Identification and validation of colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites

Abstract

To date, the sensitivity of currently available biomarkers based on the methylation of gene promoters is suboptimal for detecting adenomas and early-stage colorectal cancer (CRC). We aimed to develop biomarkers with methylated DNA binding sites of the multifunctional transcriptional factor CTCF for early detection of CRC. Using combined analyses of genome-wide occupation and the methylation profile of CTCF-binding sites, we identified candidate CTCF-binding sites. Then, we applied methylation-sensitive high-resolution melting (MS-HRM) and mass spectrometry analysis to screen and validate these candidate sites in diverse sample sets. We identified a set of colorectal neoplasia-specific biomarkers with robust performance. The top five biomarkers were selected and recommended for early detection of colorectal neoplasia. All of the five novel biomarkers exhibited a more robust discriminatory performance than that by BMP3 and NDRG4, two currently acknowledged robust methylation biomarkers. When the five new biomarkers were considered as a marker panel and tumor-positive was defined as having two or more (of the five) positive biomarkers, the marker panel could achieve a sensitivity of 91.67% for adenomas, 97.44% for Stage I CRC, 94.06% for Stage II CRC, 93.62% for Stage III CRC, and 93.54% for total colorectal tumors with a specificity of 94.05%. To our knowledge, this is the first study for colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Using a similar strategy, CTCF-binding sites could be potentially developed into biomarkers for other tumors. In summary, this study opens a new area in developing biomarkers for tumor prevention and treatment.

Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review

“…The five potential zinc-finger protein CCCTC-binding factors function as transcriptional activator, repressor, or insulator proteins; CTCF_33, CTCF_55, CTCF_94, CTCF_113, and CTCF_13 biomarkers analyzed in a study from China showed better performance than two well-known methylation biomarkers, NDRG4 and BMP3. Furthermore, with a sensitivity of 93.54% and a specificity of 94.05% ( Figure 5 ), CTCF-binding sites may be possible biomarkers in colorectal cancer detection [ 92 ].…”

“…In addition, the assessment of each mCTCF-binding site exhibited higher sensitivity and specificity for stage I-II than for terminal stages. Moreover, when a panel of five mCTCF-binding sites was examined, a sensitivity of 91.67% and a specificity of 94.05% were recorded for adenomas, pointing towards a more precise early-stage biomarker [ 92 ].…”

Prognostic and Predictive Epigenetic Biomarkers in Oncology

“…Aberrations of CTCF bindings depend on many mechanisms, including DNA methylation at the imprinting control region observed in testicular germ-cell tumors (TGCTs), CRC, bladder cancer, and ovarian cancer [87]. Liu et al [88] indicated a set of five biomarkers (CTCF_13 [chr10: 15761963-15762083], CTCF_33 [chr13: 61564369-61564467], CTCF_55 [chr17: 27940559-27940669], CTCF_94 [chr4: 165304966-165305120], and CTCF_113 [chr8: 69243102-69243188]) based on the methylation status of CTCF binding sites that were considered as a diagnostic marker panel in CRC (Table 3) [88]. This panel achieves a sensitivity of 91.67% for adenomas, 97.44% for stage I CRC, 94.06% for stage II CRC, 93.62% for stage III CRC, and 93.54% for total colorectal tumors with a specificity of 94.05%.…”