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Location-specific epigenetic regulation of the metallothionein 3 gene in esophageal adenocarcinomas.

Peng D, Hu TL, Jiang A, Washington MK, Moskaluk CA, Schneider-Stock R, El-Rifai W - PLoS ONE (2011)

Bottom Line: Moreover, the DNA hypermethylation from -127 to -8 CpG sites significantly correlated with advanced tumor stages and lymph node metastasis (P = 0.005 and P = 0.0313, respectively).The ChIP analysis demonstrated a more repressive histone modification (H3K9me2) and less active histone modifications (H3K4me2, H3K9ace) in OE33 cells than in FLO-1 cells; concordant with the presence of higher DNA methylation levels and silencing of MT3 expression in OE33 as compared to FLO-1 cells.The choice of specific regions in the CpG island is a critical step in determining the functional role and prognostic value of DNA methylation in cancer cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.

ABSTRACT

Background: Metallothionein 3 (MT3) maintains intracellular metal homeostasis and protects against reactive oxygen species (ROS)-induced DNA damage. In this study, we investigated the epigenetic alterations and gene expression of the MT3 gene in esophageal adenocarcinomas (EACs).

Methods and results: Using quantitative bisulfite pyrosequencing, we detected unique DNA methylation profiles in the MT3 promoter region. The CpG nucleotides from -372 to -306 from the transcription start site (TSS) were highly methylated in tumor (n = 64) and normal samples (n = 51), whereas CpG nucleotides closest to the TSS (-4 and +3) remained unmethylated in all normal and most tumor samples. Conversely, CpG nucleotides in two regions (from -139 to -49 and +296 to +344) were significantly hypermethylated in EACs as compared to normal samples [FDR<0.001, -log10(FDR)>3.0]. The DNA methylation levels from -127 to -8 CpG sites showed the strongest correlation with MT3 gene expression (r = -0.4, P<0.0001). Moreover, the DNA hypermethylation from -127 to -8 CpG sites significantly correlated with advanced tumor stages and lymph node metastasis (P = 0.005 and P = 0.0313, respectively). The ChIP analysis demonstrated a more repressive histone modification (H3K9me2) and less active histone modifications (H3K4me2, H3K9ace) in OE33 cells than in FLO-1 cells; concordant with the presence of higher DNA methylation levels and silencing of MT3 expression in OE33 as compared to FLO-1 cells. Treatment of OE33 cells with 5-Aza-deoxycitidine restored MT3 expression with demethylation of its promoter region and reversal of the histone modifications towards active histone marks.

Conclusion: In summary, EACs are characterized by frequent epigenetic silencing of MT3. The choice of specific regions in the CpG island is a critical step in determining the functional role and prognostic value of DNA methylation in cancer cells.

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Related in: MedlinePlus

MT3 methylation of is associated with advanced tumor stage and lymph node metastasis.A) Increased DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with advanced tumor staging (P = 0.005). B) DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with lymph node metastasis (P = 0.03). C) DNA methylation of MT3 promoter R3 (+28 to +344 sites) correlates with tumor staging (P = 0.03). D) DNA methylation of MT3 promoter R3 (+28 to +344 sites) does not correlate with lymph node status (P = 0.4).
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pone-0022009-g006: MT3 methylation of is associated with advanced tumor stage and lymph node metastasis.A) Increased DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with advanced tumor staging (P = 0.005). B) DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with lymph node metastasis (P = 0.03). C) DNA methylation of MT3 promoter R3 (+28 to +344 sites) correlates with tumor staging (P = 0.03). D) DNA methylation of MT3 promoter R3 (+28 to +344 sites) does not correlate with lymph node status (P = 0.4).

Mentions: To investigate if MT3 promoter methylation is associated with tumor biology, we performed statistical analysis between DNA methylation and clinicopathological parameters. As shown in Figure 6, DNA methylation of R2 (from −127 to −8 CpG sites) was significantly associated with advanced tumor stages (P = 0.005) and lymph node metastasis (P = 0.031). However, DNA methylation R3 (from +28 to +344 sites) was only associated with tumor stage (P = 0.033) but not with lymph node metastasis (P = 0.45).


Location-specific epigenetic regulation of the metallothionein 3 gene in esophageal adenocarcinomas.

Peng D, Hu TL, Jiang A, Washington MK, Moskaluk CA, Schneider-Stock R, El-Rifai W - PLoS ONE (2011)

MT3 methylation of is associated with advanced tumor stage and lymph node metastasis.A) Increased DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with advanced tumor staging (P = 0.005). B) DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with lymph node metastasis (P = 0.03). C) DNA methylation of MT3 promoter R3 (+28 to +344 sites) correlates with tumor staging (P = 0.03). D) DNA methylation of MT3 promoter R3 (+28 to +344 sites) does not correlate with lymph node status (P = 0.4).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139601&req=5

pone-0022009-g006: MT3 methylation of is associated with advanced tumor stage and lymph node metastasis.A) Increased DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with advanced tumor staging (P = 0.005). B) DNA methylation of MT3 promoter R2 (−127 to −8 sites) correlates with lymph node metastasis (P = 0.03). C) DNA methylation of MT3 promoter R3 (+28 to +344 sites) correlates with tumor staging (P = 0.03). D) DNA methylation of MT3 promoter R3 (+28 to +344 sites) does not correlate with lymph node status (P = 0.4).
Mentions: To investigate if MT3 promoter methylation is associated with tumor biology, we performed statistical analysis between DNA methylation and clinicopathological parameters. As shown in Figure 6, DNA methylation of R2 (from −127 to −8 CpG sites) was significantly associated with advanced tumor stages (P = 0.005) and lymph node metastasis (P = 0.031). However, DNA methylation R3 (from +28 to +344 sites) was only associated with tumor stage (P = 0.033) but not with lymph node metastasis (P = 0.45).

Bottom Line: Moreover, the DNA hypermethylation from -127 to -8 CpG sites significantly correlated with advanced tumor stages and lymph node metastasis (P = 0.005 and P = 0.0313, respectively).The ChIP analysis demonstrated a more repressive histone modification (H3K9me2) and less active histone modifications (H3K4me2, H3K9ace) in OE33 cells than in FLO-1 cells; concordant with the presence of higher DNA methylation levels and silencing of MT3 expression in OE33 as compared to FLO-1 cells.The choice of specific regions in the CpG island is a critical step in determining the functional role and prognostic value of DNA methylation in cancer cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.

ABSTRACT

Background: Metallothionein 3 (MT3) maintains intracellular metal homeostasis and protects against reactive oxygen species (ROS)-induced DNA damage. In this study, we investigated the epigenetic alterations and gene expression of the MT3 gene in esophageal adenocarcinomas (EACs).

Methods and results: Using quantitative bisulfite pyrosequencing, we detected unique DNA methylation profiles in the MT3 promoter region. The CpG nucleotides from -372 to -306 from the transcription start site (TSS) were highly methylated in tumor (n = 64) and normal samples (n = 51), whereas CpG nucleotides closest to the TSS (-4 and +3) remained unmethylated in all normal and most tumor samples. Conversely, CpG nucleotides in two regions (from -139 to -49 and +296 to +344) were significantly hypermethylated in EACs as compared to normal samples [FDR<0.001, -log10(FDR)>3.0]. The DNA methylation levels from -127 to -8 CpG sites showed the strongest correlation with MT3 gene expression (r = -0.4, P<0.0001). Moreover, the DNA hypermethylation from -127 to -8 CpG sites significantly correlated with advanced tumor stages and lymph node metastasis (P = 0.005 and P = 0.0313, respectively). The ChIP analysis demonstrated a more repressive histone modification (H3K9me2) and less active histone modifications (H3K4me2, H3K9ace) in OE33 cells than in FLO-1 cells; concordant with the presence of higher DNA methylation levels and silencing of MT3 expression in OE33 as compared to FLO-1 cells. Treatment of OE33 cells with 5-Aza-deoxycitidine restored MT3 expression with demethylation of its promoter region and reversal of the histone modifications towards active histone marks.

Conclusion: In summary, EACs are characterized by frequent epigenetic silencing of MT3. The choice of specific regions in the CpG island is a critical step in determining the functional role and prognostic value of DNA methylation in cancer cells.

Show MeSH
Related in: MedlinePlus