RNA polymerase ii holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol Cell Biol. 1997;17:6029–39.PubMedGoogle Scholar
  14. 14.
    Sanchez-Alvarez M, Goldstrohm AC, Garcia-Blanco MA, Sune C. Human transcription elongation factor ca150 localizes to splicing factor-rich nuclear speckles and assembles transcription and splicing components into complexes through its amino and carboxyl regions. Mol Cell Biol. 2006;26:4998–5014.PubMedCrossRefGoogle Scholar
  15. 15.
    Rhee I, Bachman KE, Park BH, Jair KW, Yen RW, Schuebel KE, et al. DNMT1 and DNMT3B cooperate to silence genes in human cancer cells. Nature. 2002;416:552–6.PubMedCrossRefGoogle Scholar
  16. 16.
    Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A. 1996;93:9821–6.PubMedCrossRefGoogle Scholar
  17. 17.
    Rhodes DR YJ, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, et al. Oncomine: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004;6:1–6.PubMedGoogle Scholar
  18. 18.
    Kaiser SPY, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, et al. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol. 2007;8:R131.PubMedCrossRefGoogle Scholar
  19. 19.
    Jorissen RN, Gibbs P, Christie M, Prakash S, Lipton L, Desai J, et al. Metastasis-associated gene expression changes predict poor outcomes in patients with dukes stage b and c colorectal cancer. Clin Cancer Res. 2009;15:7642–51.PubMedCrossRefGoogle Scholar
  20. 20.
    Smith JJ, Deane NG, Wu F, Merchant NB, Zhang B, Jiang A, et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology. 2010;138:958–68.PubMedCrossRefGoogle Scholar
  21. 21.
    Watanabe T, Kobunai T, Toda E, Yamamoto Y, Kanazawa T, Kazama Y, et al. Distal colorectal cancers with microsatellite instability (MSI) display distinct gene expression profiles that are different from proximal MSI cancers. Cancer Res. 2006;66:9804–8.PubMedCrossRefGoogle Scholar
  22. 22.
    Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004;429:457–63.PubMedCrossRefGoogle Scholar
  23. 23.
    Chan TA GS, Yi JM, Chen W, Van Neste L, Cope L, Herman JG, et al. Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis. PLoS Med. 2008;5:0823–38.Google Scholar
  24. 24.
    Yi JM, Dhir M, Van Neste L, Downing SR, Jeschke J, Glockner SC, et al. Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clin Cancer Res. 2011;17:1535–45.PubMedCrossRefGoogle Scholar
  25. 25.
    Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet. 2007;16:R50–9.PubMedCrossRefGoogle Scholar
  26. 26.
    Zhang W, Glockner SC, Guo M, Machida EO, Wang DH, Easwaran H, et al. Epigenetic inactivation of the canonical Wnt antagonist SRY-box containing gene 17 in colorectal cancer. Cancer Research. 2008;68:2764–72.PubMedCrossRefGoogle Scholar
  27. 27.
    Tsunoda SSE, De Young NJ, Wang X, Tian ZQ, Liu JF, Jamieson GG, et al. Methylation of CLDN6, FBN2, RBP1, RBP4, TFPI2, and TMEFF2 in esophageal squamous cell carcinoma. Oncological Report. 2009;21:1067–73.Google Scholar
  28. 28.
    Cortese R, Hartmann O, Berlin K, Eckhardt F. Correlative gene expression and DNA methylation profiling in lung development nominate new biomarkers in lung cancer. Int J Biochem Cell Biol. 2008;40:1494–508.PubMedCrossRefGoogle Scholar
  29. 29.
    Chen H, Suzuki M, Nakamura Y, Ohira M, Ando S, Iida T, et al. Aberrant methylation of FBN2 in human non-small cell lung cancer. Lung Cancer. 2005;50:43–9.PubMedCrossRefGoogle Scholar
  30. 30.
    Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer. 2003;3:253–66.PubMedCrossRefGoogle Scholar
  31. 31.
    Lofton-Day C, Model F, DeVos T, Tetzner R, Distler J, Schuster M, et al. DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem. 2008;54:414–23.PubMedCrossRefGoogle Scholar
  32. 32.
    Kim MS LJ, Sidransky D. DNA methylation markers in colorectal cancer. Cancer Metastasis Review. 2010;29:181–206.CrossRefGoogle Scholar
  33. 33.
    Melotte VLM, van den Bosch SM, Hellebrekers DM, de Hoon JP, Wouters KA, Daenen KL, et al. N-Myc downstream-regulated gene 4 (NDGR4): a candidate tumor suppressor gene and potential biomarker for colorectal cancer. J Natl Canc Inst. 2009;101:916–27.CrossRefGoogle Scholar
  34. 34.
    Melotte V, Lentjes MHFM, van den Bosch SM, Hellebrekers DMEI, de Hoon JPJ, Wouters KAD, et al. N-Myc downstream-regulated gene 4 (NDRG4): a candidate tumor suppressor gene and potential biomarker for colorectal cancer. J National Cancer Institute. 2009;101:916–27.CrossRefGoogle Scholar

Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2012

Authors and Affiliations

  • Joo Mi Yi
    • 1
  • Mashaal Dhir
    • 2
  • Angela A. Guzzetta
    • 2
  • Christine A. Iacobuzio-Donahue
    • 3
  • Kyu Heo
    • 1
  • Kwang Mo Yang
    • 1
  • Hiromu Suzuki
    • 4
  • Minoru Toyota
    • 4
  • Hwan-Mook Kim
    • 5
  • Nita Ahuja
    • 2
  1. 1.Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS)BusanSouth Korea
  2. 2.Department of SurgeryThe Johns Hopkins University School of MedicineBaltimoreUSA
  3. 3.Department of PathologyThe Johns Hopkins University School of MedicineBaltimoreUSA
  4. 4.Department of Molecular BiologySapporo Medical UniversitySapporoJapan
  5. 5.Department of Pharmacy, College of PharmacyGacheon University of Medicine and ScienceIncheonSouth Korea

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