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Peripheral Blood DNA Methylation Markers for the Early Detection of Colorectal Carcinoma in the Egyptian Population

ABSTRACT: The incidence of colorectal cancer (CRC) is on the rise on a global scale. The number of cancer-related deaths related to CRC is also rising to an alarming level. This picture is similarly seen in Egypt where the incidence of colorectal carcinoma is increasing annually, moreover, CRC in Egypt exhibits an alarming characteristic which is the affection of much younger patients than their counterparts worldwide. Fortunately, the early detection of CRC and its precursor (adenoma) has been shown to markedly decrease morbidity and mortality related to this tumor, this has prompted the development of robust screening programs for CRC in several western countries. The implementation of a CRC screening program in Egypt has been hampered by the low compliance of the patients and the relatively high cost of colonoscopy. There is a need for an affordable, non-invasive, simple, accurate and socially accepted screening test to allow such a program to succeed in Egypt. Recent studies have shown that DNA is the future target of screening tests for several malignancies. Particularly for CRC a few preliminary studies have shown encouraging results with separate DNA methylation markers both in blood and stool. In our efforts to develop a screening test with the criteria stated above, the investigators have decided to join the forces of 2 of the largest medical centers in Egypt and the middle-east: Kasr-Alaini hospital and the National cancer institute (NCI). The investigators plan to test a panel of 7 DNA methylation markers in peripheral blood for their performance as an early marker for CRC and colorectal adenomas. Data from this study will pave the way for the development of a screening test for CRC "tailored" to the Egyptian population, moreover, it will supply essential data about the genetic alterations occurring in CRC in Egyptian patients.

DISEASE(S): Colorectal Tumors,Colorectal Neoplasms,Adenoma

PROVIDER: 2140193 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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Project description:Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5 - 8.7% of CRCs. It has been shown that SAC has a worse prognosis and has different molecular and immunohistochemical features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile. We have investigated the methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array in 103 colorectal specimens from Spanish and Finnish patients. The comparison between the epigenetic signature of 36 SACs and 34 matched CCs was established with the aim of identifying the functions which characterize SAC biology and also the most differentially methylated genes for subsequent validatation by pyrosequencing, methylation-specific PCR, qPCR and immunohistochemistry, including additional cases. Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle-transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA and protein level. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing SAC with CRC showing molecular and histological features of high level microsatellite instability. This methylome study demonstrates that SAC has a distinct epigenetic regulation pattern resulting in different biological functions and that DIO3 and FOXD2 might be molecular targets for a specific histology-oriented treatment of CRC. HumanMethylation450K BeadChip (Illumina, Inc, San Diego, CA), using Infinium HD Methylation assay for genome-wide DNA methylation screening, was employed. In brief, genomic DNA (1000 ng) from each sample was bisulfite converted with the EZ DNA Methylation Kit (Zymo Research, Orange, CA) according to the manufacturer´s recommendations. Bisulfite-treated DNA was isothermally amplified at 37°C (20-24h) and the DNA product was fragmented by an endpoint enzymatic process, then precipitated, resuspended, applied to an Infinium Human Methylation450K BeadChip (Illumina, San Diego, CA, USA) and hybridized at 48°C (16-24h). The fluorescently-stained chip was imaged by the Illumina i-SCAN and Illumina's Genome Studio program (Methylation Module) was used to analyze BeadArray data to assign site-specific DNA methylation β-values to each CpG site.

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Peripheral Blood DNA Methylation Markers for the Early Detection of Colorectal Carcinoma in the Egyptian Population

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