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Similarity of aberrant DNA methylation in Barrett's esophagus and esophageal adenocarcinoma.

Smith E, De Young NJ, Pavey SJ, Hayward NK, Nancarrow DJ, Whiteman DC, Smithers BM, Ruszkiewicz AR, Clouston AD, Gotley DC, Devitt PG, Jamieson GG, Drew PA - Mol. Cancer (2008)

Bottom Line: The methylation frequency did not differ between BE and EAC samples, except for CDKN2A and RUNX3 which were significantly higher in EAC.This was significantly greater in EAC than in metaplastic BE for all genes except APC, MGMT and TIMP3.We found significant methylation in metaplastic BE, which for seven of the nine genes studied did not differ in frequency from that found in EAC.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Nursing and Midwifery, Flinders University, Bedford Park, South Australia 5042, Australia.

ABSTRACT

Background: Barrett's esophagus (BE) is the metaplastic replacement of squamous with columnar epithelium in the esophagus, as a result of reflux. It is the major risk factor for the development of esophageal adenocarcinoma (EAC). Methylation of CpG dinucleotides of normally unmethylated genes is associated with silencing of their expression, and is common in EAC. This study was designed to determine at what stage, in the progression from BE to EAC, methylation of key genes occurs.

Results: We examined nine genes (APC, CDKN2A, ID4, MGMT, RBP1, RUNX3, SFRP1, TIMP3, and TMEFF2), frequently methylated in multiple cancer types, in a panel of squamous (19 biopsies from patients without BE or EAC, 16 from patients with BE, 21 from patients with EAC), BE (40 metaplastic, seven high grade dysplastic) and 37 EAC tissues. The methylation frequency, the percentage of samples that had any extent of methylation, for each of the nine genes in the EAC (95%, 59%, 76%, 57%, 70%, 73%, 95%, 74% and 83% respectively) was significantly higher than in any of the squamous groups. The methylation frequency for each of the nine genes in the metaplastic BE (95%, 28%, 78%, 48%, 58%, 48%, 93%, 88% and 75% respectively) was significantly higher than in the squamous samples except for CDKN2A and RBP1. The methylation frequency did not differ between BE and EAC samples, except for CDKN2A and RUNX3 which were significantly higher in EAC. The methylation extent was an estimate of both the number of methylated alleles and the density of methylation on these alleles. This was significantly greater in EAC than in metaplastic BE for all genes except APC, MGMT and TIMP3. There was no significant difference in methylation extent for any gene between high grade dysplastic BE and EAC.

Conclusion: We found significant methylation in metaplastic BE, which for seven of the nine genes studied did not differ in frequency from that found in EAC. This is also the first report of gene silencing by methylation of ID4 in BE or EAC. This study suggests that metaplastic BE is a highly abnormal tissue, more similar to cancer tissue than to normal epithelium.

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Methylation frequency and methylation extent in esophageal tissues. Methylation of each gene was measured in multiple biopsies of squamous mucosa (S, n = 19) from seven patients without BE, single biopsies of squamous mucosa (S-BE, n = 16) and multiple biopsies of columnar mucosa (BE, n = 40) from 18 patients with BE, single biopsies of squamous mucosa (S-EAC, n = 21), high grade dysplastic Barrett's (D-EAC, n = 7) and tumor (EAC, n = 37) from 38 patients with EAC. The methylation was graded as unmethylated (white), methylated 1 (yellow), 2 (red), or 3 (blue), as described in the Materials and Methods.
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Figure 2: Methylation frequency and methylation extent in esophageal tissues. Methylation of each gene was measured in multiple biopsies of squamous mucosa (S, n = 19) from seven patients without BE, single biopsies of squamous mucosa (S-BE, n = 16) and multiple biopsies of columnar mucosa (BE, n = 40) from 18 patients with BE, single biopsies of squamous mucosa (S-EAC, n = 21), high grade dysplastic Barrett's (D-EAC, n = 7) and tumor (EAC, n = 37) from 38 patients with EAC. The methylation was graded as unmethylated (white), methylated 1 (yellow), 2 (red), or 3 (blue), as described in the Materials and Methods.

Mentions: The results in Figure 2 show the methylation frequency, the percentage of samples that had any extent of methylation, for each of the nine genes, in squamous tissues from either patients with no known history of BE (S), or patients with BE (S-BE) or patients with adenocarcinoma (S-EAC), in metaplastic Barrett's from patients with BE but no dysplasia or adenocarcinoma (BE), in high grade dysplastic Barrett's from patients with adenocarcinoma (D-EAC), and in adenocarcinoma (EAC). In squamous tissues the methylation frequency for each gene did not differ significantly between S and S-BE, while in S-EAC methylation was significantly higher for SFRP1 (compared to either S or S-BE) and ID4 (compared to S) and lower for APC (compared to S-BE). For all nine genes the methylation frequency in BE and D-EAC was significantly higher than each of the squamous tissues (S, S-BE and S-EAC) with the exception of CDKN2A (no difference between BE or D-EAC and S or S-BE), RBP1 (BE vs S-BE and D-EAC vs S or S-BE) and SFRP1 (D-EAC vs S-EAC). There were no differences between BE and D-EAC. The methylation frequency for all nine genes was significantly higher in EAC than any squamous tissue. There were no differences between EAC and D-EAC. There were no differences between EAC and BE, except for CDKN2A and RUNX3, which were significantly higher in EAC than BE (P = 0.0104 and 0.0358 respectively).


Similarity of aberrant DNA methylation in Barrett's esophagus and esophageal adenocarcinoma.

Smith E, De Young NJ, Pavey SJ, Hayward NK, Nancarrow DJ, Whiteman DC, Smithers BM, Ruszkiewicz AR, Clouston AD, Gotley DC, Devitt PG, Jamieson GG, Drew PA - Mol. Cancer (2008)

Methylation frequency and methylation extent in esophageal tissues. Methylation of each gene was measured in multiple biopsies of squamous mucosa (S, n = 19) from seven patients without BE, single biopsies of squamous mucosa (S-BE, n = 16) and multiple biopsies of columnar mucosa (BE, n = 40) from 18 patients with BE, single biopsies of squamous mucosa (S-EAC, n = 21), high grade dysplastic Barrett's (D-EAC, n = 7) and tumor (EAC, n = 37) from 38 patients with EAC. The methylation was graded as unmethylated (white), methylated 1 (yellow), 2 (red), or 3 (blue), as described in the Materials and Methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567345&req=5

Figure 2: Methylation frequency and methylation extent in esophageal tissues. Methylation of each gene was measured in multiple biopsies of squamous mucosa (S, n = 19) from seven patients without BE, single biopsies of squamous mucosa (S-BE, n = 16) and multiple biopsies of columnar mucosa (BE, n = 40) from 18 patients with BE, single biopsies of squamous mucosa (S-EAC, n = 21), high grade dysplastic Barrett's (D-EAC, n = 7) and tumor (EAC, n = 37) from 38 patients with EAC. The methylation was graded as unmethylated (white), methylated 1 (yellow), 2 (red), or 3 (blue), as described in the Materials and Methods.
Mentions: The results in Figure 2 show the methylation frequency, the percentage of samples that had any extent of methylation, for each of the nine genes, in squamous tissues from either patients with no known history of BE (S), or patients with BE (S-BE) or patients with adenocarcinoma (S-EAC), in metaplastic Barrett's from patients with BE but no dysplasia or adenocarcinoma (BE), in high grade dysplastic Barrett's from patients with adenocarcinoma (D-EAC), and in adenocarcinoma (EAC). In squamous tissues the methylation frequency for each gene did not differ significantly between S and S-BE, while in S-EAC methylation was significantly higher for SFRP1 (compared to either S or S-BE) and ID4 (compared to S) and lower for APC (compared to S-BE). For all nine genes the methylation frequency in BE and D-EAC was significantly higher than each of the squamous tissues (S, S-BE and S-EAC) with the exception of CDKN2A (no difference between BE or D-EAC and S or S-BE), RBP1 (BE vs S-BE and D-EAC vs S or S-BE) and SFRP1 (D-EAC vs S-EAC). There were no differences between BE and D-EAC. The methylation frequency for all nine genes was significantly higher in EAC than any squamous tissue. There were no differences between EAC and D-EAC. There were no differences between EAC and BE, except for CDKN2A and RUNX3, which were significantly higher in EAC than BE (P = 0.0104 and 0.0358 respectively).

Bottom Line: The methylation frequency did not differ between BE and EAC samples, except for CDKN2A and RUNX3 which were significantly higher in EAC.This was significantly greater in EAC than in metaplastic BE for all genes except APC, MGMT and TIMP3.We found significant methylation in metaplastic BE, which for seven of the nine genes studied did not differ in frequency from that found in EAC.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Nursing and Midwifery, Flinders University, Bedford Park, South Australia 5042, Australia.

ABSTRACT

Background: Barrett's esophagus (BE) is the metaplastic replacement of squamous with columnar epithelium in the esophagus, as a result of reflux. It is the major risk factor for the development of esophageal adenocarcinoma (EAC). Methylation of CpG dinucleotides of normally unmethylated genes is associated with silencing of their expression, and is common in EAC. This study was designed to determine at what stage, in the progression from BE to EAC, methylation of key genes occurs.

Results: We examined nine genes (APC, CDKN2A, ID4, MGMT, RBP1, RUNX3, SFRP1, TIMP3, and TMEFF2), frequently methylated in multiple cancer types, in a panel of squamous (19 biopsies from patients without BE or EAC, 16 from patients with BE, 21 from patients with EAC), BE (40 metaplastic, seven high grade dysplastic) and 37 EAC tissues. The methylation frequency, the percentage of samples that had any extent of methylation, for each of the nine genes in the EAC (95%, 59%, 76%, 57%, 70%, 73%, 95%, 74% and 83% respectively) was significantly higher than in any of the squamous groups. The methylation frequency for each of the nine genes in the metaplastic BE (95%, 28%, 78%, 48%, 58%, 48%, 93%, 88% and 75% respectively) was significantly higher than in the squamous samples except for CDKN2A and RBP1. The methylation frequency did not differ between BE and EAC samples, except for CDKN2A and RUNX3 which were significantly higher in EAC. The methylation extent was an estimate of both the number of methylated alleles and the density of methylation on these alleles. This was significantly greater in EAC than in metaplastic BE for all genes except APC, MGMT and TIMP3. There was no significant difference in methylation extent for any gene between high grade dysplastic BE and EAC.

Conclusion: We found significant methylation in metaplastic BE, which for seven of the nine genes studied did not differ in frequency from that found in EAC. This is also the first report of gene silencing by methylation of ID4 in BE or EAC. This study suggests that metaplastic BE is a highly abnormal tissue, more similar to cancer tissue than to normal epithelium.

Show MeSH
Related in: MedlinePlus