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Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability.

Richards KL, Zhang B, Baggerly KA, Colella S, Lang JC, Schuller DE, Krahe R - PLoS ONE (2009)

Bottom Line: There was only moderate correlation between LINE and Alu methylation levels, with the range of variation in methylation levels being greater for the LINE elements.Moreover, genomic instability, as measured by genome-wide loss-of-heterozygosity (LOH) single nucleotide polymorphism (SNP) analysis, was greater in HNSCC samples with more pronounced LINE hypomethylation.Global hypomethylation was variable in HNSCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

ABSTRACT
Loss of genome-wide methylation is a common feature of cancer, and the degree of hypomethylation has been correlated with genomic instability. Global methylation of repetitive elements possibly arose as a defense mechanism against parasitic DNA elements, including retrotransposons and viral pathogens. Given the alterations of global methylation in both viral infection and cancer, we examined genome-wide methylation levels in head and neck squamous cell carcinoma (HNSCC), a cancer causally associated with human papilloma virus (HPV). We assayed global hypomethylation levels in 26 HNSCC samples, compared with their matched normal adjacent tissue, using Pyrosequencing-based methylation assays for LINE repeats. In addition, we examined cell lines derived from a variety of solid tumors for LINE and SINE (Alu) repeats. The degree of LINE and Alu hypomethylation varied among different cancer cell lines. There was only moderate correlation between LINE and Alu methylation levels, with the range of variation in methylation levels being greater for the LINE elements. LINE hypomethylation was more pronounced in HPV-negative than in HPV-positive tumors. Moreover, genomic instability, as measured by genome-wide loss-of-heterozygosity (LOH) single nucleotide polymorphism (SNP) analysis, was greater in HNSCC samples with more pronounced LINE hypomethylation. Global hypomethylation was variable in HNSCC. Its correlation with both HPV status and degree of LOH as a surrogate for genomic instability may reflect alternative oncogenic pathways in HPV-positive versus HPV-negative tumors.

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Alu and LINE-1 methylation in a variety of tumor cell lines.A. Alu methylation using the Alu-3 assay. B. LINE-1 methylation using the L1-3 assay. Results are reported as the PMR (percent methylated reference) normalized to the universally methylated reference DNA. Universally unmethylated (U2M), universally methylated (UM) controls, and normal control DNA from PBLs are also shown.
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pone-0004941-g001: Alu and LINE-1 methylation in a variety of tumor cell lines.A. Alu methylation using the Alu-3 assay. B. LINE-1 methylation using the L1-3 assay. Results are reported as the PMR (percent methylated reference) normalized to the universally methylated reference DNA. Universally unmethylated (U2M), universally methylated (UM) controls, and normal control DNA from PBLs are also shown.

Mentions: Each LINE-1 and Alu methylation assay was tested on a panel of 23 cancer cell lines. Different CpG sites were compared by means of three distinct LINE-1 assays and three distinct Alu assays, each derived from different regions of the LINE-1 and Alu consensus sequences, respectively (Table 1). As a control, we also tested seven normal lymphoblastoid cell lines, which showed normal levels of methylation (all >80% in our LINE-1 assays). In contrast, as expected from previous reports [12]–[14], [21], many of the tumor cell lines showed global hypomethylation, which was most pronounced in the LINE-1 assays (Figure 1). To check the consistency between LINE and SINE methylation levels (represented by our LINE-1 and Alu assays, respectively), we compared the degree of correlation between results from the three LINE-1 assays, between results from the three Alu assays, and between the various LINE-1 and Alu assays. Linear regression analysis showed that the individual LINE-1 assay results were highly correlated with each other, for example r = 0.93 for the correlation between the L1-2 and L1-3 assay results (Figure S2A). The same high degree of correlation was present between results from the Alu assays, for example r = 0.82 for the correlation between the Alu-1 and Alu-3 assay results (Figure S2B). However, LINE-1 assay results were only moderately correlated with Alu assay results, for example r = 0.33 comparing L1-1 and Alu-1; Figure S2C). A similar level of moderate correlation between LINE-1 and Alu assays was reported previously in neuroendocrine tumors [22].


Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability.

Richards KL, Zhang B, Baggerly KA, Colella S, Lang JC, Schuller DE, Krahe R - PLoS ONE (2009)

Alu and LINE-1 methylation in a variety of tumor cell lines.A. Alu methylation using the Alu-3 assay. B. LINE-1 methylation using the L1-3 assay. Results are reported as the PMR (percent methylated reference) normalized to the universally methylated reference DNA. Universally unmethylated (U2M), universally methylated (UM) controls, and normal control DNA from PBLs are also shown.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2654169&req=5

pone-0004941-g001: Alu and LINE-1 methylation in a variety of tumor cell lines.A. Alu methylation using the Alu-3 assay. B. LINE-1 methylation using the L1-3 assay. Results are reported as the PMR (percent methylated reference) normalized to the universally methylated reference DNA. Universally unmethylated (U2M), universally methylated (UM) controls, and normal control DNA from PBLs are also shown.
Mentions: Each LINE-1 and Alu methylation assay was tested on a panel of 23 cancer cell lines. Different CpG sites were compared by means of three distinct LINE-1 assays and three distinct Alu assays, each derived from different regions of the LINE-1 and Alu consensus sequences, respectively (Table 1). As a control, we also tested seven normal lymphoblastoid cell lines, which showed normal levels of methylation (all >80% in our LINE-1 assays). In contrast, as expected from previous reports [12]–[14], [21], many of the tumor cell lines showed global hypomethylation, which was most pronounced in the LINE-1 assays (Figure 1). To check the consistency between LINE and SINE methylation levels (represented by our LINE-1 and Alu assays, respectively), we compared the degree of correlation between results from the three LINE-1 assays, between results from the three Alu assays, and between the various LINE-1 and Alu assays. Linear regression analysis showed that the individual LINE-1 assay results were highly correlated with each other, for example r = 0.93 for the correlation between the L1-2 and L1-3 assay results (Figure S2A). The same high degree of correlation was present between results from the Alu assays, for example r = 0.82 for the correlation between the Alu-1 and Alu-3 assay results (Figure S2B). However, LINE-1 assay results were only moderately correlated with Alu assay results, for example r = 0.33 comparing L1-1 and Alu-1; Figure S2C). A similar level of moderate correlation between LINE-1 and Alu assays was reported previously in neuroendocrine tumors [22].

Bottom Line: There was only moderate correlation between LINE and Alu methylation levels, with the range of variation in methylation levels being greater for the LINE elements.Moreover, genomic instability, as measured by genome-wide loss-of-heterozygosity (LOH) single nucleotide polymorphism (SNP) analysis, was greater in HNSCC samples with more pronounced LINE hypomethylation.Global hypomethylation was variable in HNSCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

ABSTRACT
Loss of genome-wide methylation is a common feature of cancer, and the degree of hypomethylation has been correlated with genomic instability. Global methylation of repetitive elements possibly arose as a defense mechanism against parasitic DNA elements, including retrotransposons and viral pathogens. Given the alterations of global methylation in both viral infection and cancer, we examined genome-wide methylation levels in head and neck squamous cell carcinoma (HNSCC), a cancer causally associated with human papilloma virus (HPV). We assayed global hypomethylation levels in 26 HNSCC samples, compared with their matched normal adjacent tissue, using Pyrosequencing-based methylation assays for LINE repeats. In addition, we examined cell lines derived from a variety of solid tumors for LINE and SINE (Alu) repeats. The degree of LINE and Alu hypomethylation varied among different cancer cell lines. There was only moderate correlation between LINE and Alu methylation levels, with the range of variation in methylation levels being greater for the LINE elements. LINE hypomethylation was more pronounced in HPV-negative than in HPV-positive tumors. Moreover, genomic instability, as measured by genome-wide loss-of-heterozygosity (LOH) single nucleotide polymorphism (SNP) analysis, was greater in HNSCC samples with more pronounced LINE hypomethylation. Global hypomethylation was variable in HNSCC. Its correlation with both HPV status and degree of LOH as a surrogate for genomic instability may reflect alternative oncogenic pathways in HPV-positive versus HPV-negative tumors.

Show MeSH
Related in: MedlinePlus