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| Status |
Public on Jun 21, 2015 |
| Title |
Methyome profiling in serrated carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
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.
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| Overall design |
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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| Contributor(s) |
Conesa-Zamora P, García-Solano J, del Carmen Turpin M, Sebastián-León P, Torres-Moreno D, Estrada E, Tuomisto A, Wilce J, Mäkinen MJ, Pérez-Guillermo M, Conesa A |
| Citation missing |
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| Submission date |
Apr 20, 2015 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Patricia Sebastian-Leon |
| E-mail(s) |
psebastian@cipf.es
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| Organization name |
CIPF
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| Department |
Bioinformatics and Genomics
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| Lab |
Genomics of Gene Expression Lab
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| Street address |
Av Autopista del Saler, 16
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| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46012 |
| Country |
Spain |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (120)
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| Relations |
| BioProject |
PRJNA281639 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68060_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of IDAT) |
| Processed data included within Sample table |
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