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Screening for epigenetically masked genes in colorectal cancer Using 5-Aza-2'-deoxycytidine, microarray and gene
Ahmed Khamas1, Toshiaki Ishikawa, Kazuro Shimokawa
1Department of Translational Oncology Graduate School of Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan.
Aim:
Unearthing of silenced genes in colorectal cancer (CRC).
Materials And Methods:
Oligonucleotide microarray was used in order to find changes in gene expression in five CRC cell lines before and after 5-aza-2'-Deoxycitidine treatment. Up-regulated genes were integrated with expression profile of matched colorectal tissue samples. Methylation-specific polymerase chain reaction and Real-time quantitative reverse transcription polymerase chain reaction were used to further analyze candidates using 15 CRC cell lines and 23 paired samples.
Results:
After applying study selection criteria for 68 genes obtained from integrated arrays, we identified 16 genes; apoptosis-stimulating of p53 protein 1(ASPP1) and Scavenger receptor class A, member 5 (SCARA5) were selected for further analysis. Methylation was only identified for SCARA5 in 20% of the cell lines and in 17% of tumor the samples. Down expression of SCARA5 was observed in CRC cell lines and in tumor samples compared to normal (p<0.001 and p=0.001, respectively).
Conclusion:
Genome-wide screening identifies genes potentially affected by methylation in CRC. SCARA5 may have a role in tumorigenesis in CRC.
Insights
Researchers identified silenced genes in colorectal cancer (CRC) by analyzing gene expression. Scavenger receptor class A, member 5 (SCARA5) showed down-regulation and methylation, suggesting a role in CRC tumorigenesis.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Colorectal cancer (CRC) is a significant global health concern.
- Identifying novel therapeutic targets requires understanding gene expression changes and epigenetic modifications in CRC.
- Silenced genes, particularly those affected by methylation, represent potential targets for intervention.
Purpose of the Study:
- To identify genes silenced by methylation in colorectal cancer (CRC).
- To investigate the role of identified genes in CRC development and progression.
- To discover potential biomarkers and therapeutic targets for CRC.
Main Methods:
- Oligonucleotide microarray analysis was performed on CRC cell lines before and after 5-aza-2'-deoxycytidine treatment to identify differentially expressed genes.
- Integrated analysis of microarray data with colorectal tissue expression profiles.
- Methylation-specific polymerase chain reaction (MSP) and Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) were used to validate candidate genes in CRC cell lines and patient samples.
Main Results:
- Genome-wide screening identified 16 potential candidate genes from 68 initial genes.
- Apoptosis-stimulating of p53 protein 1 (ASPP1) and Scavenger receptor class A, member 5 (SCARA5) were selected for further analysis.
- SCARA5 exhibited methylation in 20% of CRC cell lines and 17% of tumor samples. Down-regulation of SCARA5 was significantly observed in CRC cell lines and tumor tissues compared to normal tissues (p<0.001 and p=0.001, respectively).
Conclusions:
- Genome-wide screening effectively identifies genes potentially silenced by methylation in colorectal cancer.
- Scavenger receptor class A, member 5 (SCARA5) demonstrates altered expression and methylation patterns in CRC, suggesting its potential involvement in tumorigenesis.
- SCARA5 represents a promising candidate for further investigation as a biomarker or therapeutic target in colorectal cancer.
