Methylation profile of colon cancer genes in colorectal precursor lesions and tumor tissue: perspectives for screening

Abstract

Aims

Epigenetic alterations of genes involved in colorectal carcinogenesis are likely to be informative biomarkers for early detection. We assessed the methylation profile of a panel of seven colon cancer-related genes comparing normal colon, colorectal cancer (CRC) precursor lesions and cancer tissues from a Brazilian cohort.

Methods

The cohort comprised 114 CRC patients, including 40 matched normal tissue, 47 patients with adenomas, 33 with serrated polyps and 8 with normal colonic biopsy. DNA methylation status of SEPT9, ALX4, NDRG4, BMP3, APC, p16 and MLH1 was determined by pyrosequencing and correlated with clinicopathological features. Sensitivity, specificity, positive predictive value and negative predictive value were calculated for all genes using cancer endpoint.

Results

The most frequently methylated genes in cancer and in precancer lesions were SEPT9, ALX4, NDRG4, and BMP3, ranging from 55.3 to 95% of the samples. Overall, the frequency of methylation of these four genes in normal colonic tissue was significantly lower as compared to cancer or precursor lesions both in adenoma–carcinoma (p < .001 and p < .050) and serrated (sessile-serrated lesion) (p < .001 and p < .050) pathways. Additionally, sensitivity for the cancer endpoint ranged from 65.6 to 91.8%, and specificity from 17.9 to 62.9% for SEPT9, ALX4, NDRG4, and BMP3 genes. Moreover, the comethylation of ≥4 genes was higher in sessile-serrated lesion (87.5%) and conventional adenomas (78.7%) than in hyperplastic polyps (43.7%) (p = .025) and was significantly associated with proximal cancers (p = .042).

Conclusions

Our study suggests the DNA methylation can constitute potential biomarkers in CRC screening of Brazilian population.

Keywords:

• Colorectal cancer
• adenoma
• serrated polyps
• DNA methylation
• biomarker
• Brazil

Acknowledgments

The Biobank of Barretos Cancer Hospital was responsible for the extraction of the fresh frozen tissue samples. The authors would like to thank Dr. Jeremy Squire for carefully proofreading the English and for providing constructive criticism of the manuscript.

Ethical approval

The study was approved by the Research Ethical Committee of the Barretos Cancer Hospital on 4 February 2016 (number ID: 1074/2016). Informed consent was waived because of the retrospective nature of this study. The study protocol conforms to the ethical guidelines of the 1975 Declaration of Helsinki.

Author contributions

Conceived and designed the experiments: DPG, RMR, LA. Performed the experiments: TS, WS, MC. Analyzed the data: DPG, RMR, LA, TS, WS, MM, ACC. Contributed reagents/materials/analysis tools: DPG, RMR, LA, GNB, KS. Drafted the article: DPG, RMR, TS. Revised the manuscript critically for important intellectual content: DPG, RMR, KS. Supervised the study: DPG.

Disclosure statement

The authors declare that there is no conflict interest.

Data availability statement

The datasets generated and analyzed during the current study are not publicly available but are available from the corresponding author on reasonable request.

Additional information

Funding

Thais Sobanski and Wellington dos Santos are recipient of a fellowship of the postgraduate program of Barretos Cancer Hospital. Rui Manuel Reis is a recipient of a CNPq Productivity (Brazil) fellowship. The present study was also supported by the Public Ministry of Labor Campinas (Research, Prevention, and Education of Occupational Cancer) in Campinas, Brazil and Barretos Cancer Hospital internal (IEP) grant.