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Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer.

Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S, Vostrov A, Abdullaev Z, Lobanenkov V, Gray A, Liu C, Chang SS, Ostrow KL, Westra WH, Begum S, Dhara M, Califano J - PLoS ONE (2009)

Bottom Line: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported.We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS.Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

View Article: PubMed Central - PubMed

Affiliation: Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.

ABSTRACT

Background: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to analyze expression in primary head and neck squamous cell carcinoma (HNSCC) and pharmacologically demethylated cell lines to identify aberrantly demethylated and expressed candidate proto-oncogenes and cancer testes antigens in HNSCC.

Methodology/principal findings: We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS. Aberrant BORIS expression correlated with upregulation of candidate proto-oncogenes in multiple human malignancies including primary non-small cell lung cancers and HNSCC, induced coordinated proto-oncogene specific promoter demethylation and expression in non-tumorigenic cells, and transformed NIH3T3 cells.

Conclusions/significance: Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

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Related in: MedlinePlus

Overexpression and demethylation in other human cancers.The expO dataset repository was mined for tumor tissue gene expression measured by the Affymetrix U133 Plus 2.0 mRNA expression platform. Initially data was median-normalized by expression array and each gene was median normalized for this figure. Only the subsets of non small cell lung cancer, lymphoma, melanoma, pancreas cancer, and urothelial cancer are displayed. (a) shows the expression of H19 in these cancers. (b) MAGEA2 expression, (c) TKTL1 expression, and (d) MAGEA4. Statistical significance was measured in each tumor type by comparing gene expression in the tumor type to expression in all the remaining 1041 samples. Tumor types without p values did not approach statistical significance. Lung and urothelial showed significant expression overlap.
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pone-0004961-g005: Overexpression and demethylation in other human cancers.The expO dataset repository was mined for tumor tissue gene expression measured by the Affymetrix U133 Plus 2.0 mRNA expression platform. Initially data was median-normalized by expression array and each gene was median normalized for this figure. Only the subsets of non small cell lung cancer, lymphoma, melanoma, pancreas cancer, and urothelial cancer are displayed. (a) shows the expression of H19 in these cancers. (b) MAGEA2 expression, (c) TKTL1 expression, and (d) MAGEA4. Statistical significance was measured in each tumor type by comparing gene expression in the tumor type to expression in all the remaining 1041 samples. Tumor types without p values did not approach statistical significance. Lung and urothelial showed significant expression overlap.

Mentions: To determine if candidate proto-oncogene expression was altered in a broader range of tumor types, we analyzed expression data available through the expO datasets for 1041 human tumors of all histologies [27]. Data was first median-expression normalized by each array and subsequently by median normalization by probe set feature across the 1041 tumors from many cancer types including lung and urothelial, but not HNSCC. We chose a subset of these tumors, non-small cell lung cancer (NSCLC), lymphoma, melanoma, pancreatic cancer, prostate cancers, and urothelial cancers, for presentation (Figure 5A–D). H19 was significantly upregulated in NSCLC (p = 0.008) and in urothelial cancer (p = 0.0013), as calculated by Mann-Whitney U test comparing array-normalized expression in tumor type to all other tumors. We noted significantly increased expression of MAGEA2 in NSCLC (p = 0.005) but not in urothelial cancers (p = 0.18). TKTL1 also showed overexpression in NSCLC (p = 0.05), but not urothelial cancer (p = 0.55), and MAGEA4 was overexpressed in NSCLC (p = 0.04), but not significantly so in urothelial cancer (p = 0.12). In order to confirm target-specific demethylation noted in primary tumors, we devised a rapid, quantitative assay for specifically measuring non-methylated promoters, which we termed Quantitative Unmethylation-Specific PCR (QUMSP). Twenty-five HNSCC tumors and 11 upper aerodigestive mucosal samples were assayed for promoter demethylation (Figure 3E). Tumor-specific demethylation was found in GRIN1 (p = 0.005), MAGEA11 (p = 0.001), and MAGEA2 (p = 0.002). We performed a similar analysis using a separate, independent cohort of 13 NSCLC samples with 14 lung samples from patients without neoplastic disease and confirmed promoter hypomethylation in target genes. Significant differences at 〈<0.05 in QUMSP were found in H19 (p = 0.02), MAGEA11 (p = 0.03), MAGEA2 (p = 0.005), and MAGEA3/6 (p = 0.02). See Figure 3F.


Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer.

Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S, Vostrov A, Abdullaev Z, Lobanenkov V, Gray A, Liu C, Chang SS, Ostrow KL, Westra WH, Begum S, Dhara M, Califano J - PLoS ONE (2009)

Overexpression and demethylation in other human cancers.The expO dataset repository was mined for tumor tissue gene expression measured by the Affymetrix U133 Plus 2.0 mRNA expression platform. Initially data was median-normalized by expression array and each gene was median normalized for this figure. Only the subsets of non small cell lung cancer, lymphoma, melanoma, pancreas cancer, and urothelial cancer are displayed. (a) shows the expression of H19 in these cancers. (b) MAGEA2 expression, (c) TKTL1 expression, and (d) MAGEA4. Statistical significance was measured in each tumor type by comparing gene expression in the tumor type to expression in all the remaining 1041 samples. Tumor types without p values did not approach statistical significance. Lung and urothelial showed significant expression overlap.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2654921&req=5

pone-0004961-g005: Overexpression and demethylation in other human cancers.The expO dataset repository was mined for tumor tissue gene expression measured by the Affymetrix U133 Plus 2.0 mRNA expression platform. Initially data was median-normalized by expression array and each gene was median normalized for this figure. Only the subsets of non small cell lung cancer, lymphoma, melanoma, pancreas cancer, and urothelial cancer are displayed. (a) shows the expression of H19 in these cancers. (b) MAGEA2 expression, (c) TKTL1 expression, and (d) MAGEA4. Statistical significance was measured in each tumor type by comparing gene expression in the tumor type to expression in all the remaining 1041 samples. Tumor types without p values did not approach statistical significance. Lung and urothelial showed significant expression overlap.
Mentions: To determine if candidate proto-oncogene expression was altered in a broader range of tumor types, we analyzed expression data available through the expO datasets for 1041 human tumors of all histologies [27]. Data was first median-expression normalized by each array and subsequently by median normalization by probe set feature across the 1041 tumors from many cancer types including lung and urothelial, but not HNSCC. We chose a subset of these tumors, non-small cell lung cancer (NSCLC), lymphoma, melanoma, pancreatic cancer, prostate cancers, and urothelial cancers, for presentation (Figure 5A–D). H19 was significantly upregulated in NSCLC (p = 0.008) and in urothelial cancer (p = 0.0013), as calculated by Mann-Whitney U test comparing array-normalized expression in tumor type to all other tumors. We noted significantly increased expression of MAGEA2 in NSCLC (p = 0.005) but not in urothelial cancers (p = 0.18). TKTL1 also showed overexpression in NSCLC (p = 0.05), but not urothelial cancer (p = 0.55), and MAGEA4 was overexpressed in NSCLC (p = 0.04), but not significantly so in urothelial cancer (p = 0.12). In order to confirm target-specific demethylation noted in primary tumors, we devised a rapid, quantitative assay for specifically measuring non-methylated promoters, which we termed Quantitative Unmethylation-Specific PCR (QUMSP). Twenty-five HNSCC tumors and 11 upper aerodigestive mucosal samples were assayed for promoter demethylation (Figure 3E). Tumor-specific demethylation was found in GRIN1 (p = 0.005), MAGEA11 (p = 0.001), and MAGEA2 (p = 0.002). We performed a similar analysis using a separate, independent cohort of 13 NSCLC samples with 14 lung samples from patients without neoplastic disease and confirmed promoter hypomethylation in target genes. Significant differences at 〈<0.05 in QUMSP were found in H19 (p = 0.02), MAGEA11 (p = 0.03), MAGEA2 (p = 0.005), and MAGEA3/6 (p = 0.02). See Figure 3F.

Bottom Line: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported.We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS.Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

View Article: PubMed Central - PubMed

Affiliation: Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.

ABSTRACT

Background: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to analyze expression in primary head and neck squamous cell carcinoma (HNSCC) and pharmacologically demethylated cell lines to identify aberrantly demethylated and expressed candidate proto-oncogenes and cancer testes antigens in HNSCC.

Methodology/principal findings: We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS. Aberrant BORIS expression correlated with upregulation of candidate proto-oncogenes in multiple human malignancies including primary non-small cell lung cancers and HNSCC, induced coordinated proto-oncogene specific promoter demethylation and expression in non-tumorigenic cells, and transformed NIH3T3 cells.

Conclusions/significance: Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

Show MeSH
Related in: MedlinePlus