A two-gene blood test for methylated DNA sensitive for colorectal cancer

PLoS One. 2015 Apr 30;10(4):e0125041. doi: 10.1371/journal.pone.0125041. eCollection 2015.

Abstract

Background: Specific genes are methylated with high frequency in colorectal neoplasia, and may leak into blood. Detection of multiple methylated DNA biomarkers in blood may improve assay sensitivity for colorectal cancer (CRC) relative to a single marker. We undertook a case-control study evaluating the presence of two methylation DNA markers, BCAT1 and IKZF1, in circulation to determine if they were complementary for detection of CRC.

Methods: Methylation-specific PCR assays were developed to measure the level of methylated BCAT1 and IKZF1 in DNA extracted from plasma obtained from colonoscopy-confirmed 144 healthy controls and 74 CRC cases.

Results: DNA yields ranged from 2 to 730 ng/mL plasma (mean 18.6ng/mL; 95% CI 11-26 ng/mL) and did not correlate with gender, age or CRC status. Methylated BCAT1 and IKZF1 DNA were detected in respectively 48 (65%) and 50 (68%) of the 74 cancers. In contrast, only 5 (4%) and 7 (5%) controls were positive for BCAT1 and IKZF1 DNA methylation, respectively. A two-gene classifier model ("either or" rule) improved segregation of CRC from controls, with 57 of 74 cancers (77%) compared to only 11 of 144 (7.6%) controls being positive for BCAT1 and/or IKZF1 DNA methylation. Increasing levels of methylated DNA were observed as CRC stage progressed.

Conclusions: Detection of methylated BCAT1 and/or IKZF1 DNA in plasma may have clinical application as a novel blood test for CRC. Combining the results from the two methylation-specific PCR assays improved CRC detection with minimal change in specificity. Further validation of this two-gene blood test with a view to application in screening is now indicated.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / genetics*
  • Colorectal Neoplasms / blood supply*
  • Colorectal Neoplasms / diagnosis
  • Colorectal Neoplasms / genetics*
  • DNA Methylation / genetics*
  • Female
  • Gene Expression Regulation, Neoplastic / genetics
  • Humans
  • Ikaros Transcription Factor / genetics
  • Male
  • Neoplasm Staging
  • Transaminases / genetics

Substances

  • Biomarkers, Tumor
  • IKZF1 protein, human
  • Ikaros Transcription Factor
  • BCAT1 protein, human
  • Transaminases

Grant support

This work was co-funded by Clinical Genomics Pty Ltd, and the Commonwealth Scientific and Industrial Research Organization (CSIRO). LCL, SKP, RTB, AM, DHM and MT are employed by Clinical Genomics Pty Ltd. PLM, SM and TL are employed by CSIRO. GPY is a paid consultant of Clinical Genomics Pty. Ltd. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.