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Identification of differentially-expressed genes by DNA methylation in cervical cancer.

Lee HS, Yun JH, Jung J, Yang Y, Kim BJ, Lee SJ, Yoon JH, Moon Y, Kim JM, Kwon YI - Oncol Lett (2015)

Bottom Line: A number of the identified genes were novel cervical cancer-related genes and their differential expression was confirmed in a publicly available database.From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation.These genes may be involved in the progression or initiation of cervical cancer.

View Article: PubMed Central - PubMed

Affiliation: Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea.

ABSTRACT

To identify novel cervical cancer-related genes that are regulated by DNA methylation, integrated analyses of genome-wide DNA methylation and RNA expression profiles were performed using the normal and tumor regions of tissues from four patients; two with cervical cancer and two with pre-invasive cancer. The present study identified 19 novel cervical cancer-related genes showing differential RNA expression by DNA methylation. A number of the identified genes were novel cervical cancer-related genes and their differential expression was confirmed in a publicly available database. Among the candidate genes, the epigenetic regulation and expression of three genes, CAMK2N1, ALDH1A3 and PPP1R3C, was validated in HeLa cells treated with a demethylating reagent using methylation-specific polymerase chain reaction (PCR) and quantitative PCR, respectively. From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation. These genes may be involved in the progression or initiation of cervical cancer.

No MeSH data available.


Related in: MedlinePlus

Heatmaps of differentially-expressed genes and methylated loci. There are 19 significantly up- or downregulated genes and 28 methylated loci revealing differential mRNA expression and methylation profiles in the cervical cancer tissues. Different numbers for expression and methylation profiles are observed since some of the genes have two or more methylation loci. Red and green colors indicate the extent of the profiles in the cancer tissues versus that of the normal tissues of each patient sample. For example, red color in methylation profiles and green color in expression profiles show the hypermethylation and downregulation in cancer versus normal tissues, respectively.
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f1-ol-09-04-1691: Heatmaps of differentially-expressed genes and methylated loci. There are 19 significantly up- or downregulated genes and 28 methylated loci revealing differential mRNA expression and methylation profiles in the cervical cancer tissues. Different numbers for expression and methylation profiles are observed since some of the genes have two or more methylation loci. Red and green colors indicate the extent of the profiles in the cancer tissues versus that of the normal tissues of each patient sample. For example, red color in methylation profiles and green color in expression profiles show the hypermethylation and downregulation in cancer versus normal tissues, respectively.

Mentions: To confirm the negative correlation between DNA methylation and RNA expression profiles associated with the progression of cervical cancer, 19 genes that were selected on the basis of integrated analysis were clustered. Common methylation and expression patterns were visualized by unsupervised hierarchical clustering using an average linkage clustering method. As shown in Fig. 1, a separate cluster was formed by methylation and expression data. A negative correlation of methylation and expression was observed using TreeView. Functional annotation clustering was conducted using DAVID with default conditions to analyze the biological significance of the 19 selected genes. This showed that the selected genes were classified into five clusters to be enriched in the cell junction, membrane/plasma membrane, cytoskeletal part, glycoprotein and ion/metal binding (Table II).


Identification of differentially-expressed genes by DNA methylation in cervical cancer.

Lee HS, Yun JH, Jung J, Yang Y, Kim BJ, Lee SJ, Yoon JH, Moon Y, Kim JM, Kwon YI - Oncol Lett (2015)

Heatmaps of differentially-expressed genes and methylated loci. There are 19 significantly up- or downregulated genes and 28 methylated loci revealing differential mRNA expression and methylation profiles in the cervical cancer tissues. Different numbers for expression and methylation profiles are observed since some of the genes have two or more methylation loci. Red and green colors indicate the extent of the profiles in the cancer tissues versus that of the normal tissues of each patient sample. For example, red color in methylation profiles and green color in expression profiles show the hypermethylation and downregulation in cancer versus normal tissues, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356325&req=5

f1-ol-09-04-1691: Heatmaps of differentially-expressed genes and methylated loci. There are 19 significantly up- or downregulated genes and 28 methylated loci revealing differential mRNA expression and methylation profiles in the cervical cancer tissues. Different numbers for expression and methylation profiles are observed since some of the genes have two or more methylation loci. Red and green colors indicate the extent of the profiles in the cancer tissues versus that of the normal tissues of each patient sample. For example, red color in methylation profiles and green color in expression profiles show the hypermethylation and downregulation in cancer versus normal tissues, respectively.
Mentions: To confirm the negative correlation between DNA methylation and RNA expression profiles associated with the progression of cervical cancer, 19 genes that were selected on the basis of integrated analysis were clustered. Common methylation and expression patterns were visualized by unsupervised hierarchical clustering using an average linkage clustering method. As shown in Fig. 1, a separate cluster was formed by methylation and expression data. A negative correlation of methylation and expression was observed using TreeView. Functional annotation clustering was conducted using DAVID with default conditions to analyze the biological significance of the 19 selected genes. This showed that the selected genes were classified into five clusters to be enriched in the cell junction, membrane/plasma membrane, cytoskeletal part, glycoprotein and ion/metal binding (Table II).

Bottom Line: A number of the identified genes were novel cervical cancer-related genes and their differential expression was confirmed in a publicly available database.From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation.These genes may be involved in the progression or initiation of cervical cancer.

View Article: PubMed Central - PubMed

Affiliation: Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea.

ABSTRACT

To identify novel cervical cancer-related genes that are regulated by DNA methylation, integrated analyses of genome-wide DNA methylation and RNA expression profiles were performed using the normal and tumor regions of tissues from four patients; two with cervical cancer and two with pre-invasive cancer. The present study identified 19 novel cervical cancer-related genes showing differential RNA expression by DNA methylation. A number of the identified genes were novel cervical cancer-related genes and their differential expression was confirmed in a publicly available database. Among the candidate genes, the epigenetic regulation and expression of three genes, CAMK2N1, ALDH1A3 and PPP1R3C, was validated in HeLa cells treated with a demethylating reagent using methylation-specific polymerase chain reaction (PCR) and quantitative PCR, respectively. From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation. These genes may be involved in the progression or initiation of cervical cancer.

No MeSH data available.


Related in: MedlinePlus