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Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma.

Choudhury SR, Cui Y, Milton JR, Li J, Irudayaraj J - Clin Epigenetics (2015)

Bottom Line: Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL.AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis.Alterations in subtelomeric methylation, however, have no effects on the TL.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA.

ABSTRACT

Background: Subtelomeric regions dynamically change their epigenetic pattern during development and progression of several malignancies and degenerative disorders. However, DNA methylation of human subtelomeres and their correlation to telomere length (TL) remain undetermined in glioma.

Results: Herein, we report on the selective changes in subtelomeric DNA methylation at the end of five chromosomes (Chr.) (7q, 8q. 18p, 21q, and XpYp) and ascertain their correlation with TL in patients with glioma. Subtelomeric methylation level was invariably higher in glioma patients compared to the control group, irrespective of their age and tumor grade. In particular, a significant increase in methylation was observed at the subtelomeric CpG sites of Chr. 8q, 21q, and XpYp in tissues, obtained from the brain tumor of glioma patients. In contrast, no significant change in methylation was observed at the subtelomere of Chr. 7q and 18p. Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL. This observed phenomenon was validated in vitro by inducing demethylation in a glioblastoma cell line (SF-767) using 5-azacytidine (AZA) treatment. AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis.

Conclusions: DNA methylation level dramatically increased at the subtelomere of Chr.8q, 21q, and XpYp in malignant glioma, which could be used as an early epigenetic diagnostic biomarker of the disease. Alterations in subtelomeric methylation, however, have no effects on the TL.

No MeSH data available.


Related in: MedlinePlus

A representative result of methylation specific PCR (MSP) in the subtelomeric region on Chr. 7q (a), 8q (b), 18p (c), 21q (d), and XpYp (e). M and U refers to the amplification from the methylation- and unmethylation-specific primers respectively. Representative patients were identified by numbers. Chr. 7q subtelomere was partially methylated, and methylation level did not change significantly between the control and glioma patients. Chr.8q subtelomere was also partially methylated, but the methylation ratio increased significantly among the glioma patients. Chr. 18p subtelomere in majority of the non-glioma patients was noticeably amplified with U primers. However, distinct M-specific amplification was observed among the glioma patients. In contrast, subtelomeres of Chr. 21q and XpYp were mostly unmethylated in the non-glioma patients but showed significant increase in methylation level among the glioma patients
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Fig1: A representative result of methylation specific PCR (MSP) in the subtelomeric region on Chr. 7q (a), 8q (b), 18p (c), 21q (d), and XpYp (e). M and U refers to the amplification from the methylation- and unmethylation-specific primers respectively. Representative patients were identified by numbers. Chr. 7q subtelomere was partially methylated, and methylation level did not change significantly between the control and glioma patients. Chr.8q subtelomere was also partially methylated, but the methylation ratio increased significantly among the glioma patients. Chr. 18p subtelomere in majority of the non-glioma patients was noticeably amplified with U primers. However, distinct M-specific amplification was observed among the glioma patients. In contrast, subtelomeres of Chr. 21q and XpYp were mostly unmethylated in the non-glioma patients but showed significant increase in methylation level among the glioma patients

Mentions: The percentage of genome-wide 5-methylcytosine (5-mC %) in the cohort of control patients was in the range between 0.89 and 1.3 %, with the median value of 1.11 %. The 5-mC % assessed in the samples from glioma patients was distributed between 0.9 and 1.4 %, with a median value of 1.2 %. However, we did not find any statistically relevant difference (p = 0.81) in the mean 5-mC level between the non-glioma (1.08 ± 0.28 %) and glioma (1.19 ± 0.39 %) patients (Additional file 1: Figure S3). On the contrary, much interesting and diverse results were obtained from the methylation pattern at the observed subtelomeric regions. The subtelomere of Chr. 7q was found to be partially methylated in both the groups, since the amplification was observed against both the methylation (M)- and unmethylation (U)-specific primers. However, the methylation level for both the groups was determined to be over 50 % (hypermethylated). The mean methylation level in non-glioma individuals (65.62 ± 10.10 %) did not significantly differ from the glioma patients (75.05 ± 13.38 %) (Figs.1a and 2a). The subtelomere of Chr. 8q was also partially methylated but showed reduced methylation level (<50 %) in both the groups. The difference in the mean methylation of glioma (16.58 ± 14.1 %) and non-glioma (12.03 ± 6.70 %) groups was not significantly different (Figs.1b and 2b). The subtelomeric domain of Chr. 18p was partially methylated with the difference in mean methylation between the non-glioma to glioma patients were 35.39 ± 10.10 % and 79.68 ± 14.25 %, respectively, which exhibit a statistically significant difference (Figs.1c and 2c). In contrast, the CpG sites at the subtelomeres of Chr. 21q and XpYp showed a general trend in hypomethylation (<50 %) among the non-glioma patients and hypermethylation (>50 %) among the glioma patients. The mean methylation level in non-glioma to glioma patients varied from 17.92 ± 11.25 % to 77.70 ± 21.34 % in chromosome 21q (Figs.1d and 2d) and 26.10 ± 13.80 % to 86.23 ± 19.60 % in chromosome XpYp (Figs.1e and 2e). The mean differences in methylation level percentage between the groups for these two chromosomes hence can be considered significant.Fig. 1


Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma.

Choudhury SR, Cui Y, Milton JR, Li J, Irudayaraj J - Clin Epigenetics (2015)

A representative result of methylation specific PCR (MSP) in the subtelomeric region on Chr. 7q (a), 8q (b), 18p (c), 21q (d), and XpYp (e). M and U refers to the amplification from the methylation- and unmethylation-specific primers respectively. Representative patients were identified by numbers. Chr. 7q subtelomere was partially methylated, and methylation level did not change significantly between the control and glioma patients. Chr.8q subtelomere was also partially methylated, but the methylation ratio increased significantly among the glioma patients. Chr. 18p subtelomere in majority of the non-glioma patients was noticeably amplified with U primers. However, distinct M-specific amplification was observed among the glioma patients. In contrast, subtelomeres of Chr. 21q and XpYp were mostly unmethylated in the non-glioma patients but showed significant increase in methylation level among the glioma patients
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4597615&req=5

Fig1: A representative result of methylation specific PCR (MSP) in the subtelomeric region on Chr. 7q (a), 8q (b), 18p (c), 21q (d), and XpYp (e). M and U refers to the amplification from the methylation- and unmethylation-specific primers respectively. Representative patients were identified by numbers. Chr. 7q subtelomere was partially methylated, and methylation level did not change significantly between the control and glioma patients. Chr.8q subtelomere was also partially methylated, but the methylation ratio increased significantly among the glioma patients. Chr. 18p subtelomere in majority of the non-glioma patients was noticeably amplified with U primers. However, distinct M-specific amplification was observed among the glioma patients. In contrast, subtelomeres of Chr. 21q and XpYp were mostly unmethylated in the non-glioma patients but showed significant increase in methylation level among the glioma patients
Mentions: The percentage of genome-wide 5-methylcytosine (5-mC %) in the cohort of control patients was in the range between 0.89 and 1.3 %, with the median value of 1.11 %. The 5-mC % assessed in the samples from glioma patients was distributed between 0.9 and 1.4 %, with a median value of 1.2 %. However, we did not find any statistically relevant difference (p = 0.81) in the mean 5-mC level between the non-glioma (1.08 ± 0.28 %) and glioma (1.19 ± 0.39 %) patients (Additional file 1: Figure S3). On the contrary, much interesting and diverse results were obtained from the methylation pattern at the observed subtelomeric regions. The subtelomere of Chr. 7q was found to be partially methylated in both the groups, since the amplification was observed against both the methylation (M)- and unmethylation (U)-specific primers. However, the methylation level for both the groups was determined to be over 50 % (hypermethylated). The mean methylation level in non-glioma individuals (65.62 ± 10.10 %) did not significantly differ from the glioma patients (75.05 ± 13.38 %) (Figs.1a and 2a). The subtelomere of Chr. 8q was also partially methylated but showed reduced methylation level (<50 %) in both the groups. The difference in the mean methylation of glioma (16.58 ± 14.1 %) and non-glioma (12.03 ± 6.70 %) groups was not significantly different (Figs.1b and 2b). The subtelomeric domain of Chr. 18p was partially methylated with the difference in mean methylation between the non-glioma to glioma patients were 35.39 ± 10.10 % and 79.68 ± 14.25 %, respectively, which exhibit a statistically significant difference (Figs.1c and 2c). In contrast, the CpG sites at the subtelomeres of Chr. 21q and XpYp showed a general trend in hypomethylation (<50 %) among the non-glioma patients and hypermethylation (>50 %) among the glioma patients. The mean methylation level in non-glioma to glioma patients varied from 17.92 ± 11.25 % to 77.70 ± 21.34 % in chromosome 21q (Figs.1d and 2d) and 26.10 ± 13.80 % to 86.23 ± 19.60 % in chromosome XpYp (Figs.1e and 2e). The mean differences in methylation level percentage between the groups for these two chromosomes hence can be considered significant.Fig. 1

Bottom Line: Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL.AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis.Alterations in subtelomeric methylation, however, have no effects on the TL.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA.

ABSTRACT

Background: Subtelomeric regions dynamically change their epigenetic pattern during development and progression of several malignancies and degenerative disorders. However, DNA methylation of human subtelomeres and their correlation to telomere length (TL) remain undetermined in glioma.

Results: Herein, we report on the selective changes in subtelomeric DNA methylation at the end of five chromosomes (Chr.) (7q, 8q. 18p, 21q, and XpYp) and ascertain their correlation with TL in patients with glioma. Subtelomeric methylation level was invariably higher in glioma patients compared to the control group, irrespective of their age and tumor grade. In particular, a significant increase in methylation was observed at the subtelomeric CpG sites of Chr. 8q, 21q, and XpYp in tissues, obtained from the brain tumor of glioma patients. In contrast, no significant change in methylation was observed at the subtelomere of Chr. 7q and 18p. Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL. This observed phenomenon was validated in vitro by inducing demethylation in a glioblastoma cell line (SF-767) using 5-azacytidine (AZA) treatment. AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis.

Conclusions: DNA methylation level dramatically increased at the subtelomere of Chr.8q, 21q, and XpYp in malignant glioma, which could be used as an early epigenetic diagnostic biomarker of the disease. Alterations in subtelomeric methylation, however, have no effects on the TL.

No MeSH data available.


Related in: MedlinePlus