The development of colorectal cancer (CRC) is a multi-step process, called the polyp to cancer sequence, resulting from the accumulation of genomic alterations and epigenetic alterations in colon epithelial cells. These epigenetic alterations include the aberrant methylation of the 5' promoter region of genes with CpG islands, which can silence the expression of tumor suppressor genes. The accumulation of aberrantly methylated genes begins at the pre-cancer phase of CRC formation and is common in CRC, affecting thousands of genes, and resulting in a variety of different tumor promoting biological effects on the CRCs. An unanswered question is how the methylated genes vary between the known CRC molecular subgroups, Chromosomal Unstable (CIN), Microsatellite Unstable (MSI), and CpG Island Methylator Phenotype (CIMP) tumors. Thus, we propose to create a Research Team under the guidance of two PIs, William Grady and Sanford Markowitz, to lead an EDRN Biomarker Developmental Lab to discover novel methylated genes that can be used as early detection markers and predictive markers using cutting-edge and complementary approaches, HumanMethylation27 DNA Analysis Beadchip (lllumina Infinium platform), and deep sequencing of captured NaHSO3 treated DNA (Agilent and Solexa). These approaches will take advantage of the developed expertise of the Grady lab and of the Markowitz lab, respectively, and have the potential to identify a panel of complementary biomarkers for the early detection of colorectal neoplasms and for enhancing the care of early stage CRC. We propose the following Specific Aims: Aim 1) To develop and validate epigenetic signatures of colon adenomas and early stage non-metastatic colon cancers. Aim 2) To perform a comprehensive epigenomic characterization of colorectal cancer molecular subtypes. 2a) To develop differential methylation profiles between CIMP and nonCIMP CRCs. 2b) To develop differential methylation profiles between CIN vs. MSI CRCs. Aim 3) To identify and characterize biologically relevant novel methylation targets in colorectal cancer.
