Toward a comprehensive and systematic methylome signature in colorectal cancers

Abstract

CpG Island Methylator Phenotype (CIMP) is one of the underlying mechanisms in colorectal cancer (CRC). This study aimed to define a methylome signature in CRC through a methylation microarray analysis and a compilation of promising CIMP markers from the literature. Illumina HumanMethylation27 (IHM27) array data was generated and analyzed based on statistical differences in methylation data (1st approach) or based on overall differences in methylation percentages using lower 95% CI (2nd approach). Pyrosequencing was performed for the validation of nine genes. A meta-analysis was used to identify CIMP and non-CIMP markers that were hypermethylated in CRC but did not yet make it to the CIMP genes' list. Our 1st approach for array data analysis demonstrated the limitations in selecting genes for further validation, highlighting the need for the 2nd bioinformatics approach to adequately select genes with differential aberrant methylation. A more comprehensive list, which included non-CIMP genes, such as APC, EVL, CD109, PTEN, TWIST1, DCC, PTPRD, SFRP1, ICAM5, RASSF1A, EYA4, 30ST2, LAMA1, KCNQ5, ADHEF1, and TFPI2, was established. Array data are useful to categorize and cluster colonic lesions based on their global methylation profiles; however, its usefulness in identifying robust methylation markers is limited and rely on the data analysis method. We have identified 16 non-CIMP-panel genes for which we provide rationale for inclusion in a more comprehensive characterization of CIMP+ CRCs. The identification of a definitive list for methylome specific genes in CRC will contribute to better clinical management of CRC patients.

DNA methylome profiling identifies novel methylated genes in African American patients with colorectal neoplasia

“…We have recently published a microarray methylome study that illustrated a genome-wide methylation-based clustering of different genes and loci in colorectal neoplasia specimens as a function of disease status. 11 Herein, we used the reduced representation bisulfite sequencing (RRBS) to analyze methylome profiles in different colon tissues and validated a subset of highly methylated targets in an independent cohort of colorectal specimens.…”

“…We recently reported a list of methylated genes that have been shown to be methylated in several studies but never made it to the CIMP gene list. 11 Of this list of 15 genes (table #), 4 were methylated in this RRBS data set. These genes, SFRP1, 3OST2, LAMA1, and KCNQ5, might be eligible now to make the CIMP gene list, since our RRBS data reflect their methylation status in the analyzed samples.…”

“…5,6 Many genes are silenced by aberrant methylation in CRC, such genes have the potential to become useful biomarkers for early detection of colorectal neoplasia but need first to be validated using genome wide studies. 5,6,11,12 The ability to detect aberrant DNA methylation from a wide range of biological specimens, including blood, stool, and paraffin-embedded formalin-fixed tissue, highlights its robustness and excellent potential to detect markers of clinical utility. In addition, DNA methylation patterns can be…”

DNA Methylation and Colorectal Cancer

“…[5,6] The hypermethylation of several gene promoters including APC, p16INK4a, TIMP3 in CRC has been reported [5,6,7]. The aberrant methylation of CpG islands within gene promoters and/or first exonic/intronic regions is a recognized epigenetic event that leads to transcriptional silencing.…”

“…The aberrant methylation of CpG islands within gene promoters and/or first exonic/intronic regions is a recognized epigenetic event that leads to transcriptional silencing. Regardless of the biological consequences of methylation-induced silencing of tumor suppressor genes, this epigenetic alteration constitutes a molecular signature that can serve as a promising biomarker for early detection [5,6,8,9]. The ability to detect aberrant DNA methylation from a wide range of biological specimens highlights its robustness and excellent potential to detect markers of clinical utility in a non-invasive manner.…”