Abstract
Background: Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult. Methods. We profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm. Results: We were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the HOX and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (MDM2, DYRK2, and LYZ) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue. Conclusions: Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.
| Original language | English |
|---|---|
| Article number | 82 |
| Journal | BMC Medical Genomics |
| Volume | 4 |
| DOIs | |
| Publication status | Published - 2011 Dec 5 |
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All Science Journal Classification (ASJC) codes
- Genetics
- Genetics(clinical)
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Identification of DNA methylation changes associated with human gastric cancer. / Park, Jung Hoon; Park, Jinah; Choi, Jung Kyoon; Lyu, Jaemyun; Bae, Min Gyun; Lee, Young Gun; Bae, Jae Bum; Park, Dong Yoon; Yang, Han Kwang; Kim, Tae You; Kim, Young Joon.
In: BMC Medical Genomics, Vol. 4, 82, 05.12.2011.Research output: Contribution to journal › Article
TY - JOUR
T1 - Identification of DNA methylation changes associated with human gastric cancer
AU - Park, Jung Hoon
AU - Park, Jinah
AU - Choi, Jung Kyoon
AU - Lyu, Jaemyun
AU - Bae, Min Gyun
AU - Lee, Young Gun
AU - Bae, Jae Bum
AU - Park, Dong Yoon
AU - Yang, Han Kwang
AU - Kim, Tae You
AU - Kim, Young Joon
PY - 2011/12/5
Y1 - 2011/12/5
N2 - Background: Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult. Methods. We profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm. Results: We were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the HOX and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (MDM2, DYRK2, and LYZ) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue. Conclusions: Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.
AB - Background: Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult. Methods. We profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm. Results: We were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the HOX and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (MDM2, DYRK2, and LYZ) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue. Conclusions: Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.
UR - http://www.scopus.com/inward/record.url?scp=82455162772&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=82455162772&partnerID=8YFLogxK
U2 - 10.1186/1755-8794-4-82
DO - 10.1186/1755-8794-4-82
M3 - Article
C2 - 22133303
AN - SCOPUS:82455162772
VL - 4
JO - BMC Medical Genomics
JF - BMC Medical Genomics
SN - 1755-8794
M1 - 82
ER -