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| Status |
Public on Mar 20, 2012 |
| Title |
Screening for Epigenetically Masked Genes in Colorectal Cancer using 5-aza-2’-deoxycytidine treatment, Microarray and Gene Expression Profile |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Unearthing of silenced genes in colorectal cancer (CRC) is of great importance. We employed oligonucleotide microarray to find changes in global gene expression of five CRC cell lines. These were analyzed before and after treatment with the 5-aza-2'-Deoxycitidine. Expression of the responding genes was integrated with gene expression profiling generated by microarray analysis of matched colorectal tissue samples. Selected candidates were subjected to methylation-specific PCR (MSP) and real-time quantitative reverse transcription-PCR using CRC cell lines and paired tumor and normal samples from CRC patients. Sixty eight genes were re-expressed after 5-aza-2'-Deoxycitidine treatment and over-expressed in normal colorectal mucosa, including genes that were known to be methylated in CRC. After applying study selection criteria, we identified 16 potential genes. Two candidates were selected (ASPP1 and SCARA5). Among 15 CRC cell lines, methylation was identified in SCARA5 (20%). The methylation status of SCARA5 was subsequently investigated in 23 paired colorectal tissue samples; methylation was detected in 17%, respectively. Observed promoter methylation showed a tendency towards methylation in tumor-derived samples, in SCARA5 gene. Significant down expression of SCARA5 mRNA was observed in CRC cell lines and tumor tissues compared to adjacent normal tissues (P < 0.001 and P = 0.001, respectively). The use of genome-wide screening led to the identification of a group of candidate genes. Among them, SCARA5 was methylated and markedly down-regulated in CRC. SCARA5 gene may have a role in CRC tumorigenesis.
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| Overall design |
Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were measured by Affymetrix HG-U133 Plus 2.0 arrays. Five cell lines were also used to investigate genes upregulated after 5-aza-2'-deoxycytidine treatment. Normalization was performed by robust multi-array average (RMA) method by Gene Expression Console (affymetrix). The normalization procedure was separately performed for each data set of clinical samples and the cellline samples. The normalized gene expression levels were presented as log2-transformed values by RMA.
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| Contributor(s) |
Ahmed K, Toshiaki I, Kazuro S, Kaoru M, Satoru I, Megumi I, Hiroshi M, Hiroshi T, Hiroyuki U, Kenichi S |
| Citation(s) |
22399497 |
| Submission date |
Sep 22, 2011 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Kaoru Mogushi |
| E-mail(s) |
mogushi-k@umin.ac.jp
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| Phone |
+81-3-5802-1797
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| Organization name |
Juntendo University
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| Department |
Intractable Disease Research Center
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| Street address |
2-1-1 Hongo
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| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8421 |
| Country |
Japan |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (44)
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| GSM800745 |
patient 027b, normal, homogenized |
| GSM800746 |
patient 028b, normal, homogenized |
| GSM800747 |
patient 030b, normal, homogenized |
| GSM800748 |
patient 031b, normal, homogenized |
| GSM800749 |
patient 032b, normal, homogenized |
| GSM800750 |
patient 033b, normal, homogenized |
| GSM800751 |
patient 035b, normal, homogenized |
| GSM800752 |
patient 036b, normal, homogenized |
| GSM800753 |
patient 038b, normal, homogenized |
| GSM800754 |
patient 041b, normal, homogenized |
| GSM800755 |
patient 042b, normal, homogenized |
| GSM800756 |
patient 044b, normal, homogenized |
| GSM800757 |
patient 045b, normal, homogenized |
| GSM800758 |
patient 047b, normal, homogenized |
| GSM800759 |
patient 006b, cancer, homogenized |
| GSM800760 |
patient 011b, cancer, homogenized |
| GSM800761 |
patient 024b, cancer, homogenized |
| GSM800762 |
patient 027b, cancer, homogenized |
| GSM800763 |
patient 028b, cancer, homogenized |
| GSM800764 |
patient 030b, cancer, homogenized |
| GSM800765 |
patient 031b, cancer, homogenized |
| GSM800766 |
patient 032b, cancer, homogenized |
| GSM800767 |
patient 033b, cancer, homogenized |
| GSM800768 |
patient 035b, cancer, homogenized |
| GSM800769 |
patient 036b, cancer, homogenized |
| GSM800770 |
patient 038b, cancer, homogenized |
| GSM800771 |
patient 041b, cancer, homogenized |
| GSM800772 |
patient 042b, cancer, homogenized |
| GSM800773 |
patient 044b, cancer, homogenized |
| GSM800774 |
patient 045b, cancer, homogenized |
| GSM800775 |
patient 047b, cancer, homogenized |
| GSM800776 |
COLO320 cell line, 5aza treated |
| GSM800777 |
COLO320 cell line, control |
| GSM800778 |
HCT116 cell line, 5aza treated |
| GSM800779 |
HCT116 cell line, control |
| GSM800780 |
HT29 cell line, 5aza treated 2 |
| GSM800781 |
HT29 cell line, control 2 |
| GSM800782 |
RKO cell line, 5aza treated |
| GSM800783 |
RKO cell line, control |
| GSM800784 |
SW480 cell line, 5aza treated |
| GSM800785 |
SW480 cell line, control |
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| Relations |
| BioProject |
PRJNA147273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32323_RAW.tar |
211.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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