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Investigating the potential role of genetic and epigenetic variation of DNA methyltransferase genes in hyperplastic polyposis syndrome.

Drini M, Wong NC, Scott HS, Craig JM, Dobrovic A, Hewitt CA, Dow C, Young JP, Jenkins MA, Saffery R, Macrae FA - PLoS ONE (2011)

Bottom Line: CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1).However, the T allele of rs62106244 (intron 10 of DNMT1 gene) was over-represented in cases with HPS (p<0.01) compared with population controls.Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.

View Article: PubMed Central - PubMed

Affiliation: Colorectal Medicine and Genetics, Royal Melbourne Hospital, Department of Medicine, University of Melbourne, Parkville, Victoria, Australia. musa.drini@act.gov.au

ABSTRACT

Background: Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). At least half of CRCs arising in HPS show a CpG island methylator phenotype (CIMP), potentially linked to aberrant DNA methyltransferase (DNMT) activity. CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1). In this study, we investigated the potential for interaction of genetic and epigenetic variation in DNMT genes, in the aetiology of HPS.

Methods: We utilized high resolution melting (HRM) analysis to screen 45 cases with HPS for novel sequence variants in DNMT1, DNMT3A, DNMT3B, and DNMT3L. 21 polyps from 13 patients were screened for BRAF and KRAS mutations, with assessment of promoter methylation in the DNMT1, DNMT3A, DNMT3B, DNMT3L MLH1, MGMT, and WIF1 gene promoters.

Results: No pathologic germline mutations were observed in any DNA-methyltransferase gene. However, the T allele of rs62106244 (intron 10 of DNMT1 gene) was over-represented in cases with HPS (p<0.01) compared with population controls. The DNMT1, DNMT3A and DNMT3B promoters were unmethylated in all instances. Interestingly, the DNMT3L promoter showed low levels of methylation in polyps and normal colonic mucosa relative to matched disease free cells with methylation level negatively correlated to expression level in normal colonic tissue. DNMT3L promoter hypomethylation was more often found in polyps harbouring KRAS mutations (p = 0.0053). BRAF mutations were common (11 out of 21 polyps), whilst KRAS mutations were identified in 4 of 21 polyps.

Conclusions: Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.

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Related in: MedlinePlus

Normalized and temp-shifted difference plot for DNMT1 gene SNP rs62106244.*Seven cases were heterozygous for rs62106244. The top arrow shows the sequence of the DNMT1 gene.
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pone-0016831-g001: Normalized and temp-shifted difference plot for DNMT1 gene SNP rs62106244.*Seven cases were heterozygous for rs62106244. The top arrow shows the sequence of the DNMT1 gene.

Mentions: The T allele of the rs62106244 C>T variant (Fig. 1) was present in 7 out of 45 cases all of whom were heterozygous. To establish the frequency of this uncharacterised variant in the Caucasian population generally, we scanned 300 control samples, and found 16 that were heterozygous at this site. Chi-square analysis confirmed a statistically significant over representation of both the CT genotype and T allele in HPS cases (χ2 = 6.66, p = 0.01; χ2 = 7.45, p<0.01 respectively). We observed that cases with HPS were approximately three times more likely to carry the variant (15.6%) compared to controls (5.3%), and this difference was statistically significant (p = 0.01). However, given the rarity of the variant the confidence intervals were wide (relative risk  = 2.9; 95% confidence interval 1.1 to 6.5). DNMT3B and DNMT3L exon scanning did not reveal any SNPs in our HPS cases.


Investigating the potential role of genetic and epigenetic variation of DNA methyltransferase genes in hyperplastic polyposis syndrome.

Drini M, Wong NC, Scott HS, Craig JM, Dobrovic A, Hewitt CA, Dow C, Young JP, Jenkins MA, Saffery R, Macrae FA - PLoS ONE (2011)

Normalized and temp-shifted difference plot for DNMT1 gene SNP rs62106244.*Seven cases were heterozygous for rs62106244. The top arrow shows the sequence of the DNMT1 gene.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037390&req=5

pone-0016831-g001: Normalized and temp-shifted difference plot for DNMT1 gene SNP rs62106244.*Seven cases were heterozygous for rs62106244. The top arrow shows the sequence of the DNMT1 gene.
Mentions: The T allele of the rs62106244 C>T variant (Fig. 1) was present in 7 out of 45 cases all of whom were heterozygous. To establish the frequency of this uncharacterised variant in the Caucasian population generally, we scanned 300 control samples, and found 16 that were heterozygous at this site. Chi-square analysis confirmed a statistically significant over representation of both the CT genotype and T allele in HPS cases (χ2 = 6.66, p = 0.01; χ2 = 7.45, p<0.01 respectively). We observed that cases with HPS were approximately three times more likely to carry the variant (15.6%) compared to controls (5.3%), and this difference was statistically significant (p = 0.01). However, given the rarity of the variant the confidence intervals were wide (relative risk  = 2.9; 95% confidence interval 1.1 to 6.5). DNMT3B and DNMT3L exon scanning did not reveal any SNPs in our HPS cases.

Bottom Line: CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1).However, the T allele of rs62106244 (intron 10 of DNMT1 gene) was over-represented in cases with HPS (p<0.01) compared with population controls.Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.

View Article: PubMed Central - PubMed

Affiliation: Colorectal Medicine and Genetics, Royal Melbourne Hospital, Department of Medicine, University of Melbourne, Parkville, Victoria, Australia. musa.drini@act.gov.au

ABSTRACT

Background: Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). At least half of CRCs arising in HPS show a CpG island methylator phenotype (CIMP), potentially linked to aberrant DNA methyltransferase (DNMT) activity. CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1). In this study, we investigated the potential for interaction of genetic and epigenetic variation in DNMT genes, in the aetiology of HPS.

Methods: We utilized high resolution melting (HRM) analysis to screen 45 cases with HPS for novel sequence variants in DNMT1, DNMT3A, DNMT3B, and DNMT3L. 21 polyps from 13 patients were screened for BRAF and KRAS mutations, with assessment of promoter methylation in the DNMT1, DNMT3A, DNMT3B, DNMT3L MLH1, MGMT, and WIF1 gene promoters.

Results: No pathologic germline mutations were observed in any DNA-methyltransferase gene. However, the T allele of rs62106244 (intron 10 of DNMT1 gene) was over-represented in cases with HPS (p<0.01) compared with population controls. The DNMT1, DNMT3A and DNMT3B promoters were unmethylated in all instances. Interestingly, the DNMT3L promoter showed low levels of methylation in polyps and normal colonic mucosa relative to matched disease free cells with methylation level negatively correlated to expression level in normal colonic tissue. DNMT3L promoter hypomethylation was more often found in polyps harbouring KRAS mutations (p = 0.0053). BRAF mutations were common (11 out of 21 polyps), whilst KRAS mutations were identified in 4 of 21 polyps.

Conclusions: Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.

Show MeSH
Related in: MedlinePlus